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Md Nadzri MN, Md Zamri ASS, Singh S, Sumarni MG, Lai CH, Tan CV, Aris T, Mohd Ibrahim H, Gill BS, Mohd Ghazali N, Md Iderus NH, Lim MC, Ahmad LCRQ, Kamarudin MK, Ahmad NAR, Tee KK, Zulkifli AA. Description of the COVID-19 epidemiology in Malaysia. Front Public Health 2024; 12:1289622. [PMID: 38544725 PMCID: PMC10968133 DOI: 10.3389/fpubh.2024.1289622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/26/2024] [Indexed: 05/01/2024] Open
Abstract
Introduction Since the COVID-19 pandemic began, it has spread rapidly across the world and has resulted in recurrent outbreaks. This study aims to describe the COVID-19 epidemiology in terms of COVID-19 cases, deaths, ICU admissions, ventilator requirements, testing, incidence rate, death rate, case fatality rate (CFR) and test positivity rate for each outbreak from the beginning of the pandemic in 2020 till endemicity of COVID-19 in 2022 in Malaysia. Methods Data was sourced from the GitHub repository and the Ministry of Health's official COVID-19 website. The study period was from the beginning of the outbreak in Malaysia, which began during Epidemiological Week (Ep Wk) 4 in 2020, to the last Ep Wk 18 in 2022. Data were aggregated by Ep Wk and analyzed in terms of COVID-19 cases, deaths, ICU admissions, ventilator requirements, testing, incidence rate, death rate, case fatality rate (CFR) and test positivity rate by years (2020 and 2022) and for each outbreak of COVID-19. Results A total of 4,456,736 cases, 35,579 deaths and 58,906,954 COVID-19 tests were reported for the period from 2020 to 2022. The COVID-19 incidence rate, death rate, CFR and test positivity rate were reported at 1.085 and 0.009 per 1,000 populations, 0.80 and 7.57%, respectively, for the period from 2020 to 2022. Higher cases, deaths, testing, incidence/death rate, CFR and test positivity rates were reported in 2021 and during the Delta outbreak. This is evident by the highest number of COVID-19 cases, ICU admissions, ventilatory requirements and deaths observed during the Delta outbreak. Conclusion The Delta outbreak was the most severe compared to other outbreaks in Malaysia's study period. In addition, this study provides evidence that outbreaks of COVID-19, which are caused by highly virulent and transmissible variants, tend to be more severe and devastating if these outbreaks are not controlled early on. Therefore, close monitoring of key epidemiological indicators, as reported in this study, is essential in the control and management of future COVID-19 outbreaks in Malaysia.
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Affiliation(s)
- Mohamad Nadzmi Md Nadzri
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Ahmed Syahmi Syafiq Md Zamri
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Sarbhan Singh
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Mohd Ghazali Sumarni
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Chee Herng Lai
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Cia Vei Tan
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Tahir Aris
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | | | - Balvinder Singh Gill
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Nur’Ain Mohd Ghazali
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Nuur Hafizah Md Iderus
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Mei Cheng Lim
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Lonny Chen Rong Qi Ahmad
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Mohd Kamarulariffin Kamarudin
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Nur Ar Rabiah Ahmad
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Asrul Anuar Zulkifli
- Institute for Medical Research (IMR), National Institutes of Health (NIH), Ministry of Health Malaysia, Setia Alam, Malaysia
- International Medical School, Management and Science University, Shah Alam, Selangor, Malaysia
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Gladkikh AS, Cao TM, Klyuchnikova EO, Dao MH, Sharova AA, Melnichenko VD, Popova MR, Arbuzova TV, Sbarzaglia VA, Tsyganova NA, Ramsay E, Dedkov VG. Near complete genome sequences from Southern Vietnam revealed local features of genetic diversity and intergenerational changes in SARS- CoV-2 variants in 2020-2021. BMC Infect Dis 2023; 23:806. [PMID: 37974125 PMCID: PMC10655423 DOI: 10.1186/s12879-023-08814-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Since its beginnings in 2019, the COVID-19 pandemic is still a problem of global medical concern. Southern Vietnam is one of the country's vast regions, including 20 provinces and the densely populated metropolis Ho Chi Minh City. A randomized retrospective study was performed to investigate the epidemiology and genetic diversity of COVID-19. Whole-genome sequencing of 126 SARS-CoV-2 samples collected from Southern Vietnam between January 2020 and December 2021 revealed the main circulating variants and their distribution. METHODS Epidemiological data were obtained from the Department of Preventive Medicine of the Vietnamese Ministry of Health. To identify circulating variants, RNA, extracted from 126 nasopharyngeal swabs of patients with suspected COVID-19 were sequenced on Illunina MiSeq to obtain near complete genomes SARS-CoV-2. RESULTS Due to the effectiveness of restrictive measures in Vietnam, it was possible to keep incidence at a low level. The partial relaxation of restrictive measures, and the spread of Delta lineages, contributed to the beginning of a logarithmic increase in incidence. Lineages 20A-H circulated in Southern Vietnam during 2020. Spread of the Delta lineage in Southern Vietnam began in March 2021, causing a logarithmic rise in the number of COVID-19 cases. CONCLUSIONS Pandemic dynamics in Southern Vietnam feature specific variations in incidence, and these reflect the success of the restrictive measures put in place during the early stages of the pandemic.
