학술논문
A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys.
Document Type
Academic Journal
Author
Singh P; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Ujjainiya R; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Prakash S; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.; Naushin S; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Sardana V; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Bhatheja N; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.; Singh AP; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Barman J; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.; Kumar K; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.; Gayali S; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India.; Khan R; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Advanced Materials and Processes Research Institute, Bhopal, India.; Rawat BS; CSIR-Central Building Research Institute, Roorkee, India.; Tallapaka KB; CSIR-Centre for Cellular Molecular Biology, Hyderabad, India.; Anumalla M; CSIR-Centre for Cellular Molecular Biology, Hyderabad, India.; Lahiri A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Kar S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Bhosale V; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Srivastava M; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Mugale MN; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Pandey CP; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Khan S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Katiyar S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Raj D; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Ishteyaque S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Khanka S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Rani A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Promila; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Sharma J; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Seth A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Dutta M; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Drug Research Institute, Lucknow, India.; Saurabh N; CSIR-Central Drug Research Institute, Lucknow, India.; Veerapandian M; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR- Central Electrochemical Research Institute, Karaikudi, India.; Venkatachalam G; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR- Central Electrochemical Research Institute, Karaikudi, India.; Bansal D; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Electronics Engineering Rese arch Institute, Pilani, India.; Gupta D; CSIR-Central Electronics Engineering Rese arch Institute, Pilani, India.; Halami PM; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Food Technological Research Institute, Mysore, India.; Peddha MS; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Food Technological Research Institute, Mysore, India.; Veeranna RP; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Food Technological Research Institute, Mysore, India.; Pal A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Institute of Medicinal Aromatic Plants, Lucknow, India.; Singh RK; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Institute of Mining and Fuel Research, Dhanbad, India.; Anandasadagopan SK; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Leather Research Institute, Chennai, India.; Karuppanan P; CSIR-Central Leather Research Institute, Chennai, India.; Rahman SN; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Leather Research Institute, Chennai, India.; Selvakumar G; CSIR-Central Leather Research Institute, Chennai, India.; Venkatesan S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Leather Research Institute, Chennai, India.; Karmakar MK; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Mechanical Engineering Research Institute, Durgapur, India.; Sardana HK; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Kothari A; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Parihar DS; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Thakur A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Saifi A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Gupta N; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Singh Y; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Reddu R; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Gautam R; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Mishra A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Scientific Instruments Organization, Chandigarh, India.; Mishra A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR- Central Salt Marine Chemicals Research Institute, Bhavnagar, India.; Gogeri I; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR Fourth Paradigm Institute, Bengaluru, India.; Rayasam G; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR- Headquarters, Rafi Marg, New Delhi, India.; Padwad Y; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.; Patial V; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.; Hallan V; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.; Singh D; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.; Tirpude N; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.; Chakrabarti P; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Chemical Biology, Kolkata, India.; Maity SK; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Chemical Biology, Kolkata, India.; Ganguly D; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Chemical Biology, Kolkata, India.; Sistla R; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Chemical Technology, Hyderabad, India.; Balthu NK; CSIR-Indian Institute of Chemical Technology, Hyderabad, India.; A KK; CSIR-Indian Institute of Chemical Technology, Hyderabad, India.; Ranjith S; CSIR-Indian Institute of Chemical Technology, Hyderabad, India.; Kumar BV; CSIR-Indian Institute of Chemical Technology, Hyderabad, India.; Jamwal PS; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Wali A; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Ahmed S; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Chouhan R; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Gandhi SG; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Sharma N; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Rai G; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Irshad F; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Jamwal VL; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Paddar MA; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Khan SU; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Malik F; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Integrative Medicine, Jammu, India.; Ghosh D; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Petroleum, Dehradun, India.; Thakkar G; CSIR-Indian Institute of Petroleum, Dehradun, India.; Barik SK; CSIR-Indian Institute of Toxicology Research, Lucknow, India; CSIR-National Botanical Research Institute, Lucknow, India.; Tripathi P; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Toxicology