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

Announcing a new article publication for Zoonoses journal.   In the context of two Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) outbreaks involving local transmission and an international flight, the authors of this article used meta-transcriptome and multi-amplicon sequencing to successfully acquire the complete viral genome sequences from clinical samples with varying viral loads.

To enhance viral transcript presence, a primer pool was used for reverse transcription and the samples were sequenced with nanopore sequencing, and the entire genomic sequence of the virus was successfully acquired within less than 4 hours. In a substantial sample size of approximately 800 clinical specimens, different sequencing methods were thoroughly examined and compared.

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.

Through monitoring the viral quasi-species in individual patients, ongoing viral evolution during neutralizing antibody therapy was observed and evidence was found that vaccine administration may affect the development of viral quasi-species. Overall, the findings highlight the potential of this viral sequencing strategy for both outbreak control and patient treatment.

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eISSN 2737-7474

ISSN 2737-7466

Hong-Xiang Zeng, Wen-Hong Zu and Hai-Yan Wang et al. The Intra-Host Evolution of SARS-CoV-2 After Neutralizing Antibody Therapy, Revealed by Nanopore Sequencing. Zoonoses. 2024. Vol. 4(1). DOI: 10.15212/ZOONOSES-2023-0032