DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Response to Arguments
Claims 1, 2, 5-15, 18-23, 27, 31, 32, 41, 43, and 44 are pending, independent claims 1, 31, 43, and 44 and dependent claims 2, 5-15, 19, 22, 27, 32, and 41 are amended.
Applicant’s arguments on page 18, filed 12/08/2025, with respect to U.S.C. 112(b) rejections of claims 1, 2, 11, 18-23, 27, 31, 32, 41, 43, and 44 have been fully considered and are persuasive. The U.S.C. 112(b) rejections of claims 1, 2, 11, 18-23, 27, 31, 32, 41, 43, and 44 have been withdrawn.
Applicant’s arguments on pages 18, filed 12/08/2025 with respect to U.S.C. 112(b) rejection of claims 5-10, 12-14 have been fully considered but they are not considered persuasive.
Applicant’s arguments on pages 19-21, filed 12/08/2025 with respect to U.S.C. 101 rejection of claims 1, 2, 5-15, 18-23, 27, 31, 32, 41, 43, and 44 have been fully considered but they are not considered persuasive.
Applicant argues that the inclusion of the terms unprocessed vial culture medium and viral culture make it so the pending claim is significantly more than an abstract idea.
Examiner respectfully disagrees. One of ordinary skill in the art of Raman spectroscopy of viral cultures would know and expect the use of said material in the methods of measuring viral cultures in Raman spectroscopy. Therefore, the unprocessed viral culture medium and viral cultures is considered part of the field of use or technological environment in which when applied to the judicial exception do not amount to significantly more than the exception itself, and cannot integrate a judicial exception into a practical application.
Applicant argues that the use of Raman spectroscopy on an unprocessed viral culture medium provides a particular solution to the field of Raman spectroscopy for the monitoring and assessment of viral tire and/or viral component abundance.
Regarding Applicant's argument that the pending applications method of Raman spectroscopy is implementing a specific solution in the field, i.e., examining “unprocessed viral culture medium,” Examiner respectfully disagrees. Examiner notes that a specific abstract idea is still an abstract idea. The solution to the problem, as claimed by the applicant, must recite additional elements that integrate the judicial exception into a practical application. Examiner has examined the claims and has not found any elements that fulfill this requirement, the selection of what type of material is being examined is not significantly more than an extra solution activity. As recited in MPEP section 2106.05(g), adding insignificant extra-solution activity to the judicial exception, e.g., mere data gathering in conjunction with a law of nature or abstract idea such as a step of obtaining information so that the information can be analyzed by an abstract mental process, is found not enough to be “significantly more” when recited in a claim with a judicial exception in light of CyberSource v. Retail Decisions, Inc., 654 F.3d 1366, 1375, 99 USPQ2d 1690, 1694 (Fed. Cir. 2011). For at least these reasons, Applicant's arguments are not persuasive.
Applicant’s arguments on pages 22-26, filed 12/08/2025 with respect to U.S.C. 103 rejection of claims 1, 2, 5-15, 18-23, 27, 31, 32, 41, 43, and 44 have been fully considered but they are not considered persuasive.
Applicant argues that Dluhy and Driskell do not teach the new limitations of the amended independent claims 1, 31, 43, and 44.
Examiner respectfully disagrees and directs applicant to the rejection below.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 5-10, and 12-15 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 5-10, and 12-14, recites the limitation "the variable importance projection (VIP) calculated from the first plurality of wavenumber ranges" and “the VIP” multiple times in each claim. There is insufficient antecedent basis for this limitation in the claim. If “the variable importance projection (VIP)” is not to be put in claim 1, it should be referred to as “a variable importance projection (VIP) calculated from the first plurality of wavenumber ranges”. Therefore claims 5-10, and 12-14 and further dependent claim 15 are indefinite.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 2, 5-15, 18-23, 31, 32, 41, 43, and 44 are rejected under 35 U.S.C. 101. The claimed invention is directed to the abstract concept of performing mental steps without significantly more. The claim(s) recite(s) the following abstract concepts in BOLD of
Claim 1. A method of determining in a viral culture using Raman spectroscopy the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules, the method comprising the steps of:
(a) providing an unprocessed viral culture medium and irradiating the unprocessed viral culture medium with a light source;
(b) (i) measuring the total intensity of Raman scattered light within each one of a first plurality of wavenumber ranges to obtain a first wavenumber intensity data set for the viral culture, wherein the first plurality of wavenumber ranges are pre-selected and are characteristic of viral nucleic acids in the sample;
(ii) performing a first set of mathematical data processing steps on the first wavenumber intensity data set; and
(iii) determining the viral nucleic acid content of the viral culture based upon the output of the first set of mathematical data processing steps;
(c) (i) measuring the total intensity of Raman scattered light within each one of a second plurality of wavenumber ranges to obtain a second wavenumber intensity data set for the viral culture, wherein the second plurality of wavenumber ranges are pre-selected and are characteristic of the one or more viral structural molecules of the viruses in the sample;
(ii) performing a second set of mathematical data processing steps on the second wavenumber intensity data set; and
(iii) determining the one or more viral structural molecules content of viruses in the viral cultures based upon the output of the second set of mathematical data processing steps; and
(d) determining the ratio of viral nucleic acids to viruses comprising the one or more viral structural molecules in the viral cultures based on the values determined in steps (b)(iii) and (c)(iii).
Claim 31. A method of determining in a viral cultures using Raman spectroscopy the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules, the method comprising the steps of:
(a) (i) providing a first wavenumber intensity data set for the unprocessed viral culture medium, wherein the first data set has been obtained by irradiating the unprocessed viral culture medium with a light source and measuring the total intensity of Raman scattered light within each one of a first plurality of wavenumber ranges, wherein the first plurality of wavenumber ranges in the Raman spectrum have been selected as characteristic of viral nucleic acids in the viral culture;
(ii) performing a first set of mathematical data processing steps on the first wavenumber intensity data set; and
(iii) determining the nucleic acid content of the viral culture based upon the output of the first set of mathematical data processing steps;
(b) (i) providing a second wavenumber intensity data set for the unprocessed viral culture medium, wherein the second data set has been obtained by irradiating the unprocessed viral culture medium with a light source and measuring the total intensity of Raman scattered light within each one of a second plurality of wavenumber ranges, wherein the second plurality of wavenumber ranges in the Raman spectrum have been selected as characteristic of one or more viral structural molecules of the viruses in the viral culture;
(ii) performing a second set of mathematical data processing steps on the second wavenumber intensity data set; and
(iii) determining the one or more viral structural molecules content of viruses in the viral culture based upon the output of the second set of mathematical data processing steps;
(c) determining the ratio of viral nucleic acids to viruses comprising the one or more viral structural molecules in the viral culture based on the values determined in steps (a)(iii) and (b)(iii).
Claim 43. A method of building a multivariate data processing model which is capable of determining one or more viral structural molecules content of viruses in a viral culture from a Raman spectroscopy wavenumber intensity data set obtained for the viral culture, the method comprising:
(a) providing the unprocessed viral culture medium and irradiating the unprocessed viral culture medium with a light source;
(b) measuring the total intensity of the Raman scattered light within each one of a plurality of wavenumber ranges to obtain a wavenumber intensity data set for the viral culture, wherein the plurality of wavenumber ranges are pre-selected and are characteristic of the one or more viral structural molecules of the viruses in the viral culture;
(c) obtaining normalized wavenumber signal intensity data by pre-processing the signal intensity data using a pre-processing analytical method;
(d) obtaining model parameters by applying to the pre-processed signal intensity data a multivariate regression algorithm, wherein a calibration is performed wherein the pre- processed signal intensity data are compared with viral titre data obtained for the same sample conditions using non-Raman spectroscopy methods by visual determination by transmission electron microscopy;
(e) inferring response values using the model parameters obtained from the pre- processed data; and
(f) performing variable selection and identifying Raman spectral variables; and
And wherein the one or more viral structural molecules content of viruses in a viral culture is determined using the model parameters obtained for the identified Raman spectral variables derived from the multivariate data processing model.
Claim 44. A method of building one or more multivariate data processing models which are capable of determining the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules in a viral culture from a Raman spectroscopy wavenumber intensity data set obtained for the viral culture, the method comprising:
(a) providing the unprocessed viral culture medium and irradiating the unprocessed viral culture medium with a light source;
(b) (i) measuring the total intensity of the Raman scattered light within each one of a first plurality of wavenumber ranges to obtain a first wavenumber intensity data set for the viral culture wherein the first plurality of wavenumber ranges are pre-selected and are characteristic of viral nucleic acids in the viral culture;
(ii) measuring the total intensity of the Raman scattered light within each one of a second plurality of wavenumber ranges to obtain a second wavenumber intensity data set for the viral culture wherein the second plurality of wavenumber ranges are pre-selected and are characteristic of the one or more viral structural molecules of the viruses in the viral culture
(c) obtaining normalized wavenumber signal intensity data for the first and second wavenumber intensity data sets by pre-processing the signal intensity data using a pre-processing analytical method;
(d) obtaining model parameters to be applied to the first and second wavenumber intensity data sets by applying to each one of the pre-processed signal intensity data sets a multivariate regression algorithm, wherein a calibration is performed wherein the pre- processed signal intensity data are compared with viral titre data obtained for the same viral culture conditions using non-Raman spectroscopy methods by visual determination by transmission electron microscopy;
(e) inferring response values using the model parameters obtained from each one of the pre-processed data sets; and
(f) performing variable selection,
and wherein the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules in the viral culture is determined using the model parameters obtained for the identified Raman spectral variables derived from the multivariate data processing models.
