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. 2023 Aug 6;8(Suppl):S1-S7.
doi: 10.1016/j.ijregi.2023.07.006. eCollection 2023 Sep.

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

Ramadhan Bestari  1 , Irbah Rea Alvieda Nainggolan  2 , Mirzan Hasibuan  2 , Rima Ratnanggana  3 , Krisnoadi Rahardjo  3 , Aldise Mareta Nastri  3 , Jezzy Renova Dewantari  3 , Soetjipto Soetjipto  3 , Maria Inge Lusida  3 , Yasuko Mori  4 , Kazufumi Shimizu  4 , R Lia Kusumawati  2 , Muhammad Ichwan  2 , Inke Nadia Diniyanti Lubis  2
Affiliations

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

Ramadhan Bestari et al. IJID Reg. .

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.

Keywords: D614G; Lineage B.1.468; North Sumatera; SARS-CoV-2; Whole-genome sequence.

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Figures

Figure 1
Figure 1
Study flowchart. Ct, cycle threshold; RT-PCR, reverse transcription-polymerase chain reaction; VTM, viral transport media.
Figure 2
Figure 2
Amino acid variations of SARS-CoV-2 virus samples from North Sumatra aligned with reference genome. (White spot remarked the amino acid mutation which shown only from the translated region of each protein)
Figure 3
Figure 3
Phylogenetic analysis of SARS-CoV-2 genomes. The clustering of certain lineages is indicative of the extent of genomic variations. (Samples from North Sumatra are indicated in pink color)
See this image and copyright information in PMC

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