Nanopore sequencing reveals intra-host evolution of SARS-CoV-2 after neutralizing antibody therapy

In the context of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks involving local transmission and an international flight, researchers used meta-transcriptome and multi-amplicon sequencing to successfully acquire the complete viral genome sequences from clinical samples with varying viral loads.

The work is published in the journal Zoonoses.

To enhance viral transcript presence, a primer pool was used for reverse transcription and the samples were sequenced with nanopore sequencing. The entire genomic sequence of the virus was successfully acquired in less than four 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.

More information:
Hong-Xiang Zeng et al, The Intra-Host Evolution of SARS-CoV-2 After Neutralizing Antibody Therapy, Revealed by Nanopore Sequencing, Zoonoses (2024). DOI: 10.15212/ZOONOSES-2023-0032

Provided by Compuscript Ltd