Under step 1 of the eligibility analysis, we determine whether the claims are to a statutory category by considering whether the claimed subject matter falls within the four statutory categories of patentable subject matter identified by 35 U.S.C. 101: process, machine, manufacture, or composition of matter. The above claims are considered to be in a statutory category.
Under Step 2A, Prong One, we consider whether the claim recites a judicial exception (abstract idea). In the above claim, the highlighted portion constitutes an abstract idea because, under a broadest reasonable interpretation, it recites limitation the fall into/recite abstract idea exceptions. Specifically, under the 2019 Revised Patent Subject Matter Eligibility Guidance, it falls into the grouping of subject matter that, when recited as such in a claim limitation, covers performing mathematics or mental steps.
Next, under Step 2A, Prong Two, we consider whether the claim that recites a judicial exception is integrated into a practical application. In this step, we evaluate whether the claim recites additional elements that integrate the exception into a practical application of that exception.
This judicial exception is not integrated into a practical application because there is no improvement to another technology or technical field; improvements to the functioning of the computer itself; a particular machine; effecting a transformation or reduction of a particular article to a different state or thing. Examiner notes that since the claimed methods and system are not tied to a particular machine or apparatus, they do not represent an improvement to another technology or technical field. Similarly, there are no other meaningful limitations linking the use to a particular technological environment. Finally, there is nothing in the claims that indicates an improvement to the functioning of the computer itself or transform a particular article to a new state.
Finally, under Step 2B, we consider whether the additional elements are sufficient to amount to significantly more than the abstract idea.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because a multivariate data processing model are generic computer elements and not considered significantly more than the abstract idea. As recited in the MPEP, 2106.05(b), merely adding a generic computer, generic computer components, or a programmed computer to perform generic computer functions does not automatically overcome an eligibility rejection. Alice Corp. Pty. Ltd. v. CLS Bank Int'l, 134 S. Ct. 2347, 2359-60, 110 USPQ2d 1976, 1984 (2014). See also OIP Techs. v. Amazon.com, 788 F.3d 1359, 1364, 115 USPQ2d 1090, 1093-94.
The additional elements of unprocessed viral culture medium, and viral cultures, is well known to one of ordinary skill in the art and is considered field of use or technological environment in which when applied to the judicial exception do not amount to significantly more than the exception itself, and cannot integrate a judicial exception into a practical application.
The additional element of providing a sample and irradiating the sample with a light source; measuring the total intensity of Raman scattered light within each one of a first plurality of wavenumber ranges to obtain a first wavenumber intensity data set for the sample, wherein the first plurality of wavenumber ranges are pre-selected and are characteristic of viral nucleic acids in the sample; measuring the total intensity of Raman scattered light within each one of a second plurality of wavenumber ranges to obtain a second wavenumber intensity data set for the sample, wherein the second plurality of wavenumber ranges are pre-selected and are characteristic of the one or more viral structural molecules of the viruses in the sample; and measuring the total intensity of the Raman scattered light within each one of a plurality of wavenumber ranges to obtain a wavenumber intensity data set for the sample, wherein the plurality of wavenumber ranges are pre-selected and are characteristic of the one or more viral structural molecules of the viruses in the sample; are considered necessary data gathering and is not sufficient to integrate the abstract idea into a practical application. As recited in MPEP section 2106.05(g), necessary data gathering (i.e., receiving data) is considered extra solution activity in light of Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015).
Claims 2, 5-15, 18-23, 27, 32, 41 further limit the abstract ideas without integrating the abstract concept into a practical application or including additional limitations that can be considered significantly more than the abstract idea.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1, 2, 11, 18, 27, 31, and 32, is/are rejected under 35 U.S.C. 103 as being unpatentable over Dluhy et al. (US 2009/0086201 A1) hereinafter Dluhy in view of Driskell et al. ("Rapid and Sensitive Detection of Rotavirus Molecular Signatures Using Surface Enhanced Raman Spectroscopy", PLoS ONE, vol. 5, no. 4, 19 April 2010 (2010-04-19), page e10222.) hereinafter Driskell.
Regarding Claim 1, Dluhy teaches (a) providing an unprocessed viral culture medium, and irradiating the unprocessed viral culture medium, with a light source ([0035] “FIG. 18 illustrates the average SERS response for three HIV strains (BaL, LAV and NL) and two media controls (RMPI and DMEM) (i.e., unprocessed medium) between 600-1750 cm.sup.-1.”; [0103] “the excitation source 300 provides a stream of incident light 304 directed to the SERS substrate 202 (i.e., sample) to provide excitation for generating the Raman signal.”); (b) (i) measuring the total intensity of Raman scattered light within each one of a first plurality of wavenumber ranges to obtain a first wavenumber intensity data set for the viral culture, wherein the first plurality of wavenumber ranges are pre-selected and are characteristic of viral nucleic acids in the viral culture ( [0128] “HoloPlex grating that simultaneously measures the range of 100 to 3450 cm-1 at an excitation wavelength of 785 nm illumination supplied by a Invictus Diode Laser (Kaiser Optical Systems Incorporated, Ann Arbor, Mich.).” Where the plurality wavenumber ranges are pre-selected due to the characteristic of viral nucleic acids, because when looking to document and verify the existence of a virus on a sample (i.e., viral culture), an observer of the spectra would look in the region of the well-known and documented nucleic acid wavenumbers to ascertain if the sample has the nucleic acids. If the sample provided shows the nucleic acids in the location they are to be expected (due to the well-known documentation of the expected ranges and values) then one would be able to ascertain that the virus is in the sample (i.e., viruses have fingerprints, aka certain nucleic acids will pop at their expected range, and in the right combination the nucleic acids would reveal the type of virus being detected) for example, [0130] “The SERS spectra of the Adenovirus, Rhinovirus and HIV specimens are shown in FIGS. 9-11, respectively, and the corresponding band assignments are shown in Tables 1-3 (i.e., any one of the tables 1-3 can be a first plurality of wavenumber ranges,) .” See also [0131] which teaches the wavenumber ranges characteristic of viral nucleic acids in the sample ); (ii) performing a first set of mathematical data processing steps on the first wavenumber intensity data set ([0129] “All spectra were baseline corrected (i.e., the removal of a baseline measurement is a mathematical data processing step) for clarity.”); and (iii) determining the viral nucleic acid content of the viral culture based upon the output of the first set of mathematical data processing steps ([0140] “Instead, different viruses can be distinguished (i.e., determined) based on their unique SERS spectra.” Where the determination of the viruses comes from mapping the detected nucleic acids on the spectra, the types of nucleic acids found on the spectra would then be combined and form the specific “fingerprint” of a virus, for example [0140] “The Ad SERS spectrum is characterized by strong bands (i.e., wavenumber ranges) due to nucleic acid bases at 650 cm-1 (G), 731 cm-1 (A), 1325 cm-1 (A) and 1248 cm-1 (G). The 650 cm-1 band may also have contributions due to Tyr. The Raman lines at 1003 cm-1 and 1033 cm-1 have been assigned to the symmetric ring breathing mode and the in-plane C-H bending mode of Phe, respectively, while the bands at 1457 cm-1, 1576 cm-1, and 1655 cm-1 can be attributed to the CH2 deformation mode of proteins, the carboxylate stretching vibration (v a coo-) of Trp, and the amide I vibration of peptide groups, respectively. A notable characteristic of the Ad SERS spectrum is the relative intensity of the bands associated with the nucleic acids indicating direct binding to the silver substrate. The strong band at 731 cm-1 has been assigned to denatured DNA caused by its interaction with the silver SERS substrate.”); (c) (i) measuring the total intensity of Raman scattered light within each one of a second plurality of wavenumber ranges to obtain a second wavenumber intensity data set for the viral culture , wherein the second plurality of wavenumber ranges are pre-selected and are characteristic of the one or more viral structural molecules of the viruses in the viral culture ([0128] “HoloPlex grating that simultaneously measures the range of 100 to 3450 cm-1 at an excitation wavelength of 785 nm illumination supplied by a Invictus Diode Laser (Kaiser Optical Systems Incorporated, Ann Arbor, Mich.). Where [0127] “The samples were thawed for about 5 minutes and an Eppendorf pipette was used to withdraw about 0.5 μL from the sample vial which was then allowed to spread onto the silver nanorod substrate corresponding to about 5000 plaque forming units (pfus) of HIV, about 350 pfus of Adenovirus and about 35 pfus of Rhinovirus. The virus droplet was allowed to dry and bind to the silver surface for -1 hour prior to the Raman experiment.” each sample had its own measurement, where each sample can be labeled 1, 2, or 3, and the second sample ran is run over the second plurality of wave ranges. [0130] “The SERS spectra of the Adenovirus, Rhinovirus and HIV specimens are shown in FIGS. 9-11, respectively, and the corresponding band assignments are shown in Tables 1-3 (i.e., any one of the tables 1-3 can be a second plurality of wavenumber ranges,) .” See also [0131] which teaches the wavenumber ranges characteristic of viral nucleic acids in the sample Where the plurality wavenumber ranges are pre-selected due to the characteristic of viral nucleic acids, because when looking to document and verify the existence of a virus on a sample, an observer of the spectra would look in the region of the well-known and documented nucleic acid wavenumbers to ascertain if the sample has the nucleic acids. If the sample provided shows the nucleic acids in the location they are to be expected (due to the well-known documentation of the expected ranges and values) then one would be able to ascertain that the virus is in the sample (i.e., viruses have fingerprints, aka certain nucleic acids will pop at their expected range, and in the right combination the nucleic acids would reveal the type of virus being detected).); (ii) performing a second set of mathematical data processing steps on the second wavenumber intensity data set ([0129] “All spectra were baseline corrected (i.e., the removal of a baseline measurement is a mathematical data processing step) for clarity.”) and (iii) determining the one or more viral structural molecules content of viruses in the viral culture based upon the output of the second set of mathematical data processing steps ([0140] “Instead, different viruses can be distinguished (i.e., determined) based on their unique SERS spectra.” Where the determination of the viruses comes from mapping the detected nucleic acids on the spectra, the types of nucleic acids found on the spectra would then be combined and form the specific “fingerprint” of a virus, for example [0141] “In the SERS spectrum for rhinovirus, the major Raman bands are present at 656 cm-1 (G), 729 cm-1 (A), 853 cm-1 (Tyr), 1002 cm-1 and 1030 cm-1 (Phe), 1448 cm-1 (CH2 deformation), and 1597 cm-1 Cva coo-in Trp) (i.e., content of viruses comprising the one or more viral structural molecules in the sample, where Trp, Phe, Tyr, A, G, and CH2 are structural molecules of viruses).”