The Intra-Host Evolution of SARS-CoV-2 After Neutralizing Antibody Therapy, Revealed by Nanopore Sequencing

Zeng，Hong Xiang1,4; Zu，Wen Hong1,4; Wang，Hai Yan1,4; Yuan，Jing2; Cheng，Lin1,4; Xu，Gang1,4; Huang，Yi Gan1,4; Liu，Yang1,4; Zhang，Shu Ye3; Zhang，Zheng1,4

2024

10.15212/ZOONOSES-2023-0032

Zoonoses (Ireland)   影响因子和分区

2737-7466

2737-7474

Objective: In the context of two Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreaks involving local transmission and an international flight, we used meta-transcriptome and multi-amplicon sequencing to successfully acquire the complete viral genome sequences from clinical samples with varying viral loads. Methods: To enhance viral transcript presence, we used a primer pool for reverse transcription and sequenced the samples with nanopore sequencing, and successfully acquired the entire genomic sequence of the virus within less than 4 hours. In a substantial sample size of approximately 800 clinical specimens, we thoroughly examined and compared different sequencing methods. Results: Meta-transcriptome sequencing was effective for samples with viral reverse transcription polymerase chain reaction (RT-PCR) threshold cycle (Ct) values below 22, whereas multi-amplicon sequencing was effective across a wide Ct range. Additionally, enriched nanopore sequencing was valuable in capturing the complete genome sequence when rapid results are required. Conclusion: Through monitoring the viral quasi-species in individual patients, we observed ongoing viral evolution during neutralizing antibody therapy and found evidence that vaccine administration may affect the development of viral quasi-species. Overall, our findings highlight the potential of this viral sequencing strategy for both outbreak control and patient treatment.

Antibody Mutation SARS-CoV-2 Vaccine

英语

第一

2-s2.0-85184421783

Scopus

1.Institute for Hepatology,National Clinical Research Center for Infectious Disease,Shenzhen Third People’s Hospital,The Second Affiliated Hospital,School of Medicine,Southern University of Science and Technology,Shenzhen,Guangdong Province,518112,China
2.Department of Infectious Diseases,National Clinical Research Center for Infectious Disease,Shenzhen Third People’s Hospital,The Second Affiliated Hospital,School of Medicine,Southern University of Science and Technology,Shenzhen,Guangdong Province,518112,China
3.Clinical Center for Biotherapy at Zhongshan Hospital,Fudan University,Shanghai,200031,China
4.Shenzhen Research Center for Communicable Disease Diagnosis and Treatment,Chinese Academy of Medical Sciences,Shenzhen,China

Zeng，Hong Xiang,Zu，Wen Hong,Wang，Hai Yan,et al. The Intra-Host Evolution of SARS-CoV-2 After Neutralizing Antibody Therapy, Revealed by Nanopore Sequencing[J]. Zoonoses (Ireland),2024,4(1).

Zeng，Hong Xiang.,Zu，Wen Hong.,Wang，Hai Yan.,Yuan，Jing.,Cheng，Lin.,...&Zhang，Zheng.(2024).The Intra-Host Evolution of SARS-CoV-2 After Neutralizing Antibody Therapy, Revealed by Nanopore Sequencing.Zoonoses (Ireland),4(1).

Zeng，Hong Xiang,et al."The Intra-Host Evolution of SARS-CoV-2 After Neutralizing Antibody Therapy, Revealed by Nanopore Sequencing".Zoonoses (Ireland) 4.1(2024).