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      Challenges of SARS-CoV-2 genomic surveillance in India during low positivity rate scenario

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          Abstract

          Being the second most populous country in the world, India presents valuable lessons for the world about dealing with the SARS-CoV-2 pandemic. From this perspective, we attempted a retrospective evaluation of India’s SARS-CoV-2 genomic surveillance strategy and also gave some recommendations for undertaking effective genomic surveillance. The dynamics of the COVID-19 pandemic are continuously evolving, and there is a dire need to modulate the genomic surveillance strategy accordingly. The pandemic is now settling towards a low positivity rate scenario, so it is required to revise the practices and policies formulated for a high positivity rate scenario. The perspective also recommends adopting a decentralised approach for SARS-CoV-2 genomic surveillance with a focus on optimising the workflow of SARS-CoV-2 genomic surveillance to ensure early detection of emerging variants, especially in the low positivity rate scenario. The perspective emphasises a key observation that the SARS-CoV-2 genomic surveillance is an important mitigation effort during the pandemic, the guards of such mitigation efforts should not be lowered during the low positivity rate scenario. We attempt to highlight the limitations faced by the Indian healthcare administration during the SARS-CoV-2 genomic surveillance and, simultaneously, suggest policy interventions derived from our first-hand experience, which may be implementable in a vast, populated country like India.

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          Most cited references36

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          Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic

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            Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition

            Antibodies targeting the SARS-CoV-2 spike receptor-binding domain (RBD) are being developed as therapeutics and are a major contributor to neutralizing antibody responses elicited by infection. Here, we describe a deep mutational scanning method to map how all amino-acid mutations in the RBD affect antibody binding, and apply this method to 10 human monoclonal antibodies. The escape mutations cluster on several surfaces of the RBD that broadly correspond to structurally defined antibody epitopes. However, even antibodies targeting the same surface often have distinct escape mutations. The complete escape maps predict which mutations are selected during viral growth in the presence of single antibodies. They further enable the design of escape-resistant antibody cocktails–including cocktails of antibodies that compete for binding to the same RBD surface but have different escape mutations. Therefore, complete escape-mutation maps enable rational design of antibody therapeutics and assessment of the antigenic consequences of viral evolution.
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              N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

              The SARS-CoV-2 spike (S) glycoprotein contains an immunodominant receptor-binding domain (RBD) targeted by most neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite (designated site i) recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge, albeit selecting escape mutants in some animals. Indeed, several SARS-CoV-2 variants, including the B.1.1.7, B.1.351 and P1 lineages, harbor frequent mutations within the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs for protective immunity and vaccine design.
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                Author and article information

                Contributors
                Journal
                Front Public Health
                Front Public Health
                Front. Public Health
                Frontiers in Public Health
                Frontiers Media S.A.
                2296-2565
                27 June 2023
                2023
                27 June 2023
                : 11
                : 1117602
                Affiliations
                [1] 1Environmental Virology Cell (EVC), Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI) , Nagpur, India
                [2] 2Academy of Scientific and Innovative Research (AcSIR) , New Delhi, India
                Author notes

                Edited by: Subhas Khajanchi, Presidency University, India

                Reviewed by: Seil Kim, Korea Research Institute of Standards and Science, Republic of Korea; Xuming Zhou, Chinese Academy of Sciences (CAS), China

                *Correspondence: Krishna Khairnar, k_khairnar@ 123456neeri.res.in
                Article
                10.3389/fpubh.2023.1117602
                10335399
                ca24176b-408c-467a-a4ae-ad80ec5e43fd
                Copyright © 2023 Tomar and Khairnar.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 06 December 2022
                : 12 June 2023
                Page count
                Figures: 3, Tables: 0, Equations: 0, References: 63, Pages: 10, Words: 7869
                Categories
                Public Health
                Policy and Practice Reviews
                Custom metadata
                Infectious Diseases: Epidemiology and Prevention

                pandemic (covid-19),sars-cov-2,genomic surveilance,whole genome sequencing,public health

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