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

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.

Figure 1

Study flowchart. Ct, cycle threshold; RT-PCR, reverse transcription-polymerase chain reaction; VTM, viral transport media.

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

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)