. Furthermore, [0127] “The samples were thawed for about 5 minutes and an Eppendorf pipette was used to withdraw about 0.5 μL from the sample vial which was then allowed to spread onto the silver nanorod substrate corresponding to about 5000 plaque forming units (pfus) of HIV, about 350 pfus of Adenovirus and about 35 pfus of Rhinovirus. The virus droplet was allowed to dry and bind to the silver surface for -1 hour prior to the Raman experiment.” Where [0129] “Post processing of the collected spectra was performed using GRAMS32/AI spectral software package (Galactic Industries, Nashua, N.H.). Center of Gravity calculations were made using a GRAMS32 based program written in our laboratory (R. A. Dluhy, unpublished). All spectra were baseline corrected for clarity.”, where the second set of mathematical data comes from Table 2, and Fig 9-1, and follow the above-mentioned processing steps).
Dluhy does not teach (d) determining the ratio of viral nucleic acids to viruses comprising the one or more viral structural molecules in the viral culture based on the values.
Driskell teaches (d) determining the ratio of viral nucleic acids to viruses comprising the one or more viral structural molecules in the viral culture based on the values (“A plot of the predicted rotavirus concentration for cross-validated samples (i.e., obtained by the viral nucleic acid measured using SERS on the sample) versus the true concentration (i.e., amount of virus initially put into the sample) obtained is presented in Figure 4 (i.e., a ratio/comparison). Each data point represents the average predicted value and the error bars represent the standard deviation. The plot demonstrates the quantitative accuracy of SERS fingerprinting in combination with chemometric analysis for a small range of relatively high viral titers.” Pg. 6 col 2, paragraph 4).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the ratio determination of nucleic acids to viruses discussed in Driskell to the method of using Raman spectroscopy on viral samples discussed in Dluhy for the purpose of knowing how much viral content the Raman spectroscopy is capable of detecting. This is advantageous because Raman spectroscopy “provides the ability to rapidly detect analytes with chemical specificity intrinsic to vibrational spectroscopy and is emerging as an important tool in bioanalytical applications including identification and classification of pathogenic organisms” (e.g., Driskell pg. 1 col 2 paragraph 3).
Regarding Claim 31, Dluhy teaches (a) (i) providing a first wavenumber intensity data set for the an unprocessed viral culture medium, wherein the first data set has been obtained by irradiating the unprocessed viral culture medium with a light source and measuring the total intensity of Raman scattered light within each one of a first plurality of wavenumber ranges, wherein the first plurality of wavenumber ranges in the Raman spectrum have been selected as characteristic of viral nucleic acids in the viral culture (([0035] “FIG. 18 illustrates the average SERS response for three HIV strains (BaL, LAV and NL) and two media controls (RMPI and DMEM) (i.e., unprocessed medium) between 600-1750 cm.sup.-1.”; [0103] “the excitation source 300 provides a stream of incident light 304 directed to the SERS substrate 202 (i.e., sample) to provide excitation for generating the Raman signal.”, and [0128] “HoloPlex grating that simultaneously measures the range of 100 to 3450 cm-1 at an excitation wavelength of 785 nm illumination supplied by a Invictus Diode Laser (Kaiser Optical Systems Incorporated, Ann Arbor, Mich.).” Where the plurality wavenumber ranges are pre-selected due to the characteristic of viral nucleic acids, because when looking to document and verify the existence of a virus on a sample, an observer of the spectra would look in the region of the well-known and documented nucleic acid wavenumbers to ascertain if the sample has the nucleic acids. If the sample provided shows the nucleic acids in the location they are to be expected (due to the well-known documentation of the expected ranges and values) then one would be able to ascertain that the virus is in the sample (i.e., viruses have fingerprints, aka certain nucleic acids will pop at their expected range, and in the right combination the nucleic acids would reveal the type of virus being detected) for example, [0130] “The SERS spectra of the Adenovirus, Rhinovirus and HIV specimens (i.e., viral cultures) are shown in FIGS. 9-11, respectively, and the corresponding band assignments are shown in Tables 1-3 (i.e., any one of the tables 1-3 can be a first plurality of wavenumber ranges,) .” See also [0131] which teaches the wavenumber ranges characteristic of viral nucleic acids in the sample); (ii) performing a first set of mathematical data processing steps on the first wavenumber intensity data set ([0129] “All spectra were baseline corrected (i.e., the removal of a baseline measurement is a mathematical data processing step) for clarity.”); and (iii) determining the nucleic acid content of the viral cultures based upon the output of the first set of mathematical data processing steps ( ([0140] “Instead, different viruses can be distinguished (i.e., determined) based on their unique SERS spectra.” Where the determination of the viruses comes from mapping the detected nucleic acids on the spectra, the types of nucleic acids found on the spectra would then be combined and form the specific “fingerprint” of a virus, for example [140] “The Ad SERS spectrum is characterized by strong bands (i.e., wavenumber ranges) due to nucleic acid bases at 650 cm-1 (G), 731 cm-1 (A), 1325 cm-1 (A) and 1248 cm-1 (G). The 650 cm-1 band may also have contributions due to Tyr. The Raman lines at 1003 cm-1 and 1033 cm-1 have been assigned to the symmetric ring breathing mode and the in-plane C-H bending mode of Phe, respectively, while the bands at 1457 cm-1, 1576 cm-1, and 1655 cm-1 can be attributed to the CH2 deformation mode of proteins, the carboxylate stretching vibration (v a coo-) of Trp, and the amide I vibration of peptide groups, respectively. A notable characteristic of the Ad SERS spectrum is the relative intensity of the bands associated with the nucleic acids indicating direct binding to the silver substrate. The strong band at 731 cm-1 has been assigned to denatured DNA caused by its interaction with the silver SERS substrate.”); (b) (i) providing a second wavenumber intensity data set for the unprocessed viral culture medium, wherein the second data set has been obtained by irradiating the unprocessed viral culture medium with a light source and measuring the total intensity of Raman scattered light within each one of a second plurality of wavenumber ranges, wherein the second plurality of wavenumber ranges in the Raman spectrum have been selected as characteristic of one or more viral structural molecules of the viruses in the viral culture (([0035] “FIG. 18 illustrates the average SERS response for three HIV strains (BaL, LAV and NL) and two media controls (RMPI and DMEM) (i.e., unprocessed medium) between 600-1750 cm.sup.-1.” And [0036] “FIG. 19 illustrates the average SERS response for three HIV strains (BaL, LAV and NL) and two media controls (RMPI and DMEM) between 1000-1100 cm.sup.-1.”; [0103] “the excitation source 300 provides a stream of incident light 304 directed to the SERS substrate 202 (i.e., sample) to provide excitation for generating the Raman signal.” And [0128] “HoloPlex grating that simultaneously measures the range of 100 to 3450 cm-1 at an excitation wavelength of 785 nm illumination supplied by a Invictus Diode Laser (Kaiser Optical Systems Incorporated, Ann Arbor, Mich.). Where [0127] “The samples were thawed for about 5 minutes and an Eppendorf pipette was used to withdraw about 0.5 μL from the sample vial which was then allowed to spread onto the silver nanorod substrate corresponding to about 5000 plaque forming units (pfus) of HIV, about 350 pfus of Adenovirus and about 35 pfus of Rhinovirus. The virus droplet was allowed to dry and bind to the silver surface for -1 hour prior to the Raman experiment.” each sample had its own measurement, where each sample can be labeled 1, 2, or 3, and the second sample ran is run over the second plurality of wave ranges. [0130] “The SERS spectra of the Adenovirus, Rhinovirus and HIV specimens are shown in FIGS. 9-11, respectively, and the corresponding band assignments are shown in Tables 1-3 (i.e., any one of the tables 1-3 can be a second plurality of wavenumber ranges,) .” See also [0131] which teaches the wavenumber ranges characteristic of viral nucleic acids in the sample Where the plurality wavenumber ranges are pre-selected due to the characteristic of viral nucleic acids, because when looking to document and verify the existence of a virus on a sample, an observer of the spectra would look in the region of the well-known and documented nucleic acid wavenumbers to ascertain if the sample has the nucleic acids. If the sample provided shows the nucleic acids in the location they are to be expected (due to the well-known documentation of the expected ranges and values) then one would be able to ascertain that the virus is in the sample (i.e., viruses have fingerprints, aka certain nucleic acids will pop at their expected range, and in the right combination the nucleic acids would reveal the type of virus being detected).); (ii) performing a second set of mathematical data processing steps on the second wavenumber intensity data set ([0129] “All spectra were baseline corrected (i.e., the removal of a baseline measurement is a mathematical data processing step) for clarity.”); and (iii) determining the one or more viral structural molecules content of viruses in the viral culture based upon the output of the second set of mathematical data processing steps ([0140] “Instead, different viruses can be distinguished (i.e., determined) based on their unique SERS spectra.” Where the determination of the viruses comes from mapping the detected nucleic acids on the spectra, the types of nucleic acids found on the spectra would then be combined and form the specific “fingerprint” of a virus, for example and the second set of data shows [0141] “In the SERS spectrum for rhinovirus, the major Raman bands are present at 656 cm-1 (G), 729 cm-1 (A), 853 cm-1 (Tyr), 1002 cm-1 and 1030 cm-1 (Phe), 1448 cm-1 (CH2 deformation), and 1597 cm-1 Cva coo-in Trp).”);
Dluhy does not teach (c) determining the ratio of viral nucleic acids to viruses comprising the one or more viral structural molecules in the viral cultures based on the values.
