A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys

Prateek Singh; Rajat Ujjainiya; Satyartha Prakash; Salwa Naushin; Viren Sardana; Nitin Bhatheja; Ajay Pratap Singh; Joydeb Barman; Kartik Kumar; Saurabh Gayali; Raju Khan; Birendra Singh Rawat; Karthik Bharadwaj Tallapaka; Mahesh Anumalla; Amit Lahiri; Susanta Kar; Vivek Bhosale; Mrigank Srivastava; Madhav Nilakanth Mugale; C. P. Pandey; Shaziya Khan; Shivani Katiyar; Desh Raj; Sharmeen Ishteyaque; Sonu Khanka; Ankita Rani; Promila; Jyotsna Sharma; Anuradha Seth; Mukul Dutta; Nishant Saurabh; Murugan Veerapandian; Ganesh Venkatachalam; Deepak Bansal; Dinesh Gupta; Prakash M. Halami; Muthukumar Serva Peddha; Ravindra P. Veeranna; Anirban Pal; Ranvijay Kumar Singh; Suresh Kumar Anandasadagopan; Parimala Karuppanan; Syed Nasar Rahman; Gopika Selvakumar; Subramanian Venkatesan; Malay Kumar Karmakar; Harish Kumar Sardana; Anamika Kothari; Devendra Singh Parihar; Anupma Thakur; Anas Saifi; Naman Gupta; Yogita Singh; Ritu Reddu; Rizul Gautam; Anuj Mishra; Avinash Mishra; Iranna Gogeri; Geethavani Rayasam; Yogendra Padwad; Vikram Patial; Vipin Hallan; Damanpreet Singh; Narendra Tirpude; Partha Chakrabarti; Sujay Krishna Maity; Dipyaman Ganguly; Ramakrishna Sistla; Narender Kumar Balthu; Kiran A. Kumar; Siva Ranjith; B. Vijay Kumar; Piyush Singh Jamwal; Anshu Wali; Sajad Ahmed; Rekha Chouhan; Sumit G. Gandhi; Nancy Sharma; Garima Rai; Faisal Irshad; Vijay Lakshmi Jamwal; Masroor Ahmad Paddar; Sameer Ullah Khan; Fayaz Malik; Debashish Ghosh; Ghanshyam Thakkar; S. K. Barik; Prabhanshu Tripathi; Yatendra Kumar Satija; Sneha Mohanty; Md Tauseef Khan; Umakanta Subudhi; Pradip Sen; Rashmi Kumar; Anshu Bhardwaj; Pawan Gupta; Deepak Sharma; Amit Tuli; Saumya Ray Chaudhuri; Srinivasan Krishnamurthi; L. Prakash; Ch Rao; B. N. Singh; Arvindkumar Chaurasiya; Meera Chaurasiya; Mayuri Bhadange; Bhagyashree Likhitkar; Sharada Mohite; Yogita Patil; Mahesh Kulkarni; Rakesh Joshi; Vaibhav Pandya; Sachin Mahajan; Amita Patil; Rachel Samson; Tejas Vare; Mahesh Dharne; Ashok Giri; Shilpa Paranjape; G. Narahari Sastry; Jatin Kalita; Tridip Phukan; Prasenjit Manna; Wahengbam Romi; Pankaj Bharali; Dibyajyoti Ozah; RaviKumar Sahu; Prachurjya Dutta; Moirangthem Goutam Singh; Gayatri Gogoi; Yasmin Begam Tapadar; Elapavalooru V. S. S. K. Babu; Rajeev K. Sukumaran; Aishwarya R. Nair; Anoop Puthiyamadam; Prajeesh Kooloth Valappil; Adrash Velayudhan Pillai Prasannakumari; Kalpana Chodankar; Samir Damare; Ved Varun Agrawal; Kumardeep Chaudhary; Anurag Agrawal; Shantanu Sengupta; Debasis Dash

doi:10.1016/j.compbiomed.2022.105419

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A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys