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Affiliation(s)
- Anna S Gladkikh
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Thang M Cao
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | | | - Manh H Dao
- Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Alena A Sharova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | | | - Margarita R Popova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Tatiana V Arbuzova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Valeriya A Sbarzaglia
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Nadezhda A Tsyganova
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Edward Ramsay
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
| | - Vladimir G Dedkov
- Saint Petersburg Pasteur Institute, 14 Mira Street, Saint Petersburg, 197101, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
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Balakrishnan KN, Yew CW, Chong ETJ, Daim S, Mohamad NE, Rodrigues K, Lee PC. Timeline of SARS-CoV-2 Transmission in Sabah, Malaysia: Tracking the Molecular Evolution. Pathogens 2023; 12:1047. [PMID: 37624007 PMCID: PMC10459040 DOI: 10.3390/pathogens12081047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic poses an unprecedented public health challenge in Malaysia. The impact of COVID-19 varies between countries, including geographically divided states within a country. The deadly transmission of COVID-19 has taken a heavy toll in Sabah, Malaysia's third most populous state, contributing nearly 10% to the recorded national death toll as of 31 December 2022. Although several SARS-CoV-2 genome sequences have been analysed in Malaysia, molecular epidemiology data from Sabah focusing on the diversity and evolution of SARS-CoV-2 variants are still lacking. This study examines the major SARS-CoV-2 variants and emerging mutations from Sabah, the Malaysian Borneo, which is geographically divided from West Malaysia by the South China Sea. METHODS A total of 583 COVID-19 samples were subjected to whole genome sequencing and analysed with an additional 1123 Sabah COVID-19 sequences retrieved from the GISAID EpiCoV consortium. Nextclade and Pangolin were used to classify these sequences according to the clades and lineages. To determine the molecular evolutionary characteristics, Bayesian time-scaled phylogenetic analysis employing the maximum likelihood algorithm was performed on selected SARS-CoV-2 genome sequences, using the Wuhan-Hu-1 sequence as a reference. RESULTS Sabah was affected starting from the second COVID-19 wave in Malaysia, and the early sequences were classified under the O clade. The clade was gradually replaced during subsequent waves by G, GH, GK and GRA, with the latter being dominant as of December 2022. Phylogenetically, the Delta isolates in this study belong to the three main subclades 21A, 21J and 21I, while Omicron isolates belong to 21M, 21L and 22B. The time-scaled phylogeny suggested that SARS-CoV-2 introduced into Sabah originated from Peninsular Malaysia in early March 2020, and phylodynamic analysis indicated that increased viral spread was observed in early March and declined in late April, followed by an evolutionary stationary phase in June 2020. CONCLUSION Continuous molecular epidemiology of SARS-CoV-2 in Sabah will provide a deeper understanding of the emergence and dominance of each variant in the locality, thus facilitating public health intervention measures.
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Affiliation(s)
- Krishnan Nair Balakrishnan
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Chee Wei Yew
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Eric Tzyy Jiann Chong
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Sylvia Daim
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia;
| | - Nurul Elyani Mohamad
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Kenneth Rodrigues
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
| | - Ping-Chin Lee
- Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia; (K.N.B.); (C.W.Y.); (E.T.J.C.); (N.E.M.); (K.R.)
