The Intra-Host Evolution of SARS-CoV-2 After Neutralizing Antibody Therapy, Revealed by Nanopore Sequencing
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 varyi...
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| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Compuscript Ltd
2024-01-01
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| Series: | Zoonoses |
| Online Access: | https://www.scienceopen.com/hosted-document?doi=10.15212/ZOONOSES-2023-0032 |
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| Summary: | 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. 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. 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, 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. |
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| ISSN: | 2737-7466 2737-7474 |