Abstract
Introduction: In December 2020, World Health Organization (WHO) was informed of outbreak cases of pneumonia which related with a novel coronavirus in Wuhan City, Hubei Province (1). The epidemic then has escalated and rapidly spread around, with the WHO first declaring a Public Health Emergency of International Concern on 30th January 2020 (2) and on 11th March 2020 it was declared as pandemic (3). Until 16th June 2022, Malaysia recorded 4.5 million confirmed cases with 30,368 deaths. Many countries are facing tough battle although preventive and control measures are in place due to the virus mutation. This impacts the rate of transmission, symptoms and severity. These alarmed to strengthen the surveillance by monitoring the variant of this virus to guide responding to this pandemic. Whole genome sequencing (WGS) was started in Malaysia as early as January 2021 by selected laboratories targeting the travelers at point of entry in Malaysia. It then expanded to other samples involving many more laboratories which include the university and public health laboratories.
Objective: This study aims to describe circulating SARS-CoV-2 strains detected in Malaysia from January 2021 to May 2022.
Methods: Laboratory confirmed SARS-CoV-2 samples were selected for WGS according to criteria, which are CT Value of less than 30, involving surveillance, point of entry and unusual outbreak in a certain district/area. WGS done by respective laboratories from January 2021 until May 2022 was compiled in a single worksheet. The worksheet includes individual demographic features as well as the requestors (state/district). Data was extracted and analyzed using Microsoft Excel.
Results: A total of 12,863 SARS-CoV-2 samples underwent WGS from January 2021 to May 2022. Cumulatively, the variants detected are dominated by Variant of Concern - Delta (56%) and Omicron (42%) while the rest are below 2% from the total samples - Beta (n: 233), Alpha (n: 14), Theta (n: 13), Kappa (n: 4) and Eta (n: 3). There is an apparent transition of SARS-CoV-2 variant and its correlation with number of confirmed COVID-19 cases reported over time. The infection has increased abruptly during EW31 to EW 35/2021, Delta being the predominant strain. There was a surge starting EW 6/2022 and reached the peak at EW 10/2022 (n: 205,864), coinciding with Omicron becoming the dominating strain. More than half of the confirmed Omicron cases are local transmission with highest detection in Sarawak (n: 1,762) followed by Selangor (n: 887) and Johor (n: 448). Omicron is more transmissible than Delta evidenced by the rapid increase and highest infection within shorter period of time. Hospitalization rate has reduced by half during the peak of Omicron detection. Discussion and Conclusion: There is obvious shift of Omicron variant of over time aligning with the current trend globally. It is expected to have new variants in view of public health safety measures are lifted to accommodate the livelihood sustenance. Strengthening and expanding genomic SARS-CoV-2 surveillance is crucial to ensure emerging variants are monitored, help guide prevention of future outbreaks, country 's containment as well as clinical management.
Links
- https://apcph.cphm.my/wp-content/uploads/2022/07/APCPH2022-P-26.pdf
- https://apcph.cphm.my/wp-content/uploads/wpforms/1176-1e04940bb5d885bf8711ed1909[...]
BibTeX (Download)
@proceedings{APCPH2022-P-26,
title = {Circulating SARS-CoV-2 Variants in Malaysia},
author = {Santhi Subramaniam and Sharifah Nora Abu Bakar and Zahrin Hasran},
url = {https://apcph.cphm.my/wp-content/uploads/2022/07/APCPH2022-P-26.pdf
https://apcph.cphm.my/wp-content/uploads/wpforms/1176-1e04940bb5d885bf8711ed19095a89ed/APCPH-FINAL-d19570b2649eb1e6e7caf282b95253ac.pdf},
year = {2022},
date = {2022-08-02},
urldate = {2022-08-02},
issue = {7},
abstract = {Introduction: In December 2020, World Health Organization (WHO) was informed of outbreak cases of pneumonia which related with a novel coronavirus in Wuhan City, Hubei Province (1). The epidemic then has escalated and rapidly spread around, with the WHO first declaring a Public Health Emergency of International Concern on 30th January 2020 (2) and on 11th March 2020 it was declared as pandemic (3). Until 16th June 2022, Malaysia recorded 4.5 million confirmed cases with 30,368 deaths. Many countries are facing tough battle although preventive and control measures are in place due to the virus mutation. This impacts the rate of transmission, symptoms and severity. These alarmed to strengthen the surveillance by monitoring the variant of this virus to guide responding to this pandemic. Whole genome sequencing (WGS) was started in Malaysia as early as January 2021 by selected laboratories targeting the travelers at point of entry in Malaysia. It then expanded to other samples involving many more laboratories which include the university and public health laboratories.
Objective: This study aims to describe circulating SARS-CoV-2 strains detected in Malaysia from January 2021 to May 2022.
Methods: Laboratory confirmed SARS-CoV-2 samples were selected for WGS according to criteria, which are CT Value of less than 30, involving surveillance, point of entry and unusual outbreak in a certain district/area. WGS done by respective laboratories from January 2021 until May 2022 was compiled in a single worksheet. The worksheet includes individual demographic features as well as the requestors (state/district). Data was extracted and analyzed using Microsoft Excel.
Results: A total of 12,863 SARS-CoV-2 samples underwent WGS from January 2021 to May 2022. Cumulatively, the variants detected are dominated by Variant of Concern - Delta (56%) and Omicron (42%) while the rest are below 2% from the total samples - Beta (n: 233), Alpha (n: 14), Theta (n: 13), Kappa (n: 4) and Eta (n: 3). There is an apparent transition of SARS-CoV-2 variant and its correlation with number of confirmed COVID-19 cases reported over time. The infection has increased abruptly during EW31 to EW 35/2021, Delta being the predominant strain. There was a surge starting EW 6/2022 and reached the peak at EW 10/2022 (n: 205,864), coinciding with Omicron becoming the dominating strain. More than half of the confirmed Omicron cases are local transmission with highest detection in Sarawak (n: 1,762) followed by Selangor (n: 887) and Johor (n: 448). Omicron is more transmissible than Delta evidenced by the rapid increase and highest infection within shorter period of time. Hospitalization rate has reduced by half during the peak of Omicron detection. Discussion and Conclusion: There is obvious shift of Omicron variant of over time aligning with the current trend globally. It is expected to have new variants in view of public health safety measures are lifted to accommodate the livelihood sustenance. Strengthening and expanding genomic SARS-CoV-2 surveillance is crucial to ensure emerging variants are monitored, help guide prevention of future outbreaks, country 's containment as well as clinical management.},
howpublished = {published online at https://apcph.cphm.my},
note = {Type: POSTER PRESENTATION; Organisation: National Public Health Laboratory},
keywords = {Genome sequencing, Omicron, SARS-CoV-2},
pubstate = {published},
tppubtype = {proceedings}
}