Genomic characterization of SARS-CoV-2 identified in a reemerging COVID-19 outbreak in Beijing's Xinfadi market in 2020

Abstract

After 56 days without coronavirus disease 2019 (COVID-19) cases, reemergent cases were reported in Beijing, China on June 11, 2020. Here, we report the genetic characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequenced from the clinical specimens of 4 human cases and 2 environmental samples. The nucleotide similarity among six SARS-CoV-2 genomes ranged from 99.98% to 99.99%. Compared with the reference strain of SARS-CoV-2 (GenBank No. NC_045512), all six genome sequences shared the same substitutions at nt241 (C → T), nt3037 (C → T), nt14408 (C → T), nt23403 (A → G), nt28881 (G → A), nt28882 (G → A), and nt28883 (G → C), which are the characteristic nucleotide substitutions of L-lineage European branch I. This was also proved by the maximum likelihood phylogenetic tree based on the full-length genome of SARS-CoV-2. They also have a unique shared nucleotide substitution, nt6026 (C → T), which is the characteristic nucleotide substitution of SARS-CoV-2 in Beijing's Xinfadi outbreak. It is noteworthy that there is an amino acid D614G mutation caused by nt23403 substitution in all six genomes, which may enhance the virus's infectivity in humans and help it become the leading strain of the virus to spread around the world today. It is necessary to continuously monitor the genetic variation of SARS-CoV-2, focusing on the influence of key mutation sites of SARS-CoV-2 on viral transmission, clinical manifestations, severity, and course of disease.

Keywords: COVID-19; D614G mutation; Genomic epidemiology; L-lineage European branch I; SARS-CoV-2.

Fig. 1

Maximum likelihood phylogenetic tree based on the full-length genome sequences of the SARS-CoV-2. The tree was constructed using MEGA (v7.0) software with 1,000 bootstrap replicates. The genomes of the SARS-CoV-2 from Beijing's Xinfadi market are highlighted in shades of yellow. The genomes of the SARS-CoV-2 from Beijing (Feb-2020) and Wuhan (Dec-2019) are highlighted in shades of grey and pink, respectively. The recent reemergence of SARS-CoV-2 in Northeastern China (Shulan and Heilongjiang) that was associated with imported cases are highlighted in shades of blue and green, respectively. S- or L-lineage of the SARS-CoV-2 are marked and colored on the right. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 2

Nucleotide substitutions of six SARS-CoV-2 genome sequences identified from Beijing's Xinfadi market compared with the reference strain of SARS-CoV-2 (GenBank No. NC_045512). The characteristic nucleotide substitutions of L-lineage, nt8782C and nt28144T, are highlighted in shades of blue. The characteristic nucleotide substitutions of L-lineage European branch I, nt241(C → T), nt3037(C → T), nt14408(C → T), nt23403(A → G), nt28881(G → A), nt28882(G → A), and nt28883(G → C), are highlighted in shades of yellow. The characteristic nucleotide substitution of SARS-CoV-2 from the Xinfadi market, nt6026(C → T), is highlighted in shades of green. nt23403(A → G) is a nonsynonymous substitution in S gene, which leads to D614G mutation of S protein (indicated in red). (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)