Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging

Abstract

In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Genetic diversity of SARS-CoV-2 in South America: demographic history and structuration signals

“…The nucleotide diversity sliding window showed that the most diverse regions were located at the ORF1a, ORF3, and N loci (Fig. 1 ), agreeing with previous reports [ 59 ]. The viral populations from Peru, Argentina, and Suriname had the highest nucleotide diversity in SA.…”

“…Although nucleotide polymorphism (or Watterson estimator θ W ) was considered the best estimator of SARS-CoV-2 diversity [ 57 ], the nucleotide diversity (π) is a better estimator, since it considers the Ss frequency, and it is not influenced by the sample size. The nucleotide diversity in SA (π = 0.00028) was lower than in other continents/countries (Africa, π = 0.00047; Oceania, π = 0.00046; United States of America, π = 0.00044; Europe, π = 0.00043; Asia, π = 0.00042 [ 59 ]). All of these values were lower than those observed for other human viruses (H1N1 = 0.004-0.012 [ 60 , 61 ]; H3N2 = 0.004 [ 60 ]; hepatitis B virus = 0.015 [ 62 ]; parainfluenza virus = 0.002 [ 63 ]), which could be due to the fact that SARS-CoV-2 is a new human virus.…”

SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence

“…Three studies (one bigdata analysis [50] and two clinical studies [17,51]) reported that the SARS-CoV-2 variants were significantly associated with decrease in severity of disease. The remaining 27 studies (one animal study [18], 22 bigdata analyses [8][9][10][11][52][53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69] and four clinical studies [70][71][72][73]) described the positive association between the different variants with severity of COVID-19 (Table 3). A clinical study by Long et al showed that infection with SARS-CoV-2 variants harboring the D614G substitution was not associated with disease severity, overall mortality, transfer to ICU, mechanical ventilation and length of stay at hospital [41].…”

COVID-19 and the clinical course of rheumatic manifestations

“…Since its first detection at Wuhan in China, SARS-CoV-2 (novel coronavirus 2019) has engulfed the world with rapidly accumulating mutations and variants emerging at frequent intervals [1]. More than 100 million infections and 2.4 million deaths have been reported to the World Health Organization [2].…”