lancet-header

Preprints with The Lancet is part of SSRN´s First Look, a place where journals identify content of interest prior to publication. Authors have opted in at submission to The Lancet family of journals to post their preprints on Preprints with The Lancet. The usual SSRN checks and a Lancet-specific check for appropriateness and transparency have been applied. Preprints available here are not Lancet publications or necessarily under review with a Lancet journal. These preprints are early stage research papers that have not been peer-reviewed. The findings should not be used for clinical or public health decision making and should not be presented to a lay audience without highlighting that they are preliminary and have not been peer-reviewed. For more information on this collaboration, see the comments published in The Lancet about the trial period, and our decision to make this a permanent offering, or visit The Lancet´s FAQ page, and for any feedback please contact preprints@lancet.com.

SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen During Three Consecutive Peaks of Infection in Delhi, India – A Clinico-Genomic Study

47 Pages Posted: 17 Dec 2021

See all articles by Pramod Gautam

Pramod Gautam

Institute of Liver and Biliary Sciences

Diptanu Paul

AIIMS Vijaypur, Jammu

Varun Suroliya

Institute of Liver and Biliary Sciences

Rahul Garg

Institute of Liver and Biliary Sciences

Reshu Agarwal

Institute of Liver and Biliary Sciences - Department of Virology

Santanu Das

Institute of Liver and Biliary Sciences

Urvinder S. Kaur

Institute of Liver and Biliary Sciences

Amit Pandey

Institute of Liver and Biliary Sciences

Arjun Bhugra

Institute of Liver and Biliary Sciences

Bansidhar Tarai

Max Super Specialty Hospital - Max Healthcare

Chhagan Bihari

Institute of Liver and Biliary Sciences

Shiv Kumar Sarin

Institute of Liver and Biliary Sciences - Department of Hepatology

Ekta Gupta

Institute of Liver and Biliary Sciences - Department of Virology

More...

Abstract

Background: Since its advent, the pandemic has caused havoc in multiple waves due partly to amplified transmissibility and immune escape to vaccines. Delhi also witnessed brutal multiple peaks causing exponential rise in cases. Here we had retrospectively investigated clade variation, emergence of new lineages and varied clinical characteristics during those three peaks in order to understand the trajectory of the ongoing pandemic.

Methods: In this study a total of 1,23,378 samples were collected for a time span of fourteen months (1st June 2020, to 3rd August, 2021) encompassing three different peaks in Delhi. A subset of 747 samples was processed for sequencing. Complete clinical and demographic details of all the enrolled cases were also collected.

Findings: We detected 26 lineages across three peaks non-uniformly from 612 quality passed samples. The first peak was driven by diverse early variants, while the second one by B.1.36 and B.1.617.2, unlike third peak caused entirely by B.1.617.2. A total of 18316 mutations with median of 34 were reported. Majority of mutations were present in less than 1% of samples. Differences in clinical characteristics across three peaks was also reported.

Interpretation: In order to be ahead of the frequently changing course of the ongoing pandemic, it is of utmost importance that novel lineages to be tracked continuously. Prioritized sequencing of sudden local outburst and community hotspots must be done in order to swiftly detect a novel mutation/lineage of potential clinical importance.

Funding Information: WGS laboratory at our institute is funded by the Government of NCT, Delhi.

Declaration of Interests: The authors declare no conflict of interest.

Ethics Approval Statement: The present study was approved by Institutional Ethics Committee (IEC) at Institute of Liver and Biliary Sciences, New Delhi (Ethical no. IEC/2020/77/MA07). In this study de-identified and anonymised archived samples were subjected to whole genome sequencing. No personal details except clinically relevant information (age, sex, symptoms and outcome) were used for the purpose of the study. Hence individual consent form was waived off by the IEC.

Keywords: SARS-CoV-2 variants, COVID-19, pandemic, Lineage tracking, Delhi, India

Suggested Citation

Gautam, Pramod and Paul, Diptanu and Suroliya, Varun and Garg, Rahul and Agarwal, Reshu and Das, Santanu and Kaur, Urvinder S. and Pandey, Amit and Bhugra, Arjun and Tarai, Bansidhar and Bihari, Chhagan and Sarin, Shiv Kumar and Gupta, Ekta, SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen During Three Consecutive Peaks of Infection in Delhi, India – A Clinico-Genomic Study. Available at SSRN: https://ssrn.com/abstract=3987993 or http://dx.doi.org/10.2139/ssrn.3987993

Pramod Gautam

Institute of Liver and Biliary Sciences ( email )

India

Diptanu Paul

AIIMS Vijaypur, Jammu ( email )

Jammu & Kashmir 180001
India

Varun Suroliya

Institute of Liver and Biliary Sciences ( email )

India

Rahul Garg

Institute of Liver and Biliary Sciences ( email )

India

Reshu Agarwal

Institute of Liver and Biliary Sciences - Department of Virology ( email )

India

Santanu Das

Institute of Liver and Biliary Sciences ( email )

India

Urvinder S. Kaur

Institute of Liver and Biliary Sciences ( email )

India

Amit Pandey

Institute of Liver and Biliary Sciences ( email )

India

Arjun Bhugra

Institute of Liver and Biliary Sciences ( email )

India

Bansidhar Tarai

Max Super Specialty Hospital - Max Healthcare ( email )

India

Chhagan Bihari

Institute of Liver and Biliary Sciences ( email )

Shiv Kumar Sarin

Institute of Liver and Biliary Sciences - Department of Hepatology ( email )

New Delhi
India

Ekta Gupta (Contact Author)

Institute of Liver and Biliary Sciences - Department of Virology ( email )

India

Click here to go to TheLancet.com

Paper statistics

Abstract Views
364
Downloads
115
PlumX Metrics