Driskell teaches (c) determining the ratio of viral nucleic acids to viruses comprising the one or more viral structural molecules in the viral cultures based on the values (“A plot of the predicted rotavirus concentration for cross-validated samples (i.e., obtained by the viral nucleic acid measured using SERS on the sample) versus the true concentration (i.e., amount of virus initially put into the sample) obtained is presented in Figure 4 (i.e., a ratio/comparison). Each data point represents the average predicted value and the error bars represent the standard deviation. The plot demonstrates the quantitative accuracy of SERS fingerprinting in combination with chemometric analysis for a small range of relatively high viral titers.” Pg. 6 col 2, paragraph 4).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the ratio determination of nucleic acids to viruses discussed in Driskell to the method of using Raman spectroscopy on viral samples discussed in Dluhy for the purpose of knowing how much viral content the Raman spectroscopy is capable of detecting. This is advantageous because Raman spectroscopy “provides the ability to rapidly detect analytes with chemical specificity intrinsic to vibrational spectroscopy and is emerging as an important tool in bioanalytical applications including identification and classification of pathogenic organisms” (e.g., Driskell pg. 1 col 2 paragraph 3).
Regarding Claims 2 and 32, Dluhy and Driskell teach the limitations of claims 1 and 31.
Dluhy does not teach (i) obtaining model parameters by applying to the wavenumber signal intensity data a multivariate regression algorithm, and (ii) determining the viral nucleic acid content of the viral culture and determining the one or more viral structural molecules content of viruses in the viral culture using the model parameters obtained by applying the multivariate regression algorithm to the signal intensity data.
Driskell teaches (i) obtaining model parameters by applying to the wavenumber signal intensity data a multivariate regression algorithm, (“The normalized first derivate spectra were then mean-centered prior to PLS-DA [37,38]. The same spectral preprocessing protocol was used to generate a quantitative predictive model using partial least squares (PLS) regression analysis.” Pg 3 col 1 paragraph 6- col2 paragraph 1); and (ii) determining the viral nucleic acid content of the viral cultures and determining the one or more viral structural molecules content of viruses in the viral cultures using the model parameters obtained by applying the multivariate regression algorithm to the signal intensity data (“Preliminary studies were designed to assess the utility of the Ag nanorod substrates to generate SERS spectra of rota viruses and to evaluate the reproducibility of the method. For these studies, spectra of rotavirus samples were either baseline corrected using a concave rubber band algorithm (OPUS, Bruker Optics, Inc., Billerica, MA) computed with IO iterations and 64 points or derivatized (1 st derivative, 15 point, Savitzky-Golay). These spectral processing steps facilitate visual comparison of the Raman peak positions for spectra collected at different locations on a SERS substrate and for different substrates. Classification of the rota virus strains was achieved using partial least squares discriminant analysis that was performed using PLS Toolbox version 4.0 (Eigen Vector Research Inc., Wenatchee, WA), operating in a MATLAB environment (v7.2, The Mathworks Inc., Natick, MA). Multiple PLS-DA models were built to classify the samples according to (I) rota virus-positive or -negative, (2) strain, (3) G-genotype, or (4) P-genotype. SERS spectra used to generate the PLS-DA classification models were first processed by taking the first derivative of each spectrum (IS-point, SavitzkyGolay) and then normalizing to unit vector length [36].” Pg 3 col 1 paragraph 5-6, where Partial least squares is a multivariate data processing tool).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the mathematical modeling process of Raman spectra discussed in Driskell to the method of using Raman spectroscopy on viral samples discussed in Dluhy for the purpose of knowing how much viral content the Raman spectroscopy is capable of detecting. This is advantageous because Raman spectroscopy “provides the ability to rapidly detect analytes with chemical specificity intrinsic to vibrational spectroscopy and is emerging as an important tool in bioanalytical applications including identification and classification of pathogenic organisms” (e.g., Driskell pg. 1 col 2 paragraph 3).
Regarding Claim 11, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further teaches wherein the viruses in the viral culture are adeno-associated viruses (AAV) ([0130] “Adenovirus, belonging to the Adenoviridiae family of viruses, is about 80 nm in diameter with an icosahedral core and contains double stranded DNA within the core”).
Regarding Claim 18, Dluhy and Driskell teach the limitations of claim 1.
Dluhy does not teach the ratio provides a measure of functional viral titre.
Driskell teaches wherein the ratio provides a measure of functional viral titre (“At the outset, rotavirus was propagated in MA104 cells and harvested as cell lysates. Virus was diluted to a titer of 10^6 ffu/mL for SERS evaluation.” Pg 3, col 2 paragraph 4, where ffu/mL stands for focus forming units per milliliter and is quantified by performing a focus forming assay, which is a functional assay, and a titer is the measurement of concentration performed in an assay).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the ratio determination of nucleic acids to viruses discussed in Driskell to the method of using Raman spectroscopy on viral samples discussed in Dluhy for the purpose of knowing how much viral content the Raman spectroscopy is capable of detecting. This is advantageous because Raman spectroscopy “provides the ability to rapidly detect analytes with chemical specificity intrinsic to vibrational spectroscopy and is emerging as an important tool in bioanalytical applications including identification and classification of pathogenic organisms” (e.g., Driskell pg. 1 col 2 paragraph 3).
Regarding Claim 27, Dluhy and Driskell teach the limitations of claim 1.
Dluhy does not teach wherein the method comprises a step of comparing the ratio thereby obtained with the ratio obtained from the same viral culture by an alternative method.
Driskell teaches wherein the method comprises a step of comparing the ratio thereby obtained with the ratio obtained from the same viral culture by an alternative method (“Cells were incubated at 37°C until a cytopathic effect was evident, then lysates were frozen and thawed twice. Hemi-nested RT-PCR assays were employed to confirm the G and P genotype of each rota virus isolate using type specific primers [39].” Pg 2 col 2 paragraph 5).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the ratio determination of nucleic acids to viruses discussed in Driskell to the method of using Raman spectroscopy on viral samples discussed in Dluhy for the purpose of knowing how much viral content the Raman spectroscopy is capable of detecting. This is advantageous because Raman spectroscopy “provides the ability to rapidly detect analytes with chemical specificity intrinsic to vibrational spectroscopy and is emerging as an important tool in bioanalytical applications including identification and classification of pathogenic organisms” (e.g., Driskell pg. 1 col 2 paragraph 3).
Claim(s) 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dluhy and Driskell in view of Castillo et al. (US 2020/0318060 A1).
Regarding Claim 19, Dluhy and Driskell teach the limitations of claim 1.
Dluhy and Driskell do not teach wherein the viral culture is comprised in a bioreactor.
