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Singapore's COVID‐19 Genomic Surveillance Programme: Strategies and Insights From a Pandemic Year
ABSTRACT Background During the COVID‐19 pandemic, genomic surveillance was crucial for monitoring virus spread and identifying variants. Effective surveillance helped understand transmission dynamics. Singapore had success in combating COVID‐19 through its surveillance programmes. This paper outline...
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| Published in: | Influenza and other respiratory viruses 2024-12, Vol.18 (12), p.e70060-n/a |
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| container_title | Influenza and other respiratory viruses |
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| creator | Tan, Hao Yi Khamis, Nur Huda Goh, Alvin Mah, Tania K. L. Yeo, Benny Ngan, Jie Yin Ding, Yichen Lin, Cui Chae, Sae‐Rom Lee, Phoebe Ho, Zheng Jie Marc |
| description | ABSTRACT
Background
During the COVID‐19 pandemic, genomic surveillance was crucial for monitoring virus spread and identifying variants. Effective surveillance helped understand transmission dynamics. Singapore had success in combating COVID‐19 through its surveillance programmes. This paper outlines Singapore's strategy and its impact on public health during the transition to endemicity over 54 weeks from February 2022 to February 2023.
Methods
In May 2022, Singapore expanded its acute respiratory infections (ARI) surveillance to enhance COVID‐19 detection. COVID‐19–positive samples from ARI cases were sent to the National Public Health Laboratory for whole genome sequencing (WGS). WGS data informed public health actions based on transmission origins and case severity.
Results
Over 54 weeks, NPHL sequenced 18,918 (73%) samples. Analysis showed 29% imported and 71% local cases. Severe cases accounted for 12% and were mostly elderly, specifically those aged 80 years old and above. Variant analysis identified 11 predominant variants and 288 subvariants. Omicron BA.2, BA.5 and XBB were initially dominant, followed by increased variant heterogeneity. Severe cases mirrored these trends.
Conclusion
Genomic surveillance was integral in Singapore's COVID‐19 response, guiding timely public health decisions. Effective variant tracking supported proactive measures. The experience underscores the importance of genomic surveillance for future pandemic preparedness and emerging disease detection, emphasising its role in shaping pandemic responses and global health. |
| doi_str_mv | 10.1111/irv.70060 |
| format | article |
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Background
During the COVID‐19 pandemic, genomic surveillance was crucial for monitoring virus spread and identifying variants. Effective surveillance helped understand transmission dynamics. Singapore had success in combating COVID‐19 through its surveillance programmes. This paper outlines Singapore's strategy and its impact on public health during the transition to endemicity over 54 weeks from February 2022 to February 2023.
Methods
In May 2022, Singapore expanded its acute respiratory infections (ARI) surveillance to enhance COVID‐19 detection. COVID‐19–positive samples from ARI cases were sent to the National Public Health Laboratory for whole genome sequencing (WGS). WGS data informed public health actions based on transmission origins and case severity.
Results
Over 54 weeks, NPHL sequenced 18,918 (73%) samples. Analysis showed 29% imported and 71% local cases. Severe cases accounted for 12% and were mostly elderly, specifically those aged 80 years old and above. Variant analysis identified 11 predominant variants and 288 subvariants. Omicron BA.2, BA.5 and XBB were initially dominant, followed by increased variant heterogeneity. Severe cases mirrored these trends.
