A comparative analysis of the second and third wave of the Covid-19 pandemic: an experience from a tertiary care hospital in Western India

Abstract

Introduction. 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. Hypothesis/gap statement. Whole genome sequencing is critical for understanding a rapidly progressing pandemic. Aim. 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. Methods. 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). Results. 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. Conclusion. 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.

Early 2022 breakthrough infection sera from India target the conserved cryptic class 5 epitope to counteract immune escape by SARS-CoV-2 variants

“…In contrast to vaccination alone, hybrid immunity resulting from SARS-CoV-2 breakthrough infections has been shown to boost neutralizing antibody titers while increasing their breadth at the same time 31,32 . We shortlisted individuals who received two doses of the ChAdOx1 nCoV-19 viral vector vaccine between April and November 2021 and then were infected between November 2021 and January 2022, which marks the transition between the second and third waves of the pandemic, in India caused by the B.1.617.2 (Delta) and B.1.1.529 (Omicron) variants, respectively 33 . We hypothesized that such individuals would have developed broadly cross-reactive neutralizing antibodies that are effective against different variants of concern 31,32 .…”

“…Most of the serum samples neutralized Delta and Kappa variants better than WA.1 (Figure 1C, heatmap) due to the high similarity between the spikes of both variants 35 . Interestingly, certain sera (BCRTH 29,30,33,35,45,46) showed potent neutralization against WA.1 but failed to neutralize other tested VOCs, especially at higher dilutions (Figure 1C). This suggests that vaccination and subsequent infections have primed a strong immune response towards the parental strain but failed to generate antibodies that are broadly cross reactive against the VOCs, as also reported previously 36 .…”