Castillo teaches ([0015] “ “Biomolecule” refers to any biological material of interest that is produced in a bioreactor. Biomolecules include, for example, viruses, virus-like particles, viral products, proteins such as antibodies, carbohydrates, lipids, nucleic acids, metabolites and peptides.”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the use of a bioreactor discussed in Castillo to the viral culture analysis discussed in Dluhy and Driskell for the purpose of providing a controlled environment for the growth of the viral cultures. This is advantageous because bioreactors make it possible to obtain products suitable for clinical administration, fast and efficient methods of producing biomolecules such as virus or viral proteins in cultured cells (e.g., [0003], Castillo).
Claim(s) 20-23, and 41 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dluhy and Driskell in view of Moor et al., ("Early detection of virus infection in live human cells using Raman spectroscopy"; J. Biomed, Opt. 2018, 23(9): 097001-1-097001-7) hereinafter Moor.
Regarding Claim 20, Dluhy and Driskell teach the limitations of claim 19.
Dluhy and Driskell do not teach wherein the steps of irradiating the viral culture with a light source and measuring the total intensity of Raman scattered light is performed directly on the medium of the viral culture (in situ).
Moor teaches wherein the steps of irradiating the viral culture with a light source and measuring the total intensity of Raman scattered light is performed directly on the medium of the viral culture (in situ) (“The other Raman system was constructed in-house and involved an inverted fluorescence microscope. It was utilized for time-lapse experiments because it could keep cells for more than 24 h under the cultivation conditions.” Pg. 2 col 2 paragraph 2, where “The cells were cultured in high-glucose Dulbecco's modified Eagle's medium (Wako, Japan) supplemented with 10% of fetal bovine serum (Beit HAEMEK, Ltd., Israel) and 100 IU/mL penicillin (Wako). The cells were cultured in a CO2 incubator, SCA/SMA-163 (Astec, US), at 37°C and 5% of CO2 . A special dish with a quartz window at the bottom was purchased from Synapse-Gibko (Japan) and used for Raman analyses.” Pg. 2 col 1 paragraph 3).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine measuring a viral culture with Raman spectroscopy as discussed in Moor to the method of measure viral samples with Raman spectroscopy as discussed with Dluhy and Driskell for the purpose of measuring the cells as they cultivate and grow. This is advantageous because “Raman analysis can detect virus infection in a single cell, the experiment can be conducted with fewer virus particles than the minimal accessible number of virus particles during a clinical infection” (e.g., Moor, pg. 2 col 1 paragraph 1).
Regarding Claim 21, Dluhy and Driskell teach the limitations of claim 19.
Dluhy further teaches wherein the steps of irradiating the viral culture with a light source and measuring the total intensity of Raman scattered light is performed directly on an aliquot of the medium which has been taken from the viral culture (ex situ) ([0127]“The concentrations of the prepared virus samples in Dulbecco's Modified Eagle Medium (DMEM) were 107 plaque forming units (pfus)/mL for HIV, 105 TCID[50]/mL for Rhinovirus and 106 TCID[50]/mL for the Adenovirus. After preparation, the virus samples were stored at -80° C. until the day of the experiment. The samples were thawed for about 5 minutes and an Eppendorf pipette was used to withdraw about 0.5 μL from the sample vial (i.e., aliquot of the medium) which was then allowed to spread onto the silver nanorod substrate corresponding to about 5000 plaque forming units (pfus) of HIV, about 350 pfus of Adenovirus and about 35 pfus of Rhinovirus. The virus droplet was allowed to dry and bind to the silver surface for -1 hour prior to the Raman experiment.”)
Regarding Claim 22, Dluhy and Driskell teach the limitations of claim 1.
Dluhy and Driskell do not teach a first step of determining the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules at a first time point and one or more further steps of determining the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules at later time points; and further comprising measuring the change in the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules in the viral culture between time points, wherein each step is performed by a method according to any one of the preceding claims, preferably wherein each step is performed by the same method.
Moor teaches a first step of determining the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules at a first time point and one or more further steps of determining the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules at later time points (“The Raman analyses were carried out at 3, 6, 9, 12, 18, and 24 h after the virus injection under the stable cultivation conditions. It took 2 to 3 min for focusing on the nucleus and acquisition of the spectrum at each measuring site. To keep the synchronism in the dataset, the sample measurement was finished in 40 min at each dataset.” Pg. 4, col 1 paragraph 1, where “The PCA score plots of the datasets acquired at 3 (a) (i.e., first time), 9 (c) (i.e., later time point a), and 12 h (d) (i.e., later time point b) are shown in Fig. 3(A).” pg. 4 col 1 paragraph 1), and further comprising measuring the change in the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules in the sample between time points (“(“The Raman analyses were carried out at 3, 6, 9, 12, 18, and 24 h after the virus injection under the stable cultivation conditions. It took 2 to 3 min for focusing on the nucleus and acquisition of the spectrum at each measuring site. To keep the synchronism in the dataset, the sample measurement was finished in 40 min at each dataset.” Pg. 4, col 1 paragraph 1, where “The PCA score plots of the datasets acquired at 3 (a) (i.e., first time), 9 (c) (i.e., later time point a), and 12 h (d) (i.e., later time point b) are shown in Fig. 3(A).” pg. 4 col 1 paragraph 1, and “Those of the datasets recorded at 6, 18, and 24 hare shown in the Appendix” pg. 4 col 1 paragraph 1, where the 6 hr measurement is between 3 hr and 9 hrs), wherein each step is performed by a method according to any one of the preceding claims, preferably wherein each step is performed by the same method (implied).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine measuring a viral culture with Raman spectroscopy as discussed in Moor to the method of measure viral samples with Raman spectroscopy as discussed with Dluhy and Driskell for the purpose of measuring the cells as they cultivate and grow. This is advantageous because “Raman analysis can detect virus infection in a single cell, the experiment can be conducted with fewer virus particles than the minimal accessible number of virus particles during a clinical infection” (e.g., Moor, pg. 2 col 1 paragraph 1).
Regarding Claim 23, Dluhy, Driskell, and Moor teach the limitations of claim 22.
Dluhy and Driskell do not teach wherein the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules is determined repeatedly over a time period to provide a measure of the change in the ratio in real time.
Moor teaches wherein the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules is determined repeatedly over a time period to provide a measure of the change in the ratio in real time (“To keep the synchronism in the dataset, the sample measurement was finished in 40 min at each dataset. Therefore, each dataset has relatively small number, 10 to 15, of spectra (i.e., spectra is measured repeatedly over the course of 40 mins providing the change in ratio in real time).” Pg 4 col 1 paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine measuring a viral culture with Raman spectroscopy as discussed in Moor to the method of measure viral samples with Raman spectroscopy as discussed with Dluhy and Driskell for the purpose of measuring the cells as they cultivate and grow. This is advantageous because “Raman analysis can detect virus infection in a single cell, the experiment can be conducted with fewer virus particles than the minimal accessible number of virus particles during a clinical infection” (e.g., Moor, pg. 2 col 1 paragraph 1).
Regarding Claim 41, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further teaches (a) the viruses in the viral cultures are not HIV-1 or HIV-1 virus-like particles (HIV-1 VLPs) ([0127] “The concentrations of the prepared virus samples in Dulbecco's Modified Eagle Medium (DMEM) were 107 plaque forming units (pfus)/mL for HIV, 105 TCID[50]/mL for Rhinovirus and 106 TCID[50]/mL for the Adenovirus.” Specifically, the Rhinovirus and the Adenovirus).
Dluhy and Driskell do not teach (b) the Raman spectroscopy is not surface enhanced Raman spectroscopy.
Moor teaches (b) the Raman spectroscopy is not surface enhanced Raman spectroscopy (“The purpose of this study is to develop a technique for detection of virus infection within a short period by Raman spectroscopy (i.e., not surface enhanced Raman spectroscopy) and to investigate the origin of the spectral changes.” Pg 1 col 2 paragraph 2).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine measuring a viral culture with Raman spectroscopy as discussed in Moor to the method of measure viral samples with Raman spectroscopy as discussed with Dluhy and Driskell for the purpose of measuring the cells as they cultivate and grow. This is advantageous because “Raman analysis can detect virus infection in a single cell, the experiment can be conducted with fewer virus particles than the minimal accessible number of virus particles during a clinical infection” (e.g., Moor, pg. 2 col 1 paragraph 1).
Claim(s) 43 and 44 is/are rejected under 35 U.S.C. 103 as being unpatentable over Dluhy and Driskell in view of Homman (US 2012/0244524 A1).
