Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread and poses a major threat to public health worldwide. The whole genome sequencing plays a crucial role in virus surveillance and evolutionary analysis. In this study, five genome sequences of SARS-CoV-2 were obtained from...
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.814806/full |
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| author | Yanan Wang Duo Chen Chaofeng Zhu Zhenhua Zhao Shanshan Gao Jianjun Gou Yongjun Guo Xiangdong Kong |
| author_facet | Yanan Wang Duo Chen Chaofeng Zhu Zhenhua Zhao Shanshan Gao Jianjun Gou Yongjun Guo Xiangdong Kong |
| author_sort | Yanan Wang |
| collection | DOAJ |
| description | Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread and poses a major threat to public health worldwide. The whole genome sequencing plays a crucial role in virus surveillance and evolutionary analysis. In this study, five genome sequences of SARS-CoV-2 were obtained from nasopharyngeal swab samples from Zhengzhou, China. Following RNA extraction and cDNA synthesis, multiplex PCR was performed with two primer pools to produce the overlapped amplicons of ~1,200 bp. The viral genomes were obtained with 96% coverage using nanopore sequencing. Forty-five missense nucleotide mutations were identified; out of these, 5 mutations located at Nsp2, Nsp3, Nsp14, and ORF10 genes occurred with a <0.1% frequency in the global dataset. On the basis of mutation profiles, five genomes were clustered into two sublineages (B.1.617.2 and AY.31) or subclades (21A and 21I). The phylogenetic analysis of viral genomes from several regions of China and Myanmar revealed that five patients had different viral transmission chains. Taken together, we established a nanopore sequencing platform for genetic surveillance of SARS-CoV-2 and identified the variants circulating in Zhengzhou during August 2021. Our study provided crucial support for government policymaking and prevention and control of COVID-19. |
| first_indexed | 2024-04-13T02:34:11Z |
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| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-13T02:34:11Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Immunology |
| spelling | doaj.art-a7a488ab18b74061a85f8b5d32d0e1c52022-12-22T03:06:27ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-04-011310.3389/fimmu.2022.814806814806Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore SequencingYanan Wang0Duo Chen1Chaofeng Zhu2Zhenhua Zhao3Shanshan Gao4Jianjun Gou5Yongjun Guo6Xiangdong Kong7Genetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaGenetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaGenetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaGenetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaGenetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaDepartment of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaDepartment of Pathology, Henan Academy of Medical Sciences, Zhengzhou, ChinaGenetic and Prenatal Diagnosis Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, ChinaSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread and poses a major threat to public health worldwide. The whole genome sequencing plays a crucial role in virus surveillance and evolutionary analysis. In this study, five genome sequences of SARS-CoV-2 were obtained from nasopharyngeal swab samples from Zhengzhou, China. Following RNA extraction and cDNA synthesis, multiplex PCR was performed with two primer pools to produce the overlapped amplicons of ~1,200 bp. The viral genomes were obtained with 96% coverage using nanopore sequencing. Forty-five missense nucleotide mutations were identified; out of these, 5 mutations located at Nsp2, Nsp3, Nsp14, and ORF10 genes occurred with a <0.1% frequency in the global dataset. On the basis of mutation profiles, five genomes were clustered into two sublineages (B.1.617.2 and AY.31) or subclades (21A and 21I). The phylogenetic analysis of viral genomes from several regions of China and Myanmar revealed that five patients had different viral transmission chains. Taken together, we established a nanopore sequencing platform for genetic surveillance of SARS-CoV-2 and identified the variants circulating in Zhengzhou during August 2021. Our study provided crucial support for government policymaking and prevention and control of COVID-19.https://www.frontiersin.org/articles/10.3389/fimmu.2022.814806/fullSARS-CoV-2nanopore sequencingmultiplex PCRnucleotide mutationphylogenetic analysissequencing coverage |
| spellingShingle | Yanan Wang Duo Chen Chaofeng Zhu Zhenhua Zhao Shanshan Gao Jianjun Gou Yongjun Guo Xiangdong Kong Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing Frontiers in Immunology SARS-CoV-2 nanopore sequencing multiplex PCR nucleotide mutation phylogenetic analysis sequencing coverage |
| title | Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing |
| title_full | Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing |
| title_fullStr | Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing |
| title_full_unstemmed | Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing |
| title_short | Genetic Surveillance of Five SARS-CoV-2 Clinical Samples in Henan Province Using Nanopore Sequencing |
| title_sort | genetic surveillance of five sars cov 2 clinical samples in henan province using nanopore sequencing |
| topic | SARS-CoV-2 nanopore sequencing multiplex PCR nucleotide mutation phylogenetic analysis sequencing coverage |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.814806/full |
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