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Jalan UMS, Kota Kinabalu 88400, Sabah, Malaysia
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Lee TY, Lim WF, Ang GY, Yu CY. Genomic Surveillance of SARS-CoV-2 in Malaysia during the Era of Endemic COVID-19. Life (Basel) 2023; 13:1644. [PMID: 37629505 PMCID: PMC10455073 DOI: 10.3390/life13081644] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 08/27/2023] Open
Abstract
On 5 May 2023, WHO declared the end of coronavirus disease 2019 (COVID-19) as a public health emergency of international concern. However, the risk of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants causing rapid and high surges in cases and deaths remained. In Malaysia, five COVID-19 waves during the pandemic phase were well characterized, but similar studies focusing on the endemic phase were lacking. Hence, we retrieved 14,965 SARS-CoV-2 genomic sequences from the GISAID EpiCoV database for clade, lineage, and phylogenetic analysis in order to provide an insight into the population dynamics of SARS-CoV-2 that circulated in Malaysia from June 2022 to April 2023. The dominance of the Omicron variants was observed, and two new waves of infections driven by BA.5.2 and XBB.1, respectively, were detected. Data as of April 2023 also pointed to a possible eighth wave driven by XBB.1.9. Although new variants associated with higher transmissibility were behind the multiple surges, these subsequent waves had lower intensities as compared to the fourth and fifth waves. The on-going circulation and evolution of SARS-CoV-2 mean that COVID-19 still poses a serious threat, necessitating active genomic surveillance for early warning of potential new variants of concern.
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Affiliation(s)
- Tze Yan Lee
- School of Liberal Arts, Science and Technology (PUScLST), Perdana University, Kuala Lumpur 50490, Malaysia
| | - Wai Feng Lim
- Sunway Medical Centre, Bandar Sunway, Subang Jaya 47500, Malaysia;
| | - Geik Yong Ang
- Faculty of Sports Science and Recreation, Universiti Teknologi MARA, Shah Alam 40450, Malaysia;
| | - Choo Yee Yu
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia
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Puenpa J, Sawaswong V, Nimsamer P, Payungporn S, Rattanakomol P, Saengdao N, Chansaenroj J, Yorsaeng R, Suwannakarn K, Poovorawan Y. Investigation of the Molecular Epidemiology and Evolution of Circulating Severe Acute Respiratory Syndrome Coronavirus 2 in Thailand from 2020 to 2022 via Next-Generation Sequencing. Viruses 2023; 15:1394. [PMID: 37376693 DOI: 10.3390/v15061394] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an infectious condition caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which surfaced in Thailand in early 2020. The current study investigated the SARS-CoV-2 lineages circulating in Thailand and their evolutionary history. Complete genome sequencing of 210 SARS-CoV-2 samples collected from collaborating hospitals and the Institute of Urban Disease Control and Prevention over two years, from December 2020 to July 2022, was performed using next-generation sequencing technology. Multiple lineage introductions were observed before the emergence of the B.1.1.529 omicron variant, including B.1.36.16, B.1.351, B.1.1, B.1.1.7, B.1.524, AY.30, and B.1.617.2. The B.1.1.529 omicron variant was subsequently detected between January 2022 and June 2022. The evolutionary rate for the spike gene of SARS-CoV-2 was estimated to be between 0.87 and 1.71 × 10-3 substitutions per site per year. There was a substantial prevalence of the predominant mutations C25672T (L94F), C25961T (T190I), and G26167T (V259L) in the ORF3a gene during the Thailand outbreaks. Complete genome sequencing can enhance the prediction of future variant changes in viral genomes, which is crucial to ensuring that vaccine strains are protective against worldwide outbreaks.