Conclusion
Genomic surveillance was integral in Singapore's COVID‐19 response, guiding timely public health decisions. Effective variant tracking supported proactive measures. The experience underscores the importance of genomic surveillance for future pandemic preparedness and emerging disease detection, emphasising its role in shaping pandemic responses and global health.</description><identifier>ISSN: 1750-2640</identifier><identifier>ISSN: 1750-2659</identifier><identifier>EISSN: 1750-2659</identifier><identifier>DOI: 10.1111/irv.70060</identifier><identifier>PMID: 39701579</identifier><language>eng</language><publisher>England: John Wiley & Sons, Inc</publisher><subject>Acute Respiratory Infections (ARI) ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Antigens ; Child ; Child, Preschool ; COVID-19 ; COVID-19 - epidemiology ; COVID-19 - transmission ; COVID-19 - virology ; COVID-19 diagnostic tests ; Disease detection ; Disease transmission ; Emerging infectious diseases ; Epidemiological Monitoring ; Female ; Gene sequencing ; Genome, Viral - genetics ; Genomes ; Genomic Surveillance ; Genomics ; Global health ; Health Strategy ; Health surveillance ; Heterogeneity ; Humans ; Infant ; Infant, Newborn ; Infections ; Influenza ; Laboratories ; Male ; Middle Aged ; Original ; Pandemic preparedness ; Pandemics ; Pathogens ; Primary care ; Public Health ; Respiratory tract infection ; SARS-CoV-2 - genetics ; SARS-CoV-2 - isolation & purification ; Severe acute respiratory syndrome coronavirus 2 ; Singapore ; Singapore - epidemiology ; Surveillance ; Trends ; Viruses ; Whole Genome Sequencing ; Whole genome sequencing (WGS) ; Young Adult</subject><ispartof>Influenza and other respiratory viruses, 2024-12, Vol.18 (12), p.e70060-n/a</ispartof><rights>2024 The Author(s). published by John Wiley & Sons Ltd.</rights><rights>2024 The Author(s). Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.</rights><rights>2024. This work is published under http://creativecommons.org/licenses/by/4.0/ (the "License"). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><orcidid>0009-0005-8904-8936</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/3149320774/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/3149320774?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,11562,25753,27924,27925,37012,37013,38516,43895,44590,46052,46476,53791,53793,74412,75126</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39701579$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tan, Hao Yi</creatorcontrib><creatorcontrib>Khamis, Nur Huda</creatorcontrib><creatorcontrib>Goh, Alvin</creatorcontrib><creatorcontrib>Mah, Tania K. L.</creatorcontrib><creatorcontrib>Yeo, Benny</creatorcontrib><creatorcontrib>Ngan, Jie Yin</creatorcontrib><creatorcontrib>Ding, Yichen</creatorcontrib><creatorcontrib>Lin, Cui</creatorcontrib><creatorcontrib>Chae, Sae‐Rom</creatorcontrib><creatorcontrib>Lee, Phoebe</creatorcontrib><creatorcontrib>Ho, Zheng Jie Marc</creatorcontrib><title>Singapore's COVID‐19 Genomic Surveillance Programme: Strategies and Insights From a Pandemic Year</title><title>Influenza and other respiratory viruses</title><addtitle>Influenza Other Respir Viruses</addtitle><description>ABSTRACT
Background
During the COVID‐19 pandemic, genomic surveillance was crucial for monitoring virus spread and identifying variants. Effective surveillance helped understand transmission dynamics. Singapore had success in combating COVID‐19 through its surveillance programmes. This paper outlines Singapore's strategy and its impact on public health during the transition to endemicity over 54 weeks from February 2022 to February 2023.
Methods
In May 2022, Singapore expanded its acute respiratory infections (ARI) surveillance to enhance COVID‐19 detection. COVID‐19–positive samples from ARI cases were sent to the National Public Health Laboratory for whole genome sequencing (WGS). WGS data informed public health actions based on transmission origins and case severity.
Results
Over 54 weeks, NPHL sequenced 18,918 (73%) samples. Analysis showed 29% imported and 71% local cases. Severe cases accounted for 12% and were mostly elderly, specifically those aged 80 years old and above. Variant analysis identified 11 predominant variants and 288 subvariants. Omicron BA.2, BA.5 and XBB were initially dominant, followed by increased variant heterogeneity. Severe cases mirrored these trends.