Regarding Claim 43, Dluhy teaches (a) providing an unprocessed viral culture medium and irradiating the unprocessed viral culture medium with a light source ([0035] “FIG. 18 illustrates the average SERS response for three HIV strains (BaL, LAV and NL) and two media controls (RMPI and DMEM) (i.e., unprocessed medium) between 600-1750 cm.sup.-1.”; [0103] “the excitation source 300 provides a stream of incident light 304 directed to the SERS substrate 202 (i.e., sample) to provide excitation for generating the Raman signal.”); (b) measuring the total intensity of the Raman scattered light within each one of a plurality of wavenumber ranges to obtain a wavenumber intensity data set for the viral culture, wherein the plurality of wavenumber ranges are pre-selected and are characteristic of the one or more viral structural molecules of the viruses in the viral culture ([0128] “HoloPlex grating that simultaneously measures the range of 100 to 3450 cm-1 at an excitation wavelength of 785 nm illumination supplied by a Invictus Diode Laser (Kaiser Optical Systems Incorporated, Ann Arbor, Mich.).” Where the plurality wavenumber ranges are pre-selected due to the characteristic of viral nucleic acids, because when looking to document and verify the existence of a virus on a sample, an observer of the spectra would look in the region of the well-known and documented nucleic acid wavenumbers to ascertain if the sample has the nucleic acids. If the sample provided shows the nucleic acids in the location they are to be expected (due to the well-known documentation of the expected ranges and values) then one would be able to ascertain that the virus is in the sample (i.e., viruses have fingerprints, aka certain nucleic acids will pop at their expected range, and in the right combination the nucleic acids would reveal the type of virus being detected) for example, [0130] “The SERS spectra of the Adenovirus, Rhinovirus and HIV specimens (i.e., viral cultures) are shown in FIGS. 9-11, respectively, and the corresponding band assignments are shown in Tables 1-3 (i.e., any one of the tables 1-3 can be a first plurality of wavenumber ranges,) .” See also [0131] which teaches the wavenumber ranges characteristic of viral nucleic acids in the sample)
Dluhy does not teach (c) obtaining normalized wavenumber signal intensity data by pre-processing the signal intensity data using a pre-processing analytical method, (d) obtaining model parameters by applying to the pre-processed signal intensity data a multivariate regression algorithm, wherein the pre- processed signal intensity data are compared with viral titre data obtained for the same viral culture conditions using non-Raman spectroscopy methods by visual determination by transmission electron microscopy, (e) inferring response values using the model parameters obtained from the pre- processed data, and (f) performing variable selection; and wherein unimportant variables are removed; and wherein the one or more viral structural molecules content of viruses in a viral culture is determined using the model parameters obtained for the identified Raman spectral variables derived from the multivariate data processing model.
Driskell teaches (c) obtaining normalized wavenumber signal intensity data by pre-processing the signal intensity data using a pre-processing analytical method, (“Classification of the rota virus strains was achieved using partial least squares discriminant analysis that was performed using PLS Toolbox version 4.0 (Eigen Vector Research Inc., Wenatchee, WA), operating in a MATLAB environment (v7.2, The Mathworks Inc., Natick, MA). Multiple PLS-DA models were built to classify the samples according to (I) rota virus-positive or -negative, (2) strain, (3) G-genotype, or (4) P-genotype. SERS spectra used to generate the PLS-DA classification models were first processed by taking the first derivative of each spectrum (IS-point, SavitzkyGolay) and then normalizing to unit vector length [36].” Pg 3 col 1 paragraph 6, a first derivative method); (d) obtaining model parameters by applying to the pre-processed signal intensity data a multivariate regression algorithm, (“The normalized first derivate spectra were then mean-centered prior to PLS-DA [37,38]. The same spectral preprocessing protocol was used to generate a quantitative predictive model using partial least squares (PLS) regression analysis.” Pg 3 col 1 paragraph 6- col2 paragraph 1), wherein a calibration is performed wherein the pre- processed signal intensity data are compared with viral titre data obtained for the same sample conditions using non-Raman spectroscopy methods (“Cells were incubated at 37°C until a cytopathic effect was evident, then lysates were frozen and thawed twice. Hemi-nested RT-PCR assays were employed to confirm the G and P genotype of each rota virus isolate using type specific primers [39]. The viral tires of all virus stocks were determined by fluorescent focus neutralization assays [40].” Pg. 2 col 2 paragraph 5); (e) inferring response values using the model parameters obtained from the pre- processed data (“As is evident, the PLS predicted Concentrations (i.e., inferred response values using model parameters of the PLS model) based on intrinsic SERS spectra are accurate for concentrations
≥
10^4 ffu/ mL. The plot positively deviates at concentrations lower than 10^4 ffu/mL and the predicted concentrations are elevated with respect to the actual sample concentration. (referring to Figs. 4 and 5)” pg. 6 col 2 paragraph 5- pg. 7, col 1 paragraph 2); and (f) performing variable selection, (“Ten calibration samples were prepared between 105 and 106 ffu/mL and SERS spectra were acquired for each concentration. The root mean square error for cross validation (RMSECV) was analyzed to determine the optimum number of latent variable (i.e., performing variable selection) to include in the PLS model.” Pg 6 col 2 paragraph 4); and wherein the one or more viral structural molecules content of viruses in a viral culture is determined using the model parameters obtained for the identified Raman spectral variables derived from the multivariate data processing model (“Preliminary studies were designed to assess the utility of the Ag nanorod substrates to generate SERS spectra of rota viruses and to evaluate the reproducibility of the method. For these studies, spectra of rotavirus samples were either baseline corrected using a concave rubber band algorithm (OPUS, Bruker Optics, Inc., Billerica, MA) computed with IO iterations and 64 points or derivatized (1 st derivative, 15 point, Savitzky-Golay). These spectral processing steps facilitate visual comparison of the Raman peak positions for spectra collected at different locations on a SERS substrate and for different substrates. Classification of the rota virus strains was achieved using partial least squares discriminant analysis that was performed using PLS Toolbox version 4.0 (Eigen Vector Research Inc., Wenatchee, WA), operating in a MATLAB environment (v7.2, The Mathworks Inc., Natick, MA). Multiple PLS-DA models were built to classify the samples according to (I) rota virus-positive or -negative, (2) strain, (3) G-genotype, or (4) P-genotype. SERS spectra used to generate the PLS-DA classification models were first processed by taking the first derivative of each spectrum (IS-point, SavitzkyGolay) and then normalizing to unit vector length [36].” Pg 3 col 1 paragraph 5-6, where Partial least squares is a multivariate data processing tool).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the mathematical modeling process of Raman spectra discussed in Driskell to the method of using Raman spectroscopy on viral samples discussed in Dluhy for the purpose of knowing how much viral content the Raman spectroscopy is capable of detecting. This is advantageous because Raman spectroscopy “provides the ability to rapidly detect analytes with chemical specificity intrinsic to vibrational spectroscopy and is emerging as an important tool in bioanalytical applications including identification and classification of pathogenic organisms” (e.g., Driskell pg. 1 col 2 paragraph 3).
Dluhy and Driskell do not teach wherein non-Raman spectroscopy methods by visual determination by transmission electron microscopy.
Homman teaches wherein non-Raman spectroscopy methods by visual determination by transmission electron microscopy ([0006] “The viral particles are identified among the groups of sorted round and elliptical objects by analyzing radial density profiles of the objects in a selected group. For example, the method may be used for intracellular counting and segmentation of siRNA treated human cytomegaloviral particles in TEM images.”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the use of TEM as discussed in Hommon to the viral culture analysis discussed by Dluhy and Driskell for the purpose of providing direct, high-resolution images of atomic structure, size, and morphology of the viral cultures. This is advantageous because TEM allows for an objective, repeatable and reliable way to describe the cell components of viral cultures to accurately determine the maturity stages of the cell components (e.g., [0003], Homman).
