Prolonged detection of complete viral genomes demonstrated by SARS-CoV-2 sequencing of serial respiratory specimens

Neta S. Zuckerman, Efrat Bucris, Oran Erster, Michal Mandelboim, Amos Adler, Saar Burstein, Noam Protter, Moran Szwarcwort-Cohen, Ella Mendelson, Orna Mor

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1 Scopus citations


Accurate and timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARSCoV- 2) is clinically essential, and is required also to monitor confirmed cases aiming to prevent further spread. Positive real-time PCR results at late time points following initial diagnosis may be clinically misleading as this methodology cannot account for the infection capabilities and the existence of whole genome sequences. In this study, 47 serial respiratory samples were tested by Allplex-nCoV test (Seegene), a triplex of three assays targeting the SARS-CoV-2 RdRP, E and N genes and subsequently assessed by next generation sequencing (NGS). COVID19 patients were tested at an early stage of the disease, when all these viral gene targets were positive, and at an advanced stage, when only the N gene target was positive in the Allplex-nCoV test. The corresponding NGS results showed the presence of complete viral genome copies at both early and advanced stages of the disease, although the total number of mapped sequences was lower in samples from advanced disease stages. We conclude that reduced viral transmission at this late disease stage may result from the low quantities of complete viral sequences and not solely from transcription favoring the N gene.

Original languageEnglish
Article numbere0255691
JournalPLoS ONE
Issue number8 August
StatePublished - Aug 2021
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2021 Zuckerman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


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