Conclusion
Genomic surveillance was integral in Singapore's COVID‐19 response, guiding timely public health decisions. Effective variant tracking supported proactive measures. The experience underscores the importance of genomic surveillance for future pandemic preparedness and emerging disease detection, emphasising its role in shaping pandemic responses and global health.</description><subject>Acute Respiratory Infections (ARI)</subject><subject>Adolescent</subject><subject>Adult</subject><subject>Aged</subject><subject>Aged, 80 and over</subject><subject>Antigens</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>COVID-19</subject><subject>COVID-19 - epidemiology</subject><subject>COVID-19 - transmission</subject><subject>COVID-19 - virology</subject><subject>COVID-19 diagnostic tests</subject><subject>Disease detection</subject><subject>Disease transmission</subject><subject>Emerging infectious diseases</subject><subject>Epidemiological Monitoring</subject><subject>Female</subject><subject>Gene sequencing</subject><subject>Genome, Viral - genetics</subject><subject>Genomes</subject><subject>Genomic Surveillance</subject><subject>Genomics</subject><subject>Global health</subject><subject>Health Strategy</subject><subject>Health surveillance</subject><subject>Heterogeneity</subject><subject>Humans</subject><subject>Infant</subject><subject>Infant, Newborn</subject><subject>Infections</subject><subject>Influenza</subject><subject>Laboratories</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Original</subject><subject>Pandemic preparedness</subject><subject>Pandemics</subject><subject>Pathogens</subject><subject>Primary care</subject><subject>Public Health</subject><subject>Respiratory tract infection</subject><subject>SARS-CoV-2 - genetics</subject><subject>SARS-CoV-2 - isolation & purification</subject><subject>Severe acute respiratory syndrome coronavirus 2</subject><subject>Singapore</subject><subject>Singapore - epidemiology</subject><subject>Surveillance</subject><subject>Trends</subject><subject>Viruses</subject><subject>Whole Genome Sequencing</subject><subject>Whole genome sequencing (WGS)</subject><subject>Young Adult</subject><issn>1750-2640</issn><issn>1750-2659</issn><issn>1750-2659</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>24P</sourceid><sourceid>COVID</sourceid><sourceid>PIMPY</sourceid><recordid>eNpdkc1OGzEUhS0E4q9d8ALIEgu6Cdjj8djDpkJpoZEigQiNxMryeO4MRjPj1M4Esesj9Bn7JHVCiKBeXF_5fj46VwehI0rOaDzn1i_OBCEZ2UL7VHAySDKeb2_6lOyhgxCeCOGZ5Oku2mO5IJSLfB-Zie1qPXMeTgMe3kxH3_7-_kNzfA2da63Bk94vwDaN7gzgW-9qr9sWLvBk7vUcagsB667Eoy7Y-nEe8JV3Ldb4Nj7C8v8DaP8J7VS6CfB5fR-in1ff74c_BuOb69HwcjyYUUnIwDBTJUZUssjKgvK8qkzBGZXAmc5EUsYCHAwvKoi1lEKSjJaUlxkj2hjODtHXV91ZX7RQGuiiyUbNvG21f1FOW_Vx0tlHVbuFojTjUiYiKnxZK3j3q4cwV60NBpbrg-uDYjQVqUzSlEb05D_0yfW-i_stqZwlRIg0UsfvLW28vAUQgfNX4Nk28LKZU6KWyaqYrFolq0Z301XD_gHC5Jcp</recordid><startdate>202412</startdate><enddate>202412</enddate><creator>Tan, Hao Yi</creator><creator>Khamis, Nur Huda</creator><creator>Goh, Alvin</creator><creator>Mah, Tania K. L.</creator><creator>Yeo, Benny</creator><creator>Ngan, Jie Yin</creator><creator>Ding, Yichen</creator><creator>Lin, Cui</creator><creator>Chae, Sae‐Rom</creator><creator>Lee, Phoebe</creator><creator>Ho, Zheng Jie Marc</creator><general>John Wiley & Sons, Inc</general><general>John Wiley and Sons Inc</general><scope>24P</scope><scope>WIN</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>3V.</scope><scope>7QL</scope><scope>7T2</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>C1K</scope><scope>CCPQU</scope><scope>COVID</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>H94</scope><scope>K9.