Journal article

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Peer reviewed

A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys

Prateek Singh, Rajat Ujjainiya, Satyartha Prakash, Salwa Naushin, Viren Sardana, Nitin Bhatheja, Ajay Pratap Singh, Joydeb Barman, Kartik Kumar, Saurabh Gayali, …

Computers in biology and medicine, Vol.146, pp.105419-105419

01/07/2022

DOI: https://doi.org/10.1016/j.compbiomed.2022.105419

PMID: 35483225

Abstract

Biology

Computer Science

Computer Science, Interdisciplinary Applications

Engineering

Engineering, Biomedical

Life Sciences & Biomedicine

Life Sciences & Biomedicine - Other Topics

Mathematical & Computational Biology

Science & Technology

Technology

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.

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Title: A machine learning-based approach to determine infection status in recipients of BBV152 (Covaxin) whole-virion inactivated SARS-CoV-2 vaccine for serological surveys
Creators - without role: Prateek Singh - Institute of Genomics and Integrative Biology
Rajat Ujjainiya - Institute of Genomics and Integrative Biology
Satyartha Prakash - Institute of Genomics and Integrative Biology
Salwa Naushin - Institute of Genomics and Integrative Biology
Viren Sardana - Institute of Genomics and Integrative Biology
Nitin Bhatheja - Institute of Genomics and Integrative Biology
Ajay Pratap Singh - CSIR Inst Genom & Integrat Biol, New Delhi, India
Joydeb Barman - Institute of Genomics and Integrative Biology
Kartik Kumar - Institute of Genomics and Integrative Biology
Saurabh Gayali - CSIR Inst Genom & Integrat Biol, New Delhi, India
Raju Khan - Academy of Scientific and Innovative Research
Birendra Singh Rawat - Central Building Research Institute
Karthik Bharadwaj Tallapaka - Centre for Cellular and Molecular Biology
Mahesh Anumalla - Centre for Cellular and Molecular Biology
Amit Lahiri - Academy of Scientific and Innovative Research
Susanta Kar - Academy of Scientific and Innovative Research
Vivek Bhosale - Academy of Scientific and Innovative Research
Mrigank Srivastava - Academy of Scientific and Innovative Research
Madhav Nilakanth Mugale - Academy of Scientific and Innovative Research
C. P. Pandey - Academy of Scientific and Innovative Research
Shaziya Khan - Academy of Scientific and Innovative Research
Shivani Katiyar - Academy of Scientific and Innovative Research
Desh Raj - Academy of Scientific and Innovative Research
Sharmeen Ishteyaque - Academy of Scientific and Innovative Research
Sonu Khanka - Academy of Scientific and Innovative Research
Ankita Rani - Academy of Scientific and Innovative Research
Promila - Academy of Scientific and Innovative Research
Jyotsna Sharma - Academy of Scientific and Innovative Research
Anuradha Seth - Academy of Scientific and Innovative Research
Mukul Dutta - Academy of Scientific and Innovative Research
Nishant Saurabh - Institute of Genomics and Integrative Biology
Murugan Veerapandian - Academy of Scientific and Innovative Research
Ganesh Venkatachalam - Academy of Scientific and Innovative Research
Deepak Bansal - Academy of Scientific and Innovative Research
Dinesh Gupta - CSIR Cent Elect Engn Rese Arch Inst, Pilani, Rajasthan, India
Prakash M. Halami - Academy of Scientific and Innovative Research
Muthukumar Serva Peddha - Academy of Scientific and Innovative Research
Ravindra P. Veeranna - Academy of Scientific and Innovative Research
Anirban Pal - Academy of Scientific and Innovative Research
Ranvijay Kumar Singh - Academy of Scientific and Innovative Research