Research, Lucknow, India.; Satija YK; CSIR-Indian Institute of Toxicology Research, Lucknow, India.; Mohanty S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Toxicology Research, Lucknow, India.; Khan MT; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Indian Institute of Toxicology Research, Lucknow, India.; Subudhi U; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Minerals and Materials Technology, Bhubaneswar, India.; Sen P; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Microbial Technology, Chandigarh, India.; Kumar R; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Microbial Technology, Chandigarh, India.; Bhardwaj A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Microbial Technology, Chandigarh, India.; Gupta P; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Microbial Technology, Chandigarh, India.; Sharma D; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Microbial Technology, Chandigarh, India.; Tuli A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Microbial Technology, Chandigarh, India.; Ray Chaudhuri S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Microbial Technology, Chandigarh, India.; Krishnamurthi S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Institute of Microbial Technology, Chandigarh, India.; Prakash L; CSIR- National Aerospace Laboratories, Bengaluru, India.; Rao CV; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Botanical Research Institute, Lucknow, India.; Singh BN; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Botanical Research Institute, Lucknow, India.; Chaurasiya A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Chaurasiyar M; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Bhadange M; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Likhitkar B; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Mohite S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Patil Y; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Kulkarni M; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Joshi R; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Pandya V; CSIR-National Chemical Laboratory, Pune, India.; Mahajan S; CSIR-National Chemical Laboratory, Pune, India.; Patil A; CSIR-National Chemical Laboratory, Pune, India.; Samson R; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Vare T; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Dharne M; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Giri A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Chemical Laboratory, Pune, India.; Mahajan S; CSIR-National Chemical Laboratory, Pune, India.; Paranjape S; CSIR-National Environmental Engineering Research Institute, Nagpur, India.; Sastry GN; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Kalita J; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Phukan T; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Manna P; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Romi W; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Bharali P; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Ozah D; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Sahu RK; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Dutta P; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Singh MG; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Gogoi G; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Tapadar YB; CSIR-North - East Institute of Science and Technology, Jorhat, India.; Babu EV; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR- National Geophysical Research Institute, Hyderabad, India.; Sukumaran RK; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India.; Nair AR; CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India.; Puthiyamadam A; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India.; Valappil PK; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India.; Pillai Prasannakumari AV; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Institute for Interdisciplinary Science and Technology, Thiruvananthapuram, India.; Chodankar K; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR- National Institute of Oceanography, Goa, India.; Damare S; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR- National Institute of Oceanography, Goa, India.; Agrawal VV; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-National Physical Laboratory, New Delhi, India.; Chaudhary K; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Agrawal A; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Sengupta S; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. Electronic address: shantanus@igib.res.in.; Dash D; CSIR-Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. Electronic address: ddash@igib.res.in.
Source
Publisher: Elsevier Country of Publication: United States NLM ID: 1250250 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0534 (Electronic) Linking ISSN: 00104825 NLM ISO Abbreviation: Comput Biol Med Subsets: MEDLINE
Subject
Language
English
Abstract
Data science has been an invaluable part of the COVID-19 pandemic response with multiple applications, ranging from tracking viral evolution to understanding the vaccine effectiveness. Asymptomatic breakthrough infections have been a major problem in assessing vaccine effectiveness in populations globally. Serological discrimination of vaccine response from infection has so far been limited to Spike protein vaccines since whole virion vaccines generate antibodies against all the viral proteins. Here, we show how a statistical and machine learning (ML) based approach can be used to discriminate between SARS-CoV-2 infection and immune response to an inactivated whole virion vaccine (BBV152, Covaxin). For this, we assessed serial data on antibodies against Spike and Nucleocapsid antigens, along with age, sex, number of doses taken, and days since last dose, for 1823 Covaxin recipients. An ensemble ML model, incorporating a consensus clustering approach alongside the support vector machine model, was built on 1063 samples where reliable qualifying data existed, and then applied to the entire dataset. Of 1448 self-reported negative subjects, our ensemble ML model classified 724 to be infected. For method validation, we determined the relative ability of a random subset of samples to neutralize Delta versus wild-type strain using a surrogate neutralization assay. We worked on the premise that antibodies generated by a whole virion vaccine would neutralize wild type more efficiently than delta strain. In 100 of 156 samples, where ML prediction differed from self-reported uninfected status, neutralization against Delta strain was more effective, indicating infection. We found 71.8% subjects predicted to be infected during the surge, which is concordant with the percentage of sequences classified as Delta (75.6%-80.2%) over the same period. Our approach will help in real-world vaccine effectiveness assessments where whole virion vaccines are commonly used.
(Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
(Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)