Genetic diversity of SARS-CoV-2 and clinical, epidemiological characteristics of COVID-19 patients in Hanoi, Vietnam

Abstract

A second cluster of COVID-19 cases imported from Europe occured in Vietnam from early March 2020. We describe 44 SARS-CoV-2 RT-PCR positive patients (cycle threshold value <30) admitted to the National Hospital for Tropical Diseases in Hanoi between March 6 and April 15 2020. Whole SARS-CoV-2 genomes from these patients were sequenced using Illumina Miseq and analysed for common genetic variants and relationships to local and globally circulating strains. Results showed that 32 cases were Vietnamese with a median age of 37 years (range 15–74 years), and 23 were male. Most cases were acquired outside Vietnam, mainly from the UK (n = 15), other European countries (n = 14), Russia (n = 6) and countries in Asia (n = 3). No cases had travelled from China. Forty-one cases had symptoms at admission, typically dry cough (n = 36), fever (n = 20), sore throat (n = 14) and diarrhoea (n = 12). Hospitalisation was long with a median of 25 days, most commonly from 20–29 days. All SARS-CoV-2 genomes were similar (92–100% sequence homology) to the reference sequence Wuhan_1 (NC_045512), and 32 strains belonged to the B.1.1 lineage. The three most common variants were linked, and included C3037T, C14408T (nsp12: P323L) and A23403G (S: D614G) mutations. This group of mutations often accompanied variant C241T (39/44 genomes) or GGG 28881..28883 AAC (33/44 genomes). The prevalence of the former reflected probable European origin of viruses, and the transition D614G was dominant in Vietnam. New variants were identified; however, none could be associated with disease severity.

Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia

“…A recent study showed that the SARS-CoV-2 with the G614 variant revealed increased infectivity, competitive fitness, and transmission than the wild-type D614 virus in human airway epithelial cells and hamster ( Hou et al, 2020 ). However, this mutation was not associated with the severity of COVID-19 ( Korber et al, 2020 ; Nguyen et al, 2020 ). Here, we aimed: (1) to report full-length genome sequences of SARS-CoV-2 collected from four COVID-19 patients in the Special Region of Yogyakarta and Central Java provinces, Indonesia; (2) to compare the clade distribution of full-length genome sequences from Indonesia ( n = 60) from March to September 2020; and (3) to perform phylogenetic analysis of SARS-CoV-2 complete genomes from different countries, including Indonesia.…”

“…Recently, SARS-CoV-2 with the D614G mutation became the most frequently detected globally, including South East Asia region ( Korber et al, 2020 ; Nguyen et al, 2020 ). Interestingly, SARS-CoV-2 with the G614 variant had significantly higher infectious titers than the original D614 virus, and COVID-19 patients with the G614 variant had a higher viral load than patients without the mutation ( Korber et al, 2020 ).…”

Comparative study of predicted miRNA between Indonesia and China (Wuhan) SARS-CoV-2: a bioinformatics analysis

“…Additionally, the combination of Spike D614G and NSP12 P323L in all detected SARS-CoV-2 variants indicates the importance of these two mutations in terms of transmission and pathogenicity rate (Hartley et al 2020 ; Kannan et al 2020 ; Mutlu et al 2020 ). A study from Vietnam cases, which also found D614G and P323L as the most common mutations, suggests that there is a high probability of the European origin of viruses in their samples as these two mutations are highly dominant in European samples (Nguyen et al 2020 ). Unlike the previous two mutations, only a few studies discuss the N3 Q57H mutation (Wang et al 2020 ; Soratto et al 2020 ; Hassan et al 2020 ).…”

Peer Review #1 of "Full-length genome characterization and phylogenetic analysis of SARS-CoV-2 virus strains from Yogyakarta and Central Java, Indonesia (v0.2)"

“…A recent study showed that the SARS-CoV-2 with the G614 variant revealed increased infectivity, competitive fitness, and transmission than the wild-type D614 virus in human airway epithelial cells and hamster [7]. However, this mutation was not associated with the severity of COVID-19 [5,6].…”

“…Recently, SARS-CoV-2 with the D614G mutation became the most frequently detected globally, including South East Asia region [5,6]. Interestingly, SARS-CoV-2 with the G614 variant had significantly higher infectious titers than the original D614 virus, and COVID-19 patients with the G614 variant had a higher viral load than patients without the mutation [5].…”