</scope><scope>M0S</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0009-0005-8904-8936</orcidid></search><sort><creationdate>202412</creationdate><title>Singapore's COVID‐19 Genomic Surveillance Programme: Strategies and Insights From a Pandemic Year</title><author>Tan, Hao Yi ; Khamis, Nur Huda ; Goh, Alvin ; Mah, Tania K. L. ; Yeo, Benny ; Ngan, Jie Yin ; Ding, Yichen ; Lin, Cui ; Chae, Sae‐Rom ; Lee, Phoebe ; Ho, Zheng Jie Marc</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-p1800-c3cf2c7f8b6db159ffcb5318e53a672da67e5ec5bfeec5d878061d15d630acc53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Acute Respiratory Infections (ARI)</topic><topic>Adolescent</topic><topic>Adult</topic><topic>Aged</topic><topic>Aged, 80 and over</topic><topic>Antigens</topic><topic>Child</topic><topic>Child, Preschool</topic><topic>COVID-19</topic><topic>COVID-19 - epidemiology</topic><topic>COVID-19 - transmission</topic><topic>COVID-19 - virology</topic><topic>COVID-19 diagnostic tests</topic><topic>Disease detection</topic><topic>Disease transmission</topic><topic>Emerging infectious diseases</topic><topic>Epidemiological Monitoring</topic><topic>Female</topic><topic>Gene sequencing</topic><topic>Genome, Viral - genetics</topic><topic>Genomes</topic><topic>Genomic Surveillance</topic><topic>Genomics</topic><topic>Global health</topic><topic>Health Strategy</topic><topic>Health surveillance</topic><topic>Heterogeneity</topic><topic>Humans</topic><topic>Infant</topic><topic>Infant, Newborn</topic><topic>Infections</topic><topic>Influenza</topic><topic>Laboratories</topic><topic>Male</topic><topic>Middle Aged</topic><topic>Original</topic><topic>Pandemic preparedness</topic><topic>Pandemics</topic><topic>Pathogens</topic><topic>Primary care</topic><topic>Public Health</topic><topic>Respiratory tract infection</topic><topic>SARS-CoV-2 - genetics</topic><topic>SARS-CoV-2 - isolation & purification</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Singapore</topic><topic>Singapore - epidemiology</topic><topic>Surveillance</topic><topic>Trends</topic><topic>Viruses</topic><topic>Whole Genome Sequencing</topic><topic>Whole genome sequencing (WGS)</topic><topic>Young Adult</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tan, Hao Yi</creatorcontrib><creatorcontrib>Khamis, Nur Huda</creatorcontrib><creatorcontrib>Goh, Alvin</creatorcontrib><creatorcontrib>Mah, Tania K. L.</creatorcontrib><creatorcontrib>Yeo, Benny</creatorcontrib><creatorcontrib>Ngan, Jie Yin</creatorcontrib><creatorcontrib>Ding, Yichen</creatorcontrib><creatorcontrib>Lin, Cui</creatorcontrib><creatorcontrib>Chae, Sae‐Rom</creatorcontrib><creatorcontrib>Lee, Phoebe</creatorcontrib><creatorcontrib>Ho, Zheng Jie Marc</creatorcontrib><collection>Open Access: Wiley-Blackwell Open Access Journals</collection><collection>Wiley Free Archive</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Health and Safety Science Abstracts (Full archive)</collection><collection>Virology and AIDS Abstracts</collection><collection>ProQuest - Health & Medical Complete保健、医学与药学数据库</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>Coronavirus Research Database</collection><collection>ProQuest Central</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Publicly Available Content (ProQuest)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Influenza and other respiratory viruses</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tan, Hao Yi</au><au>Khamis, Nur Huda</au><au>Goh, Alvin</au><au>Mah, Tania K. L.