Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022
The continuously emerging new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made the global coronavirus disease 2019 (COVID-19) pandemic unpredictable. Since the beginning of the pandemic, densely populated South and Southeast Asia have suffered great losses due to mu...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/6/1355 |
| _version_ | 1827735366987153408 |
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| author | Qiong Yu Xi Tong Li Zuo Xinyu Tao Zhonghui Xu Xiaocui Li Haizhou Liu Wuxiang Guan Di Liu Haibin Liu Fang Huang Lijia Jia |
| author_facet | Qiong Yu Xi Tong Li Zuo Xinyu Tao Zhonghui Xu Xiaocui Li Haizhou Liu Wuxiang Guan Di Liu Haibin Liu Fang Huang Lijia Jia |
| author_sort | Qiong Yu |
| collection | DOAJ |
| description | The continuously emerging new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made the global coronavirus disease 2019 (COVID-19) pandemic unpredictable. Since the beginning of the pandemic, densely populated South and Southeast Asia have suffered great losses due to multiple COVID-19 surges because of vaccine and other medical resource shortages. Therefore, it is crucial to closely monitor the SARS-CoV-2 epidemic and to understand the evolutionary and transmission characteristics of SARS-CoV-2 in these regions. Here, we document the evolution of epidemic strains in the Philippines, Pakistan, and Malaysia from late 2021 to early 2022. Our results confirmed the circulation of at least five SARS-CoV-2 genotypes in these countries in January 2022, when Omicron BA.2, with a detection rate of 69.11%, replaced Delta B.1.617 as the dominant strain. Single-nucleotide polymorphism analysis indicated the distinct evolutionary directions of the Omicron and Delta isolates, with <i>S</i>, <i>Nsp1</i>, and <i>Nsp6</i> genes potentially playing a significant role in the host adaptation of the Omicron strain. These findings are able to provide insights for predicting the evolutionary direction of SARS-CoV-2 in terms of variant competition, developing multi-part vaccines, and to support the evaluation and adjustment of current surveillance, prevention, and control strategies in South and Southeast Asia. |
| first_indexed | 2024-03-11T01:50:02Z |
| format | Article |
| id | doaj.art-6086054f2ab54451ac30a36113dffc4e |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-11T01:50:02Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-6086054f2ab54451ac30a36113dffc4e2023-11-18T13:02:39ZengMDPI AGViruses1999-49152023-06-01156135510.3390/v15061355Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022Qiong Yu0Xi Tong1Li Zuo2Xinyu Tao3Zhonghui Xu4Xiaocui Li5Haizhou Liu6Wuxiang Guan7Di Liu8Haibin Liu9Fang Huang10Lijia Jia11Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaKey Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaKey Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaKey Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaLivzon Bio Inc., Zhuhai 519045, ChinaLivzon Bio Inc., Zhuhai 519045, ChinaKey Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaKey Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaKey Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaKey Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaHubei Jiangxia Laboratory, Wuhan 430200, ChinaKey Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, ChinaThe continuously emerging new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have made the global coronavirus disease 2019 (COVID-19) pandemic unpredictable. Since the beginning of the pandemic, densely populated South and Southeast Asia have suffered great losses due to multiple COVID-19 surges because of vaccine and other medical resource shortages. Therefore, it is crucial to closely monitor the SARS-CoV-2 epidemic and to understand the evolutionary and transmission characteristics of SARS-CoV-2 in these regions. Here, we document the evolution of epidemic strains in the Philippines, Pakistan, and Malaysia from late 2021 to early 2022. Our results confirmed the circulation of at least five SARS-CoV-2 genotypes in these countries in January 2022, when Omicron BA.2, with a detection rate of 69.11%, replaced Delta B.1.617 as the dominant strain. Single-nucleotide polymorphism analysis indicated the distinct evolutionary directions of the Omicron and Delta isolates, with <i>S</i>, <i>Nsp1</i>, and <i>Nsp6</i> genes potentially playing a significant role in the host adaptation of the Omicron strain. These findings are able to provide insights for predicting the evolutionary direction of SARS-CoV-2 in terms of variant competition, developing multi-part vaccines, and to support the evaluation and adjustment of current surveillance, prevention, and control strategies in South and Southeast Asia.https://www.mdpi.com/1999-4915/15/6/1355SARS-CoV-2variantgenomic epidemiologyevolutionary dynamics |
| spellingShingle | Qiong Yu Xi Tong Li Zuo Xinyu Tao Zhonghui Xu Xiaocui Li Haizhou Liu Wuxiang Guan Di Liu Haibin Liu Fang Huang Lijia Jia Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022 Viruses SARS-CoV-2 variant genomic epidemiology evolutionary dynamics |
| title | Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022 |
| title_full | Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022 |
| title_fullStr | Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022 |
| title_full_unstemmed | Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022 |
| title_short | Genomic Surveillance of SARS-CoV-2 Variants That Emerged in South and Southeast Asia during Early 2022 |
| title_sort | genomic surveillance of sars cov 2 variants that emerged in south and southeast asia during early 2022 |
| topic | SARS-CoV-2 variant genomic epidemiology evolutionary dynamics |
| url | https://www.mdpi.com/1999-4915/15/6/1355 |
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