Regarding Claim 44, Dluhy teaches (a) providing an unprocessed viral culture medium and irradiating the unprocessed viral culture medium with a light source ([0035] “FIG. 18 illustrates the average SERS response for three HIV strains (BaL, LAV and NL) and two media controls (RMPI and DMEM) (i.e., unprocessed medium) between 600-1750 cm.sup.-1.”; [0103] “the excitation source 300 provides a stream of incident light 304 directed to the SERS substrate 202 (i.e., sample) to provide excitation for generating the Raman signal.”); (b) (i) measuring the total intensity of the Raman scattered light within each one of a first plurality of wavenumber ranges to obtain a first wavenumber intensity data set for the viral culture wherein the first plurality of wavenumber ranges are pre-selected and are characteristic of viral nucleic acids in the viral culture ([0128] “HoloPlex grating that simultaneously measures the range of 100 to 3450 cm-1 at an excitation wavelength of 785 nm illumination supplied by a Invictus Diode Laser (Kaiser Optical Systems Incorporated, Ann Arbor, Mich.).” Where the plurality wavenumber ranges are pre-selected due to the characteristic of viral nucleic acids, because when looking to document and verify the existence of a virus on a sample, an observer of the spectra would look in the region of the well-known and documented nucleic acid wavenumbers to ascertain if the sample has the nucleic acids. If the sample provided shows the nucleic acids in the location they are to be expected (due to the well-known documentation of the expected ranges and values) then one would be able to ascertain that the virus is in the sample (i.e., viruses have fingerprints, aka certain nucleic acids will pop at their expected range, and in the right combination the nucleic acids would reveal the type of virus being detected) for example, [0130] “The SERS spectra of the Adenovirus, Rhinovirus and HIV specimens (i.e., viral cultures) are shown in FIGS. 9-11, respectively, and the corresponding band assignments are shown in Tables 1-3 (i.e., any one of the tables 1-3 can be a first plurality of wavenumber ranges,) .” See also [0131] which teaches the wavenumber ranges characteristic of viral nucleic acids in the sample); (ii) measuring the total intensity of the Raman scattered light within each one of a second plurality of wavenumber ranges to obtain a second wavenumber intensity data set for the viral culture wherein the second plurality of wavenumber ranges are pre-selected and are characteristic of the one or more viral structural molecules of the viruses in the viral culture [0128] “HoloPlex grating that simultaneously measures the range of 100 to 3450 cm-1 at an excitation wavelength of 785 nm illumination supplied by a Invictus Diode Laser (Kaiser Optical Systems Incorporated, Ann Arbor, Mich.). Where [0127] “The samples were thawed for about 5 minutes and an Eppendorf pipette was used to withdraw about 0.5 μL from the sample vial which was then allowed to spread onto the silver nanorod substrate corresponding to about 5000 plaque forming units (pfus) of HIV, about 350 pfus of Adenovirus and about 35 pfus of Rhinovirus. The virus droplet was allowed to dry and bind to the silver surface for -1 hour prior to the Raman experiment.” each sample had its own measurement, where each sample can be labeled 1, 2, or 3, and the second sample ran is run over the second plurality of wave ranges. [0130] “The SERS spectra of the Adenovirus, Rhinovirus and HIV specimens are shown in FIGS. 9-11, respectively, and the corresponding band assignments are shown in Tables 1-3 (i.e., any one of the tables 1-3 can be a second plurality of wavenumber ranges,) .” See also [0131] which teaches the wavenumber ranges characteristic of viral nucleic acids in the sample Where the plurality wavenumber ranges are pre-selected due to the characteristic of viral nucleic acids, because when looking to document and verify the existence of a virus on a sample, an observer of the spectra would look in the region of the well-known and documented nucleic acid wavenumbers to ascertain if the sample has the nucleic acids. If the sample provided shows the nucleic acids in the location they are to be expected (due to the well-known documentation of the expected ranges and values) then one would be able to ascertain that the virus is in the sample (i.e., viruses have fingerprints, aka certain nucleic acids will pop at their expected range, and in the right combination the nucleic acids would reveal the type of virus being detected).).
Dluhy does not teach (c) obtaining normalized wavenumber signal intensity data for the first and second wavenumber intensity data sets by pre-processing the signal intensity data using a pre-processing analytical method, (d) obtaining model parameters to be applied to the first and second wavenumber intensity data sets by applying to each one of the pre-processed signal intensity data sets a multivariate regression algorithm, wherein a calibration is performed wherein the pre- processed signal intensity data are compared with viral titre data obtained for the same viral culture conditions using non-Raman spectroscopy methods by visual determination by transmission electron microscopy; (e) inferring response values using the model parameters obtained from each one of the pre-processed data sets and (f) performing variable selection; and wherein the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules in the viral culture is determined using the model parameters obtained for the identified Raman spectral variables derived from the multivariate data processing models.
Driskell teaches (c) obtaining normalized wavenumber signal intensity data for the first and second wavenumber intensity data sets by pre-processing the signal intensity data using a pre-processing analytical method, (“Classification of the rota virus strains was achieved using partial least squares discriminant analysis that was performed using PLS Toolbox version 4.0 (Eigen Vector Research Inc., Wenatchee, WA), operating in a MATLAB environment (v7.2, The Mathworks Inc., Natick, MA). Multiple PLS-DA models were built to classify the samples according to (I) rota virus-positive or -negative, (2) strain, (3) G-genotype, or (4) P-genotype. SERS spectra used to generate the PLS-DA classification models were first processed by taking the first derivative of each spectrum (IS-point, SavitzkyGolay) and then normalizing to unit vector length [36].” Pg 3 col 1 paragraph 6, a first derivative method); (d) obtaining model parameters to be applied to the first and second wavenumber intensity data sets by applying to each one of the pre-processed signal intensity data sets a multivariate regression algorithm, (“The normalized first derivate spectra were then mean-centered prior to PLS-DA [37,38]. The same spectral preprocessing protocol was used to generate a quantitative predictive model using partial least squares (PLS) regression analysis.” Pg 3 col 1 paragraph 6- col2 paragraph 1), wherein a calibration is performed wherein the pre- processed signal intensity data are compared with viral titre data obtained for the same sample conditions using non-Raman spectroscopy methods (“Cells were incubated at 37°C until a cytopathic effect was evident, then lysates were frozen and thawed twice. Hemi-nested RT-PCR assays were employed to confirm the G and P genotype of each rota virus isolate using type specific primers [39]. The viral tires of all virus stocks were determined by fluorescent focus neutralization assays [40].” Pg. 2 col 2 paragraph 5); (e) inferring response values using the model parameters obtained from each one of the pre-processed data sets (“As is evident, the PLS predicted Concentrations (i.e., inferred response values using model parameters of the PLS model) based on intrinsic SERS spectra are accurate for concentrations
≥
10^4 ffu/ mL. The plot positively deviates at concentrations lower than 10^4 ffu/mL and the predicted concentrations are elevated with respect to the actual sample concentration. (referring to Figs. 4 and 5)” pg. 6 col 2 paragraph 5- pg. 7, col 1 paragraph 2); and (f) performing variable selection, (“Ten calibration samples were prepared between 105 and 106 ffu/mL and SERS spectra were acquired for each concentration. The root mean square error for cross validation (RMSECV) was analyzed to determine the optimum number of latent variable (i.e., performing variable selection) to include in the PLS model.” Pg 6 col 2 paragraph 4); and wherein the ratio of viral nucleic acids to viruses comprising one or more viral structural molecules in the viral culture is determined using the model parameters obtained for the identified Raman spectral variables derived from the multivariate data processing models (“Preliminary studies were designed to assess the utility of the Ag nanorod substrates to generate SERS spectra of rota viruses and to evaluate the reproducibility of the method. For these studies, spectra of rotavirus samples were either baseline corrected using a concave rubber band algorithm (OPUS, Bruker Optics, Inc., Billerica, MA) computed with IO iterations and 64 points or derivatized (1 st derivative, 15 point, Savitzky-Golay). These spectral processing steps facilitate visual comparison of the Raman peak positions for spectra collected at different locations on a SERS substrate and for different substrates. Classification of the rota virus strains was achieved using partial least squares discriminant analysis that was performed using PLS Toolbox version 4.0 (Eigen Vector Research Inc., Wenatchee, WA), operating in a MATLAB environment (v7.2, The Mathworks Inc., Natick, MA). Multiple PLS-DA models were built to classify the samples according to (I) rota virus-positive or -negative, (2) strain, (3) G-genotype, or (4) P-genotype. SERS spectra used to generate the PLS-DA classification models were first processed by taking the first derivative of each spectrum (IS-point, SavitzkyGolay) and then normalizing to unit vector length [36].” Pg 3 col 1 paragraph 5-6, where Partial least squares is a multivariate data processing tool).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the mathematical modeling process of Raman spectra discussed in Driskell to the method of using Raman spectroscopy on viral samples discussed in Dluhy for the purpose of knowing how much viral content the Raman spectroscopy is capable of detecting. This is advantageous because Raman spectroscopy “provides the ability to rapidly detect analytes with chemical specificity intrinsic to vibrational spectroscopy and is emerging as an important tool in bioanalytical applications including identification and classification of pathogenic organisms” (e.g., Driskell pg. 1 col 2 paragraph 3).
Dluhy and Driskell do not teach wherein non-Raman spectroscopy methods by visual determination by transmission electron microscopy.
Homman teaches wherein non-Raman spectroscopy methods by visual determination by transmission electron microscopy ([0006] “The viral particles are identified among the groups of sorted round and elliptical objects by analyzing radial density profiles of the objects in a selected group. For example, the method may be used for intracellular counting and segmentation of siRNA treated human cytomegaloviral particles in TEM images.”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to combine the use of TEM as discussed in Hommon to the viral culture analysis discussed by Dluhy and Driskell for the purpose of providing direct, high-resolution images of atomic structure, size, and morphology of the viral cultures. This is advantageous because TEM allows for an objective, repeatable and reliable way to describe the cell components of viral cultures to accurately determine the maturity stages of the cell components (e.g., [0003], Homman).
Examiner’s Note
Regarding Claims 5-10, and 12-15, the closest prior art Dluhy et al. (US 2009/0086201 A1) hereinafter Dluhy in view of Driskell et al. ("Rapid and Sensitive Detection of Rotavirus Molecular Signatures Using Surface Enhanced Raman Spectroscopy", PLoS ONE, vol. 5, no. 4, 19 April 2010 (2010-04-19), page e10222.) hereinafter Driskell. teaches several limitations and their specifications are rejected below.
