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

Ramadhan Bestari, Irbah Rea Alvieda Nainggolan, Mirzan Hasibuan, Rima Ratnanggana, Krisnoadi Rahardjo, Aldise Mareta Nastri, Jezzy Renova Dewantari, Soetjipto Soetjipto, Maria Inge Lusida, Yasuko Mori, Kazufumi Shimizu, R. Lia Kusumawati, Muhammad Ichwan, Inke Nadia Diniyanti Lubis

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish
Pages (from-to)S1-S7
JournalIJID Regions
Volume8
DOIs
Publication statusPublished - Sept 2023

Keywords

  • D614G
  • Lineage B.1.468
  • North Sumatera
  • SARS-CoV-2
  • Whole-genome sequence

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