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. 2023 May-Jun:43:58-65.
doi: 10.1016/j.ijmmb.2022.10.011. Epub 2022 Nov 9.

Seroepidemiological and genomic investigation of SARS-CoV-2 spread in North East region of India

Romi Wahengbam  1 , Pankaj Bharali  2 , Prasenjit Manna  2 , Tridip Phukan  2 , Moirangthem Goutam Singh  2 , Gayatri Gogoi  3 , Yasmin Begam Tapadar  3 , Anil Kumar Singh  4 , Rituraj Konwar  4 , Channakeshavaiah Chikkaputtaiah  4 , Natarajan Velmurugan  5 , Selvaraman Nagamani  6 , Hridoy Jyoti Mahanta  6 , Himakshi Sarma  7 , Ravi Kumar Sahu  4 , Prachurjya Dutta  8 , Sawlang Borsingh Wann  2 , Jatin Kalita  2 , G Narahari Sastry  9
Affiliations

Seroepidemiological and genomic investigation of SARS-CoV-2 spread in North East region of India

Romi Wahengbam et al. Indian J Med Microbiol. 2023 May-Jun.

Abstract

Purpose: Seroepidemiology and genomic surveillance are valuable tools to investigate infection transmission during a pandemic. North East (NE) India is a strategically important region being the gateway connecting the country with Southeast Asia. Here, we examined the spread of SARS-CoV-2 in NE India during the first and second waves of COVID-19 using serological and whole genome sequencing approaches.

Methods: qRT-PCR analysis was performed on a selected population (n ​= ​16,295) from June 2020 to July 2021, and metadata was collected. Immunoassays were studied (n ​= ​2026) at three-time points (August 2020, February 2021, and June 2021) and in a cohort (n ​= ​35) for a year. SARS-CoV-2 whole genomes (n ​= ​914) were sequenced and analyzed with those obtained from the databases.

Results: Test positivity rates (TPR) in the first and second waves were 6.34% and 6.64% in Assam, respectively, and a similar pattern was observed in other NE states. Seropositivity in the three time points was 10.63%, 40.3%, and 46.33%, respectively, and neutralizing antibody prevalence was 90.91%, 52.14%, and 69.30%, respectively. Persistence of pan-IgG-N SARS-CoV-2 antibody for over a year was observed among three subjects in the cohort group. Normal variants dominated the first wave, while B.1.617.2 and AY-sublineages dominated the second wave in the region. The prevalence of the variants co-related well with high TPR and seropositivity rate in the region and identified mostly among vaccinated individuals.

Conclusion: The COVID-19 first wave in the region witnessed low transmission with the evolution of diverse variants. Seropositivity increased during the study period with over half of the individuals carrying neutralizing antibodies against SARS-CoV-2. High infection and seroprevalence in NE India during the second wave were associated with the dominant emergence of variants of concern.

Keywords: COVID-19; Neutralizing antibody; Seroprevalence; Test positivity rate; Whole genome sequencing.

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Figures

Fig. 1
Fig. 1
Trend of COVID-19 (a) positivity (b) recovery (c) death in India and states of North East India during first wave and second wave. The data were sourced from www.covid19india.org (retrieved on July 17, 2021).
Fig. 2
Fig. 2
COVID-19 spread in various states of North East region of India and in the neighboring countries sharing international border with the region. (a) Demographics of test positivity rate (TPR), recovery rate, death rate, vaccination rate and variants detected for the states of North East India, and variants identified in the neighboring countries during the study period. The data related to COVID-19 test, recovery, death and vaccination were sourced from www.covid19india.org (retrieved on July 17, 2021). Only the variants of concern and variant of interest are shown. The variant data was retrieved from the Indian SARS-CoV-2 Genomics Consortium (INSACOG) (http://clingen.igib.res.in/covid19genomes/), and GISAID databases (https://www.gisaid.org/) (retrieved on October 15, 2021). The variant dataset for the state of Assam also included the variants identified from the whole genome sequencing conducted in the present study. (b) COVID-19 confirmed cases, (c) TPR, and (d) death cases in the neighboring countries of North East region of India. Data were sourced from Our World in Data (https://ourworldindata.org/coronavirus) (retrieved on October 15, 2021). (e) Seropositivity rate of India and neighboring countries. Data were sourced from Serotracker (https://serotracker.com/en/Explore) (retrieved on October 24, 2021). Seropositivity rate for India, China and Nepal are shown as the average of three different time points of each year. Seropositivity data was not available for Bangladesh, Bhutan and Myanmar.
Fig. 3
Fig. 3
Evolution of SARS-CoV-2 variants at different time points of their detection in the states of North East India. The variant data was sourced from the Indian SARS-CoV-2 Genomics Consortium (INSACOG) (http://clingen.igib.res.in/covid19genomes/), and GISAID databases (https://www.gisaid.org/) (retrieved on October 15, 2021). The variant dataset for the state of Assam also included the variants identified from the whole genome sequencing conducted in the present study.
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