Regarding Claim 5, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further teaches wherein the first plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the first wavenumber intensity data set for the viral culture comprises 4 or more of the wavenumber ranges: (i) 420-420 cm-1; (ii) 510-517 cm-1; (iii) 844-863 cm-1; (iv) 992-1037 cm-1; (v) 1057-1069 cm-1; (vi) 1112-1137 cm-1; (vii) 1182-1184 cm-1; (viii) 1193-1199 cm-1; (ix) 1333- 1380 cm-1; (x) 1410-1461 cm-1; (xi) 1583-1586 cm-1 and (xii) 1594-1692 cm-1; (Table 1: Raman Shift (cm^-1) list, see also [0128]).
However, Dluhy and Driskell fail to disclose the use of a variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, and specifically VIP
≥
1.0
, and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims.
Regarding Claim 6, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further teaches wherein the first plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the first wavenumber intensity data set for the viral cultures comprises 4 or more of the wavenumber ranges: (i) 512-515 cm-1; (ii) 846-862 cm-1; (iii) 993-1036 cm-1; (iv) 1060-1066 cm 1; (v) 1115-1134 cm-1; (vi) 1352-1376 cm-1; (vii)1415-1455 cm-1; (viii) 1596-1611 cm-1; (ix) 1626- 1626 cm-1 and (x) 1635-1678 cm-1 (Table 1: Raman Shift (cm^-1) list).
However, Dluhy and Driskell fail to disclose the use of a variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, and specifically VIP
≥
1.25
, and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims.
Regarding Claim 7, Dluhy and Driskell teach the limitations of claim 1.
However, Dluhy and Driskell fail to disclose wherein the first plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the first wavenumber intensity data set for the viral cultures comprises 4 or more of the wavenumber ranges: (i) 848-861 cm-1; (ii) 994-1035 cm-1; (iii) 1119-1129; (iv) 1355-1363 cm-1; (v) 1425-1431 cm-1; (vi) 1597-1608 cm-1; (vii) 1638-1644 cm-1 and (viii) 1652-1658 cm-1; and wherein a variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, is
≥
1.50; and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims
Regarding Claim 8, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further teaches wherein the second plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the second wavenumber intensity data set for the viral cultures comprises 4 or more of the wavenumber ranges: (i) 420-426 cm-1; (ii) 447-448 cm-1; (iii) 514-519 cm-1; (iv) 824-833 cm-1; (v) 838-866 cm-1; (vi) 879-884 cm-1; (vii) 993-1037cm-1; (viii) 1055-1074 cm-1; (ix) 1107-1140 cm-1; (x) 1332-1338 cm-1; (xi) 1350-1376 cm-1; (xii) 1412-1429 cm-1; (xiii) 1438-1441 cm-1; (xiv) 1445- 1464 cm-1; (xv) 1471-1475 cm-1; (xvi) 1486-1506 cm-1; (xvii) 1513-1546 cm-1; (xviii) 1558-1562 cm-1; (xix) 1597-1609 cm-1 and (xx) 1671-1703 cm-1(Table 2: Raman Shift (cm^-1) list).
However, Dluhy and Driskell fail to disclose the use of a variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, and specifically VIP
≥
1.0
, and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims.
Regarding Claim 9, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further teaches wherein the second plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the second wavenumber intensity data set for the viral cultures comprises 4 or more of the wavenumber ranges: (i) 422-423 cm-1; (ii) 843-864 cm-1; (iii) 994-1019 cm-1; (iv) 1026-1035 cm 1; (v) 1057-1069 cm-1; (vi) 1110-1137 cm-1; (vii)1356-1362 cm-1; (viii) 1415-1420 cm-1; (ix) 1450- 1452 cm-1; (x) 1530-1543 cm-1; (xi) 1598-1607 cm-1; (xii) 1675-1675 cm-1 and (xiii) 1689-1690 cm-1 (Table 3: Raman Shift (cm^-1) list).
However, Dluhy and Driskell fail to disclose the use of a variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, and specifically VIP
≥
1.25
, and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims
Regarding Claim 10, Dluhy and Driskell teach the limitations of claim 1.
However, Dluhy and Driskell fail to disclose wherein the second plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the second wavenumber intensity data set for the viral cultures comprises 4 or more of the wavenumber ranges: (i) 845-862 cm-1; (ii) 995-1010 cm-1; (iii) 1028-1034 cm-1; (iv) 1060-1066 cm-1; (v) 1113-1135 cm-1; (vi) 1535-1539 cm-1 and (vii) 1599-1607 cm-1; and wherein the variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, is
≥
1.50; and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims.
Regarding Claim 12, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further teaches wherein the first plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the first wavenumber intensity data set for the viral culture comprises 5 or more of the wavenumber ranges: (i) 420-438 cm-1; (ii) 457-497 cm-1; (iii) 503-552 cm-1; (iv) 576-580 cm-1; (v) 588-589 cm-1; (vi) 604-608 cm-1; (vii) 617-621 cm-1; (viii) 796-805 cm-1; (ix) 808-809 cm-1; (x) 824-911 cm-1; (xi)918-939 cm-1; (xii)971-1168 cm-1; (xiii) 1191-1197 cm-1; (xiv) 1206-1212 cm1; (xv) 1234-1237 cm-1; (xvi) 1246-1252 cm-1; (xvii) 1259-1481 cm-1; (xviii) 1497-1500 cm-1; (xix) 1526-1540 cm-1; (xx) 1545-1550 cm-1; (xxi) 1584-1591 cm-1; (xxii) 1598-1685 cm-1; (xxiii) 1699- 1699 cm-1; (xxiv) 1717-1719 cm-1; (xxv) 1754-1754 cm-1; (xxvi) 1768-1771 cm-1; (xxvii) 1782- 1783 cm-1 and (xxviii) 1789-1800 cm-1 (Table 1: Raman Shift( cm^-1) list).
However, Dluhy and Driskell fail to disclose the use the variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, and specifically VIP
≥
1.0
, and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims.
Similarly, no art rejection is applied to dependent claim 15.
Regarding Claim 13, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further teaches wherein the first plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the first wavenumber intensity data set for the viral culture comprises 5 or more of the wavenumber ranges: (i) 420-421 cm-1; (ii) 426-429 cm-1; (iii) 434-436; (iv) 459-486 cm-1; (v) 490- 496 cm-1; (vi) 504-549 cm-1; (vii) 798-800 cm-1; (viii) 834-885 cm-1; (ix) 892-907 cm-1; (x) 919- 938 cm-1; (xi) 973-973 cm-1; (xii) 981-983 cm-1; (xiii) 990-1145 cm-1; (xiv) 1207-1211 cm-1; (xv) 1248-1250 cm-1 (xvi) 1270-1322 cm-1 (xvii) 1328-1331 cm-1 (xviii) 1346-1380 cm-1 (xix) 1383- 1473 cm-1 (xx) 1476-1478 cm-1 (xxi) 1498-1499 cm-1 (xxii) 1528-1528 cm-1 (xxiii) 1590-1590 cm-1 (xxiv) 1599-1602 cm-1 (xxv) 1609-1613 cm-1 (xxvi) 1616-1620 cm-1 (xxvii) 1628-1634 cm-1 (xxviii) 1640-1672 cm-1 (xxix) 1678-1679 cm-1 (xxx) 1769-1769 cm-1 and (xxxi) 1800- 1800 cm-1(Table 1: Raman Shift( cm^-1) list).
However, Dluhy and Driskell fail to disclose the use the variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, and specifically VIP
≥
1.25
, and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims.
Regarding Claim 14, Dluhy and Driskell teach the limitations of claim 1.
Dluhy further wherein the first plurality of wavenumber ranges in the Raman spectrum which are measured to obtain the first wavenumber intensity data set for the viral cultures comprises 5 or more of wavenumber ranges: (i) 420-420 cm-1; (ii) 467-471 cm-1; (iii) 474-481 cm-1; (iv) 505-529 cm-1; (v) 537-543 cm 1; (vi) 836-884 cm-1; (vii) 897-902 cm-1; (viii) 919-937 cm-1; (ix) 995-1043 cm-1; (x) 1046-1046 cm-1; (xi) 1049-1071 cm-1; (xii) 1084-1144 cm-1; (xiii) 1209-1210 cm-1; (xiv) 1271-1273 cm-1; (xv) 1277-1302 cm-1 (xvi) 1347-1366 cm-1 (xvii) 1386-1433 cm-1 (xviii) 1444-1461 cm-1 (xix) 1467- 1469 cm-1 (xx) 1610-1612 cm-1 (xxi) 1629-1630 cm-1 and (xxii) 1655-1671 cm-1 (Table 3: Raman Shift( cm^-1) list).
However, Dluhy and Driskell fail to disclose the use the variable importance projection (VIP) calculated from the first plurality of wavenumber ranges, and specifically VIP
≥
1.50
, and there are no motivations absent the applicant’s own disclose, to modify Dluhy and Driskell in the manner required by the pending application’s claims.
Since claims 5-10, 12-15 are rejected under 35 U.S.C 101 and 112(b) the claims are not allowed.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/EMMA ALEXANDER/ Patent Examiner, Art Unit 2863
/Catherine T. Rastovski/ Supervisory Primary Examiner, Art Unit 2857