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Affiliation(s)
- Jiratchaya Puenpa
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Vorthon Sawaswong
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pattaraporn Nimsamer
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sunchai Payungporn
- Center of Excellence in Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Patthaya Rattanakomol
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nutsada Saengdao
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jira Chansaenroj
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ritthideach Yorsaeng
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kamol Suwannakarn
- Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok 10300, Thailand
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Puenpa J, Rattanakomol P, Saengdao N, Chansaenroj J, Yorsaeng R, Suwannakarn K, Thanasitthichai S, Vongpunsawad S, Poovorawan Y. Molecular characterisation and tracking of severe acute respiratory syndrome coronavirus 2 in Thailand, 2020-2022. Arch Virol 2023; 168:26. [PMID: 36593392 PMCID: PMC9807426 DOI: 10.1007/s00705-022-05666-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/30/2022] [Indexed: 01/04/2023]
Abstract
The global COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was first detected in China in December 2019. To date, there have been approximately 3.4 million reported cases of COVID-19 and over 24,000 deaths in Thailand. In this study, we investigated the molecular characteristics and evolution of SARS-CoV-2 in Thailand from 2020 to 2022. Two hundred sixty-eight SARS-CoV-2 isolates, collected mostly in Bangkok from COVID-19 patients, were characterised by partial genome sequencing. Moreover, the viruses in 5,627 positive SARS-CoV-2 samples were identified as viral variants - B.1.1.7 (Alpha), B.1.617.2 (Delta), B.1.1.529 (Omicron/BA.1), or B.1.1.529 (Omicron/BA.2) - by multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) assays. The results revealed that B.1.36.16 caused the predominant outbreak in the second wave (December 2020-January 2021), B.1.1.7 (Alpha) in the third wave (April-June 2021), B.1.617.2 (Delta) in the fourth wave (July-December 2021), and B.1.1.529 (Omicron) in the fifth wave (January-March 2022). The evolutionary rate of the viral genome was 2.60 × 10-3 (95% highest posterior density [HPD], 1.72 × 10-3 to 3.62 × 10-3) nucleotide substitutions per site per year. Continued molecular surveillance of SARS-CoV-2 is crucial for monitoring emerging variants with the potential to cause new COVID-19 outbreaks.
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Affiliation(s)
- Jiratchaya Puenpa
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Patthaya Rattanakomol
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Nutsada Saengdao
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.416009.aDepartment of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jira Chansaenroj
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ritthideach Yorsaeng
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kamol Suwannakarn
- grid.416009.aDepartment of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Somchai Thanasitthichai
- grid.415836.d0000 0004 0576 2573Institute of Medical Research and Technology Assessment, Ministry of Public Health, Bangkok, Thailand
| | - Sompong Vongpunsawad
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- grid.7922.e0000 0001 0244 7875Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand ,grid.512985.2FRS(T), The Royal Society of Thailand, Sanam Sueapa, Dusit, Bangkok, Thailand
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Yu CY, Wong SY, Liew NWC, Joseph N, Zakaria Z, Nurulfiza I, Soe HJ, Kairon R, Amin-Nordin S, Chee HY. Whole genome sequencing analysis of SARS-CoV-2 from Malaysia: From alpha to Omicron. Front Med (Lausanne) 2022; 9:1001022. [PMID: 36213636 PMCID: PMC9537942 DOI: 10.3389/fmed.2022.1001022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/05/2022] [Indexed: 11/18/2022] Open
Abstract
Countries around the world are gearing for the transition of the coronavirus disease 2019 (COVID-19) from pandemic to endemic phase but the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants could lead to a prolonged pandemic. SARS-CoV-2 has continued to evolve as it optimizes its adaptation to the human host and the successive waves of COVID-19 have been linked to the explosion of particular variant of concern. As the genetic diversity and epidemiological landscape of SARS-CoV-2 differ from country to country, this study aims to provide insights into the variants that are circulating in Malaysia. Whole genome sequencing was performed for 204 SARS-CoV-2 from COVID-19 cases and an additional 18,667 SARS-CoV-2 genome sequences were retrieved from the GISAID EpiCoV database for clade, lineage and genetic variation analyses. Complete genome sequences with high coverage were then used for phylogeny investigation and the resulting phylogenetic tree was constructed from 8,716 sequences. We found that the different waves of COVID-19 in Malaysia were dominated by different clades with the L and O clade for first and second wave, respectively, whereas the progressive replacement by G, GH, and GK of the GRA clade were observed in the subsequence waves. Continuous monitoring of the genetic diversity of SARS-CoV-2 is important to identify the emergence and dominance of new variant in different locality so that the appropriate countermeasures can be taken to effectively contain the spread of SARS-CoV-2.
