Genomic Tracking of SARS-CoV-2 Variants in Myanmar

Abstract

In December 2019, the COVID-19 disease started in Wuhan, China. The WHO declared a pandemic on 12 March 2020, and the disease started in Myanmar on 23 March 2020. In December 2020, different variants were brought worldwide, threatening global health. To counter those threats, Myanmar started the COVID-19 variant surveillance program in late 2020. Whole genome sequencing was done six times between January 2021 and March 2022. Among them, 83 samples with a PCR threshold cycle of less than 25 were chosen. Then, we used MiSeq FGx for sequencing and Illumina DRAGEN COVIDSeq pipeline, command line interface, GISAID, and MEGA version 7 for data analysis. In January 2021, no variant was detected. The second run, during the rise of cases in June 2021, showed Alpha, Delta, and Kappa variants. The third and the fourth runs in August and December showed only a Delta variant. Omicron and Delta variants were detected during the fifth run in January 2022. The sixth run in March 2022 showed only Omicron BA.2. Amino acid mutation at the receptor binding domain of Spike glycoprotein started since the second run coupling with high transmission, recurrence, and vaccine escape. We also found the mutation at the primer targets used in current RT-PCR platforms, but there was no mutation at the existing antiviral drug targets. The occurrence of multiple variants and mutations claimed vigilance at ports of entry and preparedness for effective control measures. Genomic surveillance with the observation of evolutionary data is required to predict imminent threats of the current disease and diagnose emerging infectious diseases.

Keywords: COVID-19; Myanmar; SARS-CoV-2; sequencing; variant.

Figure 1

Phylogenetic tree comparing Myanmar SARS-CoV-2 sequences with 78 previously published sequences. Label: Yellow = First Run, Green = Second Run, Red = Third Run, Blue = Fourth Run, Purple = Fifth Run, and Orange = Sixth Run; We performed sequence alignment using MEGA version 7 with the MUSCLE algorithm, neighbor-joining analysis method, and the Kimura 2-parameter model with 1000 bootstrap replications for phylogenetic analysis.