key: cord-0882657-8r6u3e3i
authors: Chong, Yoong Min; Sam, I-Ching; Ponnampalavanar, Sasheela; Syed Omar, Sharifah Faridah; Kamarulzaman, Adeeba; Munusamy, Vijayan; Wong, Chee Kuan; Jamaluddin, Fadhil Hadi; Gan, Han Ming; Chong, Jennifer; Teh, Cindy Shuan Ju; Chan, Yoke Fun
title: Complete Genome Sequences of SARS-CoV-2 Strains Detected in Malaysia
date: 2020-05-14
journal: Microbiol Resour Announc
DOI: 10.1128/mra.00383-20
sha: ac8ea2b6afdbbf50e057615cb945200774eb95a5
doc_id: 882657
cord_uid: 8r6u3e3i

We sequenced four severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Malaysia during the second wave of infection and found unique mutations which suggest local evolution. Circulating Malaysian strains represent introductions from different countries, particularly during the first wave of infection. Genome sequencing is important for understanding local epidemiology.

MinION (23,390 reads) sequencing with Geneious mapper using default parameters. The four genome sizes ranged from 29,486 to 29,898 bp with GC contents of 36.6 to 37.9% (Table 1) . Multiple sequence alignment was performed with MAFFT with default parameters (3) . Phylogenetic analysis was conducted with FastTree 2.1.11 (4) implemented in Geneious with default parameters using whole genomes available at GISAID (www.gisaid.org), including six other previously deposited Malaysian strains (EPI_ISL_416829, EPI_ISL_416866, EPI_ISL_416884, EPI_ISL_416885, EPI_ISL_416886, and EPI_ISL_416907).

The four complete genome sequences reported here date from the main second wave of infections in Malaysia (Fig. 1A) . Strain 188407 was linked to a religious mass gathering which has been associated with 48% of national cases and clusters with strains from Japan, Australia, and Saudi Arabia (Fig. 1B) . Strain 189332 clusters with strain 188407, but the patient from whom it was isolated had no clear link to the gathering. This suggests that the strains associated with the gathering have established community transmission. The person with strain 186197 had travelled to Vietnam, while strain 190300, from a patient with no history of travelling or attending gatherings, was clustered with strains from Europe (Fig. 1B) . Compared to reference strain Wuhan-Hu-1, Malaysian sequences have 16 nucleotide substitutions (Table 1) . Four substitutions in the nonstructural region (ORF1a-T2737A, ORF1a-C6310A, ORF1b- 

More genomic data will clarify virus spread in Malaysia, particularly with respect to the role played by the mass gathering. Data availability. These sequences have been deposited in the GISAID EpiCoV newly emerging coronavirus SARS-CoV-2 platform under identifiers EPI_ISL_417917 to EPI_ISL_417920. The sequences were also deposited in the following NCBI databases: GenBank (accession numbers MT372480 to MT372483

Press statement from the Director-General of Health

ARTIC Network. 2020. nCoV-2019 sequencing protocol

MAFFT multiple sequence alignment software version 7: improvements in performance and usability

FastTree 2: approximately maximumlikelihood trees for large alignments

We gratefully acknowledge the authors from the originating and submitting laboratories of GISAID sequence data on which this analysis is based. We are part of the University of Malaya COVID-19 Research Group, which includes the health care workers involved in the care of COVID-19 patients in the University of Malaya Medical Centre.