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

Abstract

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.