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Abstract

As the world was still recovering from the 2020 pandemic, the devastating impact of Covid-19 driven by the Delta variant shook the world in 2021. As the second wave was declining, there was an unusual surge in Covid-19 positive cases by the end of 2021 which led to global concern about the change in virus characteristics.

Whole genome sequencing is critical for understanding a rapidly progressing pandemic.

. To provide an insight into the major differences encountered in the changing characteristics between the second and third waves of the pandemic at a tertiary care hospital in India.

A retrospective observational cohort analysis was conducted on Covid-positive patients during the second wave of the Covid-19 pandemic (from March 2021 to April 2021) and the third wave of the Covid-19 pandemic (from December 2021 to January 2022).

Out of 303 Covid-19 positive cases, 52 samples were tested by whole genome sequencing during the second wave and 108 during the third wave. A decline of 18.5 % was observed in the case fatality rate from the second wave to the third wave. There was a 5 % decline in the number of patients admitted with ARDS and a 16.3 % decline in the number of patients with co-morbidities.

In total, 51.9 percent of cases were due to the Delta variant during the second wave and 95 percent due to the Omicron variant during the third wave. We found that 36.5 % of Covid-positive patients during the second wave had been vaccinated compared to 40 % in the third wave.

Whole genome sequencing of clinical samples from a wide range of individuals during a viral epidemic will enable us to develop a more rapid public health response to new variants and identify the required vaccine modifications more quickly.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
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2023-05-12
2024-12-13
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References

  1. Welfare M of H and F 2022 https://www.mohfw.gov.in/ accessed 1 August 2022
  2. Samarasekera U. India grapples with second wave of COVID-19. Lancet Microbe 2021; 2:e238 [View Article] [PubMed]
    [Google Scholar]
  3. Kavitha C, Gowrisankar A, Banerjee S. The second and third waves in India: when will the pandemic be culminated?. Eur Phys J Plus 2021; 136:596 [View Article] [PubMed]
    [Google Scholar]
  4. Thakur V, Bhola S, Thakur P, Patel SKS, Kulshrestha S et al. Waves and variants of SARS-CoV-2: understanding the causes and effect of the COVID-19 catastrophe. Infection 2022; 50:309–325 [View Article] [PubMed]
    [Google Scholar]
  5. World Health Organisation 2016 https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ accessed 2 August 2022
  6. Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 2021; 599:114–119 [View Article] [PubMed]
    [Google Scholar]
  7. Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020; 5:1403–1407 [View Article] [PubMed]
    [Google Scholar]
  8. Ramani S, Bahuguna M, Tiwari A, Shende S, Waingankar A et al. Corona was scary, lockdown was worse: a mixed-methods study of community perceptions on COVID-19 from urban informal settlements of Mumbai. PLoS One 2022; 17:e0268133 [View Article] [PubMed]
    [Google Scholar]
  9. Cepheid Diagnostics Xpert ® Xpress SARS-CoV-2; 2022May
  10. La Marca A, Capuzzo M, Paglia T, Roli L, Trenti T et al. Testing for SARS-CoV-2 (COVID-19): a systematic review and clinical guide to molecular and serological in-vitro diagnostic assays. Reprod Biomed Online 2020; 41:483–499 [View Article] [PubMed]
    [Google Scholar]
  11. CDC The Whole Genome Sequencing (WGS) Process; 2016 264789
  12. Fan G, Yang Z, Lin Q, Zhao S, Yang L et al. Decreased case fatality rate of COVID-19 in the second wave: a study in 53 countries or regions. Transbound Emerg Dis 2021; 68:213–215 [View Article] [PubMed]
    [Google Scholar]
  13. S. Chandrasekhar FRS, Laily Noor I. Jurusan teknik mesin. First and second waves of coronavirus disease-19: a comparative study in hospitalized patients in Reus, Spain. Liq Cryst 2020; 21:1–17
    [Google Scholar]
  14. Coccia M. The impact of first and second wave of the COVID-19 pandemic in society: comparative analysis to support control measures to cope with negative effects of future infectious diseases. Environ Res 2021; 197:111099 [View Article] [PubMed]
    [Google Scholar]
  15. Aggarwal A, Mehta S, Gupta D, Sheikh S, Pallagatti S et al. Clinical & immunological erythematosus patients characteristics in systemic lupus maryam. J Dent Educ 2012; 76:1532–1539 [View Article] [PubMed]
    [Google Scholar]
  16. Chakraborty C, Sharma AR, Bhattacharya M, Agoramoorthy G, Lee S-S. The current second wave and COVID-19 vaccination status in India. Brain Behav Immun 2021; 96:1–4 [View Article] [PubMed]
    [Google Scholar]
  17. Philomina J B, Jolly B, John N, Bhoyar RC, Majeed N et al. Genomic survey of SARS-CoV-2 vaccine breakthrough infections in healthcare workers from Kerala, India. J Infect 2021; 83:237–279 [View Article] [PubMed]
    [Google Scholar]
  18. Welfare M of H and F n.d. List of INSACOG Laboratories with suggested distribution of States/UTs.
  19. Indian Council for Medical Research Genomic surveillance for SARS-cov-2 in India Indian SARS-cov-2 genomics consortium (INSACOGG). My Gov, Government India 20211–18
    [Google Scholar]
  20. Chen Z, Azman AS, Chen X, Zou J, Tian Y et al. Global landscape of SARS-CoV-2 genomic surveillance and data sharing. Nat Genet 2022; 54:499–507 [View Article] [PubMed]
    [Google Scholar]
  21. Yang W, Shaman J. COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant and implications for vaccination. J R Soc Interface 2022; 19:20210900 [View Article] [PubMed]
    [Google Scholar]
  22. Tian D, Sun Y, Zhou J, Ye Q. The global epidemic of the SARS-CoV-2 Delta variant, key spike mutations and immune escape. Front Immunol 2021; 12:751778 [View Article] [PubMed]
    [Google Scholar]
  23. Gowrisankar A, Priyanka TMC, Banerjee S. Omicron: a mysterious variant of concern. Eur Phys J Plus 2022; 137:100 [View Article] [PubMed]
    [Google Scholar]
  24. Pandey A, Sah P, Moghadas SM, Mandal S, Banerjee S et al. Challenges facing COVID-19 vaccination in India: lessons from the initial vaccine rollout. J Glob Health 2021; 11:1–5 [PubMed]
    [Google Scholar]
  25. Arora P, Zhang L, Rocha C, Sidarovich A, Kempf A et al. Comparable neutralisation evasion of SARS-CoV-2 omicron subvariants BA.1, BA.2, and BA.3. Lancet Infect Dis 2022; 22:766–767 [View Article] [PubMed]
    [Google Scholar]
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