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Affiliation(s)
- Choo Yee Yu
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sie Yeng Wong
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nancy Woan Charn Liew
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Narcisse Joseph
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Zunita Zakaria
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Malaysia
| | - Isa Nurulfiza
- Laboratory of Vaccine and Biomolecules, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | | | | | - Syafinaz Amin-Nordin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hui Yee Chee
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
- *Correspondence: Hui Yee Chee,
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Vassilaki N, Papadimitriou K, Ioannidis A, Papandreou NC, Milona RS, Iconomidou VA, Chatzipanagiotou S. SARS-CoV-2 Amino Acid Mutations Detection in Greek Patients Infected in the First Wave of the Pandemic. Microorganisms 2022; 10:microorganisms10071430. [PMID: 35889149 PMCID: PMC9322066 DOI: 10.3390/microorganisms10071430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel virus that belongs to the Coronoviridae family, emerged in December 2019, causing the COVID-19 pandemic in March 2020. Unlike previous SARS and Middle East respiratory syndrome (MERS) outbreaks, this virus has a higher transmissibility rate, albeit a lower case fatality rate, which results in accumulation of a significant number of mutations and a faster evolution rate. Genomic studies on the mutation rate of the virus, as well as the identification of mutations that prevail and their impact on disease severity, are of great importance for pandemic surveillance and vaccine and drug development. Here, we aim to identify mutations on the SARS-CoV-2 viral genome and their effect on the proteins they are located in, in Greek patients infected in the first wave of the pandemic. To this end, we perform SARS-CoV-2 amplicon-based NGS sequencing on nasopharyngeal swab samples from Greek patients and bioinformatic analysis of the results. Although SARS-CoV-2 is considered genetically stable, we discover a variety of mutations on the viral genome. In detail, 18 mutations are detected in total on 10 SARS-CoV-2 isolates. The mutations are located on ORF1ab, S protein, M protein, ORF3a and ORF7a. Sixteen are also detected in patients from other regions around the world, and two are identified for the first time in the present study. Most of them result in amino acid substitutions. These substitutions are analyzed using computational tools, and the results indicate minor or major impact on the proteins’ structural stability, which could probably affect viral transmissibility and pathogenesis. The correlation of these variations with the viral load levels is examined, and their implication for disease severity and the biology of the virus are discussed.
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Affiliation(s)
- Niki Vassilaki
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece; (N.V.); (R.S.M.)
| | - Konstantinos Papadimitriou
- Laboratory of Food Quality Control and Hygiene, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece;
| | - Anastasios Ioannidis
- Department of Nursing, Faculty of Health Sciences, University of Peloponnese, Sehi Area, 22100 Tripoli, Greece;
| | - Nikos C. Papandreou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (N.C.P.); (V.A.I.)
| | - Raphaela S. Milona
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521 Athens, Greece; (N.V.); (R.S.M.)
| | - Vassiliki A. Iconomidou
- Section of Cell Biology and Biophysics, Department of Biology, School of Science, National and Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece; (N.C.P.); (V.A.I.)
| | - Stylianos Chatzipanagiotou
- Department of Medical Biopathology, Eginition Hospital, Athens Medical School, National and Kapodistrian University of Athens, 72–74 Vasilissis Sofias Avenue, 11528 Athens, Greece
- Correspondence:
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Cheong YL, Ghazali SM, Che Ibrahim MKB, Kee CC, Md Iderus NH, Ruslan QB, Gill BS, Lee FCH, Lim KH. Assessing the Spatiotemporal Spread Pattern of the COVID-19 Pandemic in Malaysia. Front Public Health 2022; 10:836358. [PMID: 35309230 PMCID: PMC8931737 DOI: 10.3389/fpubh.2022.836358] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
Introduction The unprecedented COVID-19 pandemic has greatly affected human health and socioeconomic backgrounds. This study examined the spatiotemporal spread pattern of the COVID-19 pandemic in Malaysia from the index case to 291,774 cases in 13 months, emphasizing on the spatial autocorrelation of the high-risk cluster events and the spatial scan clustering pattern of transmission. Methodology We obtained the confirmed cases and deaths of COVID-19 in Malaysia from the official GitHub repository of Malaysia's Ministry of Health from January 25, 2020 to February 24, 2021, 1 day before the national vaccination program was initiated. All analyses were based on the daily cumulated cases, which are derived from the sum of retrospective 7 days and the current day for smoothing purposes. We examined the daily global, local spatial autocorrelation and scan statistics of COVID-19 cases at district level using Moran's I and SaTScan™. Results At the initial stage of the outbreak, Moran's I index > 0.5 (p < 0.05) was observed. Local Moran's I depicted the high-high cluster risk expanded from west to east of Malaysia. The cases surged exponentially after September 2020, with the high-high cluster in Sabah, from Kinabatangan on September 1 (cumulative cases = 9,354; Moran's I = 0.34; p < 0.05), to 11 districts on October 19 (cumulative cases = 21,363, Moran's I = 0.52, p < 0.05). The most likely cluster identified from space-time scanning was centered in Jasin, Melaka (RR = 11.93; p < 0.001) which encompassed 36 districts with a radius of 178.8 km, from November 24, 2020 to February 24, 2021, followed by the Sabah cluster. Discussion and Conclusion Both analyses complemented each other in depicting underlying spatiotemporal clustering risk, giving detailed space-time spread information at district level. This daily analysis could be valuable insight into real-time reporting of transmission intensity, and alert for the public to avoid visiting the high-risk areas during the pandemic. The spatiotemporal transmission risk pattern could be used to monitor the spread of the pandemic.
