Bestari R, Nainggolan IRA, Hasibuan M, Ratnanggana R, Rahardjo K, Nastri AM, Dewantari JR, Soetjipto S, Lusida MI, Mori Y, Shimizu K, Kusumawati RL, Ichwan M, Lubis IND. SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia.
IJID REGIONS 2023;
8:S1-S7. [PMID:
37799539 PMCID:
PMC10548867 DOI:
10.1016/j.ijregi.2023.07.006]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 10/07/2023]
Abstract
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.
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