New sequencing tool speeds up SARS-CoV-2 outbreak response and informs treatment

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.