Suresh Kumar Anandasadagopan - Academy of Scientific and Innovative Research
Parimala Karuppanan - CSIR Cent Leather Res Inst, Chennai, Tamil Nadu, India
Syed Nasar Rahman - Academy of Scientific and Innovative Research
Gopika Selvakumar - CSIR Cent Leather Res Inst, Chennai, Tamil Nadu, India
Subramanian Venkatesan - Academy of Scientific and Innovative Research
Malay Kumar Karmakar - Academy of Scientific and Innovative Research
Harish Kumar Sardana - Institute of Genomics and Integrative Biology
Anamika Kothari - CSIR Cent Sci Instruments Org, Chandigarh, India
Devendra Singh Parihar - Academy of Scientific and Innovative Research
Anupma Thakur - Academy of Scientific and Innovative Research
Anas Saifi - Academy of Scientific and Innovative Research
Naman Gupta - Academy of Scientific and Innovative Research
Yogita Singh - Central Building Research Institute
Ritu Reddu - Academy of Scientific and Innovative Research
Rizul Gautam - Academy of Scientific and Innovative Research
Anuj Mishra - Academy of Scientific and Innovative Research
Avinash Mishra - Academy of Scientific and Innovative Research
Iranna Gogeri - Academy of Scientific and Innovative Research
Geethavani Rayasam - Academy of Scientific and Innovative Research
Yogendra Padwad - Academy of Scientific and Innovative Research
Vikram Patial - Academy of Scientific and Innovative Research
Vipin Hallan - Academy of Scientific and Innovative Research
Damanpreet Singh - Central Building Research Institute
Narendra Tirpude - Academy of Scientific and Innovative Research
Partha Chakrabarti - Academy of Scientific and Innovative Research
Sujay Krishna Maity - Academy of Scientific and Innovative Research
Dipyaman Ganguly - Academy of Scientific and Innovative Research
Ramakrishna Sistla - Academy of Scientific and Innovative Research
Narender Kumar Balthu - CSIR Indian Inst Chem Technol, Hyderabad, India
Kiran A. Kumar - CSIR Indian Inst Chem Technol, Hyderabad, India
Siva Ranjith - CSIR Indian Inst Chem Technol, Hyderabad, India
B. Vijay Kumar - CSIR Indian Inst Chem Technol, Hyderabad, India
Piyush Singh Jamwal - College Station Medical Center
Anshu Wali - College Station Medical Center
Sajad Ahmed - College Station Medical Center
Rekha Chouhan - College Station Medical Center
Sumit G. Gandhi - Academy of Scientific and Innovative Research
Nancy Sharma - Academy of Scientific and Innovative Research
Garima Rai - Academy of Scientific and Innovative Research
Faisal Irshad - Academy of Scientific and Innovative Research
Vijay Lakshmi Jamwal - Academy of Scientific and Innovative Research
Masroor Ahmad Paddar - Academy of Scientific and Innovative Research
Sameer Ullah Khan - Academy of Scientific and Innovative Research
Fayaz Malik - Academy of Scientific and Innovative Research
Debashish Ghosh - Academy of Scientific and Innovative Research
Ghanshyam Thakkar - CSIR Indian Inst Petr, Dehra Dun, Uttarakhand, India
S. K. Barik - CSIR Indian Inst Toxicol Res, Lucknow, Uttar Pradesh, India
Prabhanshu Tripathi - Academy of Scientific and Innovative Research
Yatendra Kumar Satija - CSIR Indian Inst Toxicol Res, Lucknow, Uttar Pradesh, India
Sneha Mohanty - Academy of Scientific and Innovative Research
Md Tauseef Khan - Academy of Scientific and Innovative Research
Umakanta Subudhi - Academy of Scientific and Innovative Research
Pradip Sen - Academy of Scientific and Innovative Research
Rashmi Kumar - Institute of Genomics and Integrative Biology
Anshu Bhardwaj - Academy of Scientific and Innovative Research
Pawan Gupta - Academy of Scientific and Innovative Research
Deepak Sharma - Academy of Scientific and Innovative Research
