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

doi:10.1016/j.ijregi.2023.07.006

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 journal › Article › peer-review

2 Citations (Scopus)

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 language	English
Pages (from-to)	S1-S7
Journal	IJID Regions
Volume	8
DOIs	https://doi.org/10.1016/j.ijregi.2023.07.006
Publication status	Published - Sept 2023

Keywords

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

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.ijregi.2023.07.006

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Bestari, R., Nainggolan, I. R. A., Hasibuan, M., Ratnanggana, R., Rahardjo, K., Nastri, A. M., Dewantari, J. R., Soetjipto, S., Lusida, M. I., Mori, Y., Shimizu, K., Kusumawati, R. L., Ichwan, M., & Lubis, I. N. D. (2023). SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia. IJID Regions, 8, S1-S7. https://doi.org/10.1016/j.ijregi.2023.07.006

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title = "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",

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

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year = "2023",

month = sep,

doi = "10.1016/j.ijregi.2023.07.006",

language = "English",

volume = "8",

pages = "S1--S7",

journal = "IJID Regions",

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T1 - SARS-CoV-2 lineages circulating during the first wave of the pandemic in North Sumatra, Indonesia

AU - Bestari, Ramadhan

AU - Nainggolan, Irbah Rea Alvieda

AU - Hasibuan, Mirzan

AU - Ratnanggana, Rima

AU - Rahardjo, Krisnoadi

AU - Nastri, Aldise Mareta

AU - Dewantari, Jezzy Renova

AU - Soetjipto, Soetjipto

AU - Lusida, Maria Inge

AU - Mori, Yasuko

AU - Shimizu, Kazufumi

AU - Kusumawati, R. Lia

AU - Ichwan, Muhammad

AU - Lubis, Inke Nadia Diniyanti

PY - 2023/9

Y1 - 2023/9

N2 - 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.

AB - 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.

KW - D614G

KW - Lineage B.1.468

KW - North Sumatera

KW - SARS-CoV-2

KW - Whole-genome sequence

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U2 - 10.1016/j.ijregi.2023.07.006

DO - 10.1016/j.ijregi.2023.07.006

M3 - Article

AN - SCOPUS:85167971689

SN - 2772-7076

VL - 8

SP - S1-S7

JO - IJID Regions

JF - IJID Regions

ER -

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

Abstract

Keywords

UN SDGs

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