The Emergence and Spread of Novel SARS-CoV-2 Variants

Abstract

Since severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) began to spread in late 2019, laboratories around the world have widely used whole genome sequencing (WGS) to continuously monitor the changes in the viral genes and discovered multiple subtypes or branches evolved from SARS-CoV-2. Recently, several novel SARS-CoV-2 variants have been found to be more transmissible. They may affect the immune response caused by vaccines and natural infections and reduce the sensitivity to neutralizing antibodies. We analyze the distribution characteristics of prevalent SARS-CoV-2 variants and the frequency of mutant sites based on the data available from GISAID and PANGO by R 4.0.2 and ArcGIS 10.2. Our analysis suggests that B.1.1.7, B.1.351, and P.1 are more easily spreading than other variants, and the key mutations of S protein, including N501Y, E484K, and K417N/T, have high mutant frequencies, which may have become the main genotypes for the spread of SARS-CoV-2.

SARS-CoV-2 Serological and Biomolecular Analyses among Companion Animals in Campania Region (2020–2021)

“…On the other hand, lower susceptibility to SARS-CoV-2 in dogs, with low amounts of viral RNA shedding, has been observed [7][8][9][10]. Due to SARS-CoV-2's error-prone nature during replication, several mutations have rapidly arisen that, in a few months, have led to the evolution of new variants, and some of them have rapidly spread worldwide [11]. Moreover, several studies have reported SARS-CoV-2 infections in companion animals by variants that appeared early in the pandemic [1,12,13], and later with B.1.1.7 Alpha [14,15] and the B.1.617.2 Delta variants [10].…”

Clinico-Genomic Analysis Reiterates Mild Symptoms Post-vaccination Breakthrough: Should We Focus on Low-Frequency Mutations?

“…Such mutations can be classified as high- and low-frequency mutations based on their occurrence in the sample compared with the global datasets ( Table 2 ). All the mutations observed in higher frequencies were well studied due to their stability and global distribution ( Cele et al, 2021 ; Collier et al, 2021 ; Yi et al, 2021 ), with some of them being used as lineage-defining mutations ( Dhar et al, 2021 ; Lauring and Hodcroft, 2021 ; Tegally et al, 2021 ; Figure 2 ). Understanding and reporting low-frequency mutations with potential implications in functional modulation is a valuable resource for rapid strain containment response after performing validation studies ( Pandey and Agrawal, 2020 ).…”

Rapid screening assays of N501Y and E484K SARS-CoV-2 variants and identification of an emerging N501T variant in France

“…1.1.7) found in a retrospective study in the UK on September 20, 2020 [3]. B.1.1.7 was characterized by an unusually large number of mutations including 14 non-synonymous mutations, 6 synonymous mutations and 4 deletions [4]. Three mutations in the S gene, N501Y located in the receptorbinding motif (RBM), 69-70 deletion lead to conformational changes of S protein and P681H adjacent to the furin cleavage site are particularly implicated in the dissemination of the variant.…”