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Affiliation(s)
- Yoon Ling Cheong
- Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
- *Correspondence: Yoon Ling Cheong
| | - Sumarni Mohd Ghazali
- Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | | | - Chee Cheong Kee
- Sector for Biostatistics and Data Repository, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Malaysia
| | - Nuur Hafizah Md Iderus
- Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Qistina binti Ruslan
- Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Balvinder Singh Gill
- Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Florence Chi Hiong Lee
- Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Kuang Hock Lim
- Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
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Xu H, Xie CY, Li PH, Ji ZL, Sun JF, Hu B, Li X, Fang M. Demographic, Virological Characteristics and Prognosis of Asymptomatic COVID-19 Patients in South China. Front Med (Lausanne) 2022; 9:830942. [PMID: 35155505 PMCID: PMC8831799 DOI: 10.3389/fmed.2022.830942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/05/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Asymptomatic transmission is a major concern for SARS-CoV-2 community spread; however, little information is available on demographic, virological characteristics and prognosis of asymptomatic cases. METHODS All COVID-19 patients hospitalized in Guangdong Province from September 1, 2020 to February 28, 2021, were included and were divided into asymptomatic and symptomaticgroup. The source country of all patients, clinical laboratory test results, the genotype of virus and the time of SARS-CoV-2 RNA turning negative or hospitalization were confirmed. RESULTS Total 233 patients from 57 different countries or regions were included, with 83 (35.6%) asymptomatic and 150 (64.4%) symptomatic patients. Asymptomatic cases were younger (P = 0.019), lower rate in comorbidities (P = 0.021) such as hypertension (P = 0.083) and chronic liver disease (P = 0.045), lower PCT (P = 0.021), DDI (P < 0.001) and ALT (P = 0.029), but higher WBC count (P = 0.002) and lymphocyte (P = 0.011) than symptomatic patients. As for SARS-CoV-2 subtypes, patients infected with B.1.1 (53.8%), B.1.351 (81.8%) and B.1.524 (60%) are mainly asymptomatic, while infected with B, B.1, B.1.1.63, B.1.1.7, B.1.36, B.1.36.1, B.1.36.16, B.1.5 and B.6 were inclined to be symptomatic. Patients infected with variant B.1.351 and B.1.524 spent longer time in SARS-CoV-2 RNA turn negative (26 days, P = 0.085; 41 days, P = 0.007) and hospitalization (28 days, P = 0.085; 43 days, P = 0.004). CONCLUSIONS The asymptomatic cases are prone to develop in patients with younger age, less comorbidities andinfected with B.1.1 and B.1.524 variants. More attention should be paid for lineage B.1.524 because it can significantly prolong the SARS-CoV-2 RNA negative conversion time and hospitalization in infected cases.
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Affiliation(s)
- Hui Xu
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cheng-yuan Xie
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Pei-hong Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Shantou University Medical College, Shantou, China
| | - Zhong-liang Ji
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Department of Emergency, Shenzhen University General Hospital, Shenzhen, China
| | - Jiu-feng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Bei Hu
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xin Li
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ming Fang
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Shantou University Medical College, Shantou, China
- *Correspondence: Ming Fang
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