</au><au>Yeo, Benny</au><au>Ngan, Jie Yin</au><au>Ding, Yichen</au><au>Lin, Cui</au><au>Chae, Sae‐Rom</au><au>Lee, Phoebe</au><au>Ho, Zheng Jie Marc</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Singapore's COVID‐19 Genomic Surveillance Programme: Strategies and Insights From a Pandemic Year</atitle><jtitle>Influenza and other respiratory viruses</jtitle><addtitle>Influenza Other Respir Viruses</addtitle><date>2024-12</date><risdate>2024</risdate><volume>18</volume><issue>12</issue><spage>e70060</spage><epage>n/a</epage><pages>e70060-n/a</pages><issn>1750-2640</issn><issn>1750-2659</issn><eissn>1750-2659</eissn><abstract>ABSTRACT
Background
During the COVID‐19 pandemic, genomic surveillance was crucial for monitoring virus spread and identifying variants. Effective surveillance helped understand transmission dynamics. Singapore had success in combating COVID‐19 through its surveillance programmes. This paper outlines Singapore's strategy and its impact on public health during the transition to endemicity over 54 weeks from February 2022 to February 2023.
Methods
In May 2022, Singapore expanded its acute respiratory infections (ARI) surveillance to enhance COVID‐19 detection. COVID‐19–positive samples from ARI cases were sent to the National Public Health Laboratory for whole genome sequencing (WGS). WGS data informed public health actions based on transmission origins and case severity.
Results
Over 54 weeks, NPHL sequenced 18,918 (73%) samples. Analysis showed 29% imported and 71% local cases. Severe cases accounted for 12% and were mostly elderly, specifically those aged 80 years old and above. Variant analysis identified 11 predominant variants and 288 subvariants. Omicron BA.2, BA.5 and XBB were initially dominant, followed by increased variant heterogeneity. Severe cases mirrored these trends.
Conclusion
Genomic surveillance was integral in Singapore's COVID‐19 response, guiding timely public health decisions. Effective variant tracking supported proactive measures. The experience underscores the importance of genomic surveillance for future pandemic preparedness and emerging disease detection, emphasising its role in shaping pandemic responses and global health.</abstract><cop>England</cop><pub>John Wiley & Sons, Inc</pub><pmid>39701579</pmid><doi>10.1111/irv.70060</doi><tpages>11</tpages><orcidid>https://orcid.org/0009-0005-8904-8936</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Open Access: Wiley-Blackwell Open Access Journals; Publicly Available Content (ProQuest); PubMed Central; Coronavirus Research Database |
| subjects | Acute Respiratory Infections (ARI) Adolescent Adult Aged Aged, 80 and over Antigens Child Child, Preschool COVID-19 COVID-19 - epidemiology COVID-19 - transmission COVID-19 - virology COVID-19 diagnostic tests Disease detection Disease transmission Emerging infectious diseases Epidemiological Monitoring Female Gene sequencing Genome, Viral - genetics Genomes Genomic Surveillance Genomics Global health Health Strategy Health surveillance Heterogeneity Humans Infant Infant, Newborn Infections Influenza Laboratories Male Middle Aged Original Pandemic preparedness Pandemics Pathogens Primary care Public Health Respiratory tract infection SARS-CoV-2 - genetics SARS-CoV-2 - isolation & purification Severe acute respiratory syndrome coronavirus 2 Singapore Singapore - epidemiology Surveillance Trends Viruses Whole Genome Sequencing Whole genome sequencing (WGS) Young Adult |
| title | Singapore's COVID‐19 Genomic Surveillance Programme: Strategies and Insights From a Pandemic Year |
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