Amit Tuli - Academy of Scientific and Innovative Research
Saumya Ray Chaudhuri - Academy of Scientific and Innovative Research
Srinivasan Krishnamurthi - Academy of Scientific and Innovative Research
L. Prakash - CSIR Natl Aerosp Labs, Bengaluru, India
Ch Rao - Academy of Scientific and Innovative Research
B. N. Singh - Academy of Scientific and Innovative Research
Arvindkumar Chaurasiya - Academy of Scientific and Innovative Research
Meera Chaurasiya - Academy of Scientific and Innovative Research
Mayuri Bhadange - Academy of Scientific and Innovative Research
Bhagyashree Likhitkar - Academy of Scientific and Innovative Research
Sharada Mohite - Academy of Scientific and Innovative Research
Yogita Patil - Academy of Scientific and Innovative Research
Mahesh Kulkarni - Academy of Scientific and Innovative Research
Rakesh Joshi - Academy of Scientific and Innovative Research
Vaibhav Pandya - CSIR Natl Chem Lab, Pune, Maharashtra, India
Sachin Mahajan - CSIR Natl Chem Lab, Pune, Maharashtra, India
Amita Patil - CSIR Natl Chem Lab, Pune, Maharashtra, India
Rachel Samson - Academy of Scientific and Innovative Research
Tejas Vare - Academy of Scientific and Innovative Research
Mahesh Dharne - Academy of Scientific and Innovative Research
Ashok Giri - Academy of Scientific and Innovative Research
Sachin Mahajan - Academy of Scientific and Innovative Research
Shilpa Paranjape - CSIR Natl Environm Engn Res Inst, Nagpur, Maharashtra, India
G. Narahari Sastry - Academy of Scientific and Innovative Research
Jatin Kalita - Academy of Scientific and Innovative Research
Tridip Phukan - Academy of Scientific and Innovative Research
Prasenjit Manna - Academy of Scientific and Innovative Research
Wahengbam Romi - Academy of Scientific and Innovative Research
Pankaj Bharali - Academy of Scientific and Innovative Research
Dibyajyoti Ozah - Academy of Scientific and Innovative Research
RaviKumar Sahu - Academy of Scientific and Innovative Research
Prachurjya Dutta - Academy of Scientific and Innovative Research
Moirangthem Goutam Singh - CSIR North East Inst Sci & Technol, Jorhat, Assam, India
Gayatri Gogoi - CSIR North East Inst Sci & Technol, Jorhat, Assam, India
Yasmin Begam Tapadar - CSIR North East Inst Sci & Technol, Jorhat, Assam, India
Elapavalooru V. S. S. K. Babu - Academy of Scientific and Innovative Research
Rajeev K. Sukumaran - Academy of Scientific and Innovative Research
Aishwarya R. Nair - CSIR Natl Inst Interdisciplinary Sci & Technol, Thiruvananthapuram, Kerala, India
Anoop Puthiyamadam - Academy of Scientific and Innovative Research
Prajeesh Kooloth Valappil - Academy of Scientific and Innovative Research
Adrash Velayudhan Pillai Prasannakumari - Academy of Scientific and Innovative Research
Kalpana Chodankar - Academy of Scientific and Innovative Research
Samir Damare - Academy of Scientific and Innovative Research
Ved Varun Agrawal - Academy of Scientific and Innovative Research
Kumardeep Chaudhary - CSIR Inst Genom & Integrat Biol, New Delhi, India
Anurag Agrawal - CSIR Inst Genom & Integrat Biol, New Delhi, India
Shantanu Sengupta - CSIR Inst Genom & Integrat Biol, New Delhi, India
Debasis Dash - CSIR Inst Genom & Integrat Biol, New Delhi, India
Publication Details: Computers in biology and medicine, Vol.146, pp.105419-105419
Publisher: Elsevier
Number of pages: 10
Grant note: DST; Department of Science & Technology (India) DBT-BINC MLP 2007; MLP 1811; MLP-1811; MLP-2002; GAP-0192 / CSIR; Council of Scientific & Industrial Research (CSIR) - India
Identifiers: 9922866008331
Academic Unit: King Khalid University; University Ha'il
Language: English
Resource Type: Journal article