{"title":"2020-2024 年菲律宾流行的 SARS-CoV-2 变种的基因组分析","authors":"Arnie Dimaano , Kiana Dominique Carreon , Giselle Sophia Camaya , Irvin Rondolo , Jarel Elgin Tolentino","doi":"10.1016/j.dialog.2024.100193","DOIUrl":null,"url":null,"abstract":"<div><h3>Purpose</h3><p>Genomic sequencing has been an invaluable tool to determine the evolution of SARS-CoV-2. In the present study, we provided a comprehensive description of the SARS-CoV-2 variants circulated in the Philippines.</p></div><div><h3>Methods</h3><p>The dataset from the human COVID-19 infections was acquired by downloading the sequences and their associated metadata spanning from March 2020 to April 2024. Then, we executed several filtering criteria to acquire the final dataset for the Philippine samples and performed spatial distribution analysis and phylogenetic tree construction of the reported SARS-CoV-2 sequences.</p></div><div><h3>Results</h3><p>A total of 16,679,203 SARS-CoV sequences were obtained, of which 17,393 (0.10 %) were sampled in the Philippines. Western Visayas reported the highest SARS-CoV-2 sequences (21.33 %), while the Bangsamoro Autonomous Region in Muslim Mindanao reported the least (0.48 %). The phylogenetic tree revealed the evolution of the detected SARS-CoV-2 variants circulating in the Philippines with 19 A as the first reported case (based on the GISAID submission), and 24 A (JN.1) as the currently circulating variant. Omicron variants have dominated the Philippines with 21 L (Omicron, BA.2) having 5102 cases (29.33 %), followed by 22B (BA.5) having 2184 cases (12.57 %). Using Pearson's Chi-square test of independence, we showed that there is a significant association between the age-groups and gender with the detection years.</p></div><div><h3>Conclusion</h3><p>Altogether, this analysis showed the updated epidemiological trends of the reported SARS-CoV-2 variants in the Philippines. This increases the importance of conducting surveillance on viral infectious diseases such as COVID-19 to provide the scope and trajectory of viral spread in a country.</p></div>","PeriodicalId":72803,"journal":{"name":"Dialogues in health","volume":"5 ","pages":"Article 100193"},"PeriodicalIF":0.0000,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772653324000297/pdfft?md5=c2d3976b5c454541656dc2dae68e0f59&pid=1-s2.0-S2772653324000297-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Genomic analysis of the SARS-CoV-2 variants circulated in the Philippines, 2020–2024\",\"authors\":\"Arnie Dimaano , Kiana Dominique Carreon , Giselle Sophia Camaya , Irvin Rondolo , Jarel Elgin Tolentino\",\"doi\":\"10.1016/j.dialog.2024.100193\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Purpose</h3><p>Genomic sequencing has been an invaluable tool to determine the evolution of SARS-CoV-2. In the present study, we provided a comprehensive description of the SARS-CoV-2 variants circulated in the Philippines.</p></div><div><h3>Methods</h3><p>The dataset from the human COVID-19 infections was acquired by downloading the sequences and their associated metadata spanning from March 2020 to April 2024. Then, we executed several filtering criteria to acquire the final dataset for the Philippine samples and performed spatial distribution analysis and phylogenetic tree construction of the reported SARS-CoV-2 sequences.</p></div><div><h3>Results</h3><p>A total of 16,679,203 SARS-CoV sequences were obtained, of which 17,393 (0.10 %) were sampled in the Philippines. Western Visayas reported the highest SARS-CoV-2 sequences (21.33 %), while the Bangsamoro Autonomous Region in Muslim Mindanao reported the least (0.48 %). The phylogenetic tree revealed the evolution of the detected SARS-CoV-2 variants circulating in the Philippines with 19 A as the first reported case (based on the GISAID submission), and 24 A (JN.1) as the currently circulating variant. Omicron variants have dominated the Philippines with 21 L (Omicron, BA.2) having 5102 cases (29.33 %), followed by 22B (BA.5) having 2184 cases (12.57 %). Using Pearson's Chi-square test of independence, we showed that there is a significant association between the age-groups and gender with the detection years.</p></div><div><h3>Conclusion</h3><p>Altogether, this analysis showed the updated epidemiological trends of the reported SARS-CoV-2 variants in the Philippines. This increases the importance of conducting surveillance on viral infectious diseases such as COVID-19 to provide the scope and trajectory of viral spread in a country.</p></div>\",\"PeriodicalId\":72803,\"journal\":{\"name\":\"Dialogues in health\",\"volume\":\"5 \",\"pages\":\"Article 100193\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-09-12\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2772653324000297/pdfft?md5=c2d3976b5c454541656dc2dae68e0f59&pid=1-s2.0-S2772653324000297-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Dialogues in health\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2772653324000297\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Dialogues in health","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2772653324000297","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Genomic analysis of the SARS-CoV-2 variants circulated in the Philippines, 2020–2024
Purpose
Genomic sequencing has been an invaluable tool to determine the evolution of SARS-CoV-2. In the present study, we provided a comprehensive description of the SARS-CoV-2 variants circulated in the Philippines.
Methods
The dataset from the human COVID-19 infections was acquired by downloading the sequences and their associated metadata spanning from March 2020 to April 2024. Then, we executed several filtering criteria to acquire the final dataset for the Philippine samples and performed spatial distribution analysis and phylogenetic tree construction of the reported SARS-CoV-2 sequences.
Results
A total of 16,679,203 SARS-CoV sequences were obtained, of which 17,393 (0.10 %) were sampled in the Philippines. Western Visayas reported the highest SARS-CoV-2 sequences (21.33 %), while the Bangsamoro Autonomous Region in Muslim Mindanao reported the least (0.48 %). The phylogenetic tree revealed the evolution of the detected SARS-CoV-2 variants circulating in the Philippines with 19 A as the first reported case (based on the GISAID submission), and 24 A (JN.1) as the currently circulating variant. Omicron variants have dominated the Philippines with 21 L (Omicron, BA.2) having 5102 cases (29.33 %), followed by 22B (BA.5) having 2184 cases (12.57 %). Using Pearson's Chi-square test of independence, we showed that there is a significant association between the age-groups and gender with the detection years.
Conclusion
Altogether, this analysis showed the updated epidemiological trends of the reported SARS-CoV-2 variants in the Philippines. This increases the importance of conducting surveillance on viral infectious diseases such as COVID-19 to provide the scope and trajectory of viral spread in a country.
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