Surge of severe acute respiratory syndrome coronavirus 2 infections linked to single introduction of a virus strain in Myanmar, 2020

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a major health concern globally. Genomic epidemiology is an important tool to assess the pandemic of coronavirus disease 2019 (COVID-19). Several mutations have been reported by genome analysis of the SARS-CoV-2. In the present study, we investigated the mutational and phylogenetic analysis of 30 whole-genome sequences for the virus's genomic characteristics in the specimens collected in the early phase of the pandemic (March–June, 2020) and the sudden surge of local transmission (August–September, 2020). The four samples in the early phase of infection were B.6 lineage and located within a clade of the samples collected at the same time in Singapore and Malaysia, while five returnees by rescue flights showed the lineage B. 1.36.1 (three from India), B.1.1 (one from India) and B.1.80 (one from China). However, there was no evidence of local spread from these returnees. Further, all 19 whole-genome sequences collected in the sudden surge of local transmission showed lineage B.1.36. The surge of the second wave on SARS-CoV-2 infection was linked to the single-introduction of a variant (B.1.36) that may result from the strict restriction of international travel and containment efforts. These genomic data provides the useful information to disease control and prevention strategy.

Epidemiology and Genetic Analysis of SARS-CoV-2 in Myanmar during the Community Outbreaks in 2020

“…The genetic analysis of 41 strains (10 from this study and 31 downloaded from GI-SAID) showed that first, five Myanmar sequences during April to early May 2020 belonged to GISAID clade O, Nextstrain clade 19A, and PANGOLIN B.6 (Figure 3A and Table S2) [14]. Thereafter, the genotypes diversified and changed into GISAID clade G (Nextstrain 20A; PANGOLIN B.…”

“…To clarify the genotypes of strains in Myanmar, 10 sequences in this study and an additional 31 sequences already registered in the public database were analyzed by Nextstrain to find out Nexstrain and GISAID clades (https://clades.nextstrain.org (accessed on 30 November 2021)) [14,20,21]. The 10 whole genomes sequenced in the current study have been deposited in the GISAID EpiCoV coronavirus SARS-CoV2 database (www.gisaid.org (accessed on 12 June 2021) (Table S1), and 31 strains previously submitted from the Department of Medical Research (DMR), Myanmar, were downloaded from the GISAID (EPI_ISL_896572-EPI_ISL_896601) (Table S2) [22].…”

“…According to the previously published report from other group in Myanmar, they analyzed the demographic characteristics of 31 COVID-19 patients from April to September 2020. Among them, 21 patients were from Yangon City, and ten patients were from the Rakhine States [14]. The patients were adults, ages ranging from 21 to 84 years, and female (54.8%, 17/31) were similar number of male cases (45.2%, 14/31).…”

“…Out of 31 cases, 14 local transmission cases had a history of contact with known COVID-19 patients, but no traveling history to foreign countries. The remaining 17 patients had no contact history with a known positive case [14]. Additionally, the clinical symptoms were extracted from the matching cases from the official website of Ministry of Health [13].…”

“…We have used the official surveillance data of COVID-19 in Myanmar, described characteristics of the two epidemic waves with case fatality rates, and estimated the effective reproductive number for the epidemics. In this study, the SARS-CoV-2 whole-genome sequences from 10 patients in Myanmar collected in August 2020 at the beginning of the second wave were investigated to identify the genetic diversity among the viruses together with 31 sequences [14] deposited in the public genetic database from Myanmar during 2020, to understand the molecular epidemiology of the SARS-CoV-2 virus in Myanmar.…”