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

Abstract

We aimed to analyze the situation of the first two epidemic waves in Myanmar using the publicly available daily situation of COVID-19 and whole-genome sequencing data of SARS-CoV-2. From March 23 to December 31, 2020, there were 33,917 confirmed cases and 741 deaths in Myanmar (case fatality rate of 2.18%). The first wave in Myanmar from March to July was linked to overseas travel, and then a second wave started from Rakhine State, a western border state, leading to the second wave spreading countrywide in Myanmar from August to December 2020. The estimated effective reproductive number (R_t) nationwide reached 6-8 at the beginning of each wave and gradually decreased as the epidemic spread to the community. The whole-genome analysis of 10 Myanmar SARS-CoV-2 strains together with 31 previously registered strains showed that the first wave was caused by GISAID clade O or PANGOLIN lineage B.6 and the second wave was changed to clade GH or lineage B.1.36.16 with a close genetic relationship with other South Asian strains. Constant monitoring of epidemiological situations combined with SARS-CoV-2 genome analysis is important for adjusting public health measures to mitigate the community transmissions of COVID-19.

Keywords: COVID-19; SARS-CoV-2; case fatality rate; community transmission; molecular epidemiology; reproductive number; whole-genome sequences.

Figure 1

Location of Rakhine State (orange) and Yangon (pink) in Myanmar. Source: This map was generated by ArcMap 10.0 software (ESRI, Tokyo, Japan).

Figure 2

The epidemic situation of coronavirus disease-2019 (COVID-19) in Myanmar from 23 March to 30 December 2020. (A) The daily number of laboratory-confirmed cases by reporting date colored as yellow and green and timeline of events. (B) The daily number of reported death cases by reporting date colored as light blue. (C) Estimated daily reproductive number (R_t). Solid blue indicates time-varying R_t during the study period. Dashed blue lines show 95% credible intervals.

Figure 3

Phylogenetic tree showing the evolutionary relationship of SARS-CoV-2 with 41 Myanmar strains including 10 strains obtained in this study and 6195 global strains collected from December 2019 to September 2020. Sequence data were downloaded from Global Initiative on Sharing All Influenza Data (GISAID), and figures were created by the Nextstrain platform. (A) Time-aware phylogenetic tree showing 10 strains from this study (indicated by arrow) and 31 from another study [14], colored by GISAID clade. (B) Phylogeographic map showing an estimated geographic relationship among SARS-CoV-2 sequences colored by country. Myanmar was indicated by red. (C) Time-aware phylogenetic tree focused on sequences from Myanmar (red), Bangladesh (purple), India (yellow-green), and Thailand (green). The lineage related to local transmission in the second wave in Myanmar in 2020 was indicated by the arrow. (D) Phylogeographic map focused on the relationship of the sequences from Myanmar, Bangladesh, India, and Thailand.

Figure 4

Phylogenetic tree of SARS-CoV-2 in Myanmar. Maximum-likelihood (ML) tree was created with 41 Myanmar strains, 509 global strains, and 770 strains in neighboring Asian countries collected from December 2019 to September 2020, downloaded from Global Initiative on Sharing All Influenza Data (GISIAD). Countries with more than 10 strains were used in the phylogenetic tree. The 41 strains from Myanmar are marked in pink, and different colors denote different countries. (A) Clade O, (B) Clade GR, (C) Clade GH, (D) Clade GH.