Genomic surveillance of SARS-CoV-2 in Thailand reveals mixed imported populations, a local lineage expansion and a virus with truncated ORF7a

Abstract

Coronavirus Disease 2019 (COVID-19) is a global public health threat. Genomic surveillance of SARS-CoV-2 was implemented in March of 2020 at a major diagnostic hub in Bangkok, Thailand. Several virus lineages supposedly originated in many countries were found, and a Thai-specific lineage, designated A/Thai-1, has expanded to be predominant in Thailand. A virus sample in the SARS-CoV-2 A/Thai-1 lineage contains a frame-shift deletion at ORF7a, encoding a putative host antagonizing factor of the virus.

Keywords: COVID-19; Genomic surveillance; SARS-CoV-2; Thailand.

Fig. 1

Cladogram based on a maximum-likelihood tree showing Thai populations of SARS-CoV-2. The cladogram represents a matching maximum-likelihood tree (1,000 bootstrap replicates) shown in Supplementary Fig. 1. Genomes generated in this study are labelled in blue with remaining lineage representatives labelled in black. Bootstrap values (≥ 75) are shown at the nodes. Thai virus genomes independently generated by other groups and deposited in GISAID are labelled in green. Genomes collected from January 2020 are similar to that of reference Wuhan-Hu-1. Our data showed at least four independently lineages, and two additional events of lineage B from January 2020 and lineage B.6 (shown in green), could be recognized as potential introduction events. The A and B lineages are coloured in orange and cyan, respectively. * indicates the sample with the ORF7a deletion.

Fig. 2

Maximum-likelihood tree containing A/Thai-1 subset. For visualization of A/Thai-1 lineage, the A/Thai-1 genomes from Fig. 1 generated in this study are presented. The lineage defining node has a bootstrap value of 99 (1,000 replicates) as shown in Supplementary Fig. 1. Mutations that define each branch point are shown. 20,134G→U in Thailand_Bangkok-0030 could not be called. * indicates the sample with the ORF7a deletion.

Fig. 3

Diagram depicting Thailand/Bangkok-0018 frame-shift deletion in ORF7a. The upper diagram shows the gene organization of the SARS-CoV-2 genome. The functional domains of ORF7a are indicated based on SARS-CoV. Sequences from SARS-CoV, the SARS-CoV-2 Wuhan-Hu-1 reference, the Arizona sample with an 81-nucleotide deletion (EPI_ISL_424669) and Thailand/Bangkok-0018 are aligned to demonstrate the altered region in red box.