SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia

OBJECTIVES: To determine the lineage distribution of the virus during the first wave of the pandemic in North Sumatra, Indonesia. METHODS: A total of 20 samples with positive results based on reverse transcription-polymerase chain reaction were selected for virus culture and then performed whole-genome sequence analysis using next-generation sequencing which was applied by the Illumina MiSeq instrument. RESULTS: Whole-genome sequence analysis revealed that the majority of our samples belong to lineages B.1.468 (n = 10), B.1 (n = 5), B.1.1 (n = 2), B.1.1.398 (n = 2), and B.6 (n = 1). Other unique amino acid mutations found in our samples were present in A58T on non-structural protein (NSP3) (70%), P323L on NSP12 (95%), Q57H on NS3 protein (75%), and D614G on S (100%). CONCLUSION: The SARS-CoV-2 lineage B.1.468 may be the main virus variant circulating in North Sumatra at the beginning of the emergence of COVID-19 cases in this province.