Prolonged detection of complete viral genomes demonstrated by SARS-CoV-2 sequencing of serial respiratory specimens
| Autor: | Amos Adler, Ella Mendelson, Oran Erster, Noam E. Protter, Neta S. Zuckerman, Efrat Bucris, Moran Szwarcwort-Cohen, Orna Mor, Michal Mandelboim, Saar Burstein |
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| Rok vydání: | 2021 |
| Předmět: |
RNA viruses
Male Viral Diseases Coronaviruses viruses Artificial Gene Amplification and Extension Disease Polymerase Chain Reaction Genome Medical Conditions Transcription (biology) Genome Sequencing DNA sequencing Respiratory system Pathology and laboratory medicine Aged 80 and over Viral Genomics Multidisciplinary High-Throughput Nucleotide Sequencing Genomics Medical microbiology Middle Aged Infectious Diseases Viruses Viral Genome Medicine RNA Viral Female SARS CoV 2 Pathogens Transcriptome Analysis Research Article Next-Generation Sequencing Adult SARS coronavirus Adolescent Science Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Microbial Genomics Genome Viral Biology Research and Analysis Methods Real-Time Polymerase Chain Reaction Microbiology Virology Genetics Humans Molecular Biology Techniques Sequencing Techniques Molecular Biology Gene Aged Medicine and health sciences Biology and life sciences Whole Genome Sequencing SARS-CoV-2 Organisms Viral pathogens Computational Biology COVID-19 Covid 19 Reverse Transcriptase-Polymerase Chain Reaction Genome Analysis Microbial pathogens |
| Zdroj: | PLoS ONE PLoS ONE, Vol 16, Iss 8 (2021) PLoS ONE, Vol 16, Iss 8, p e0255691 (2021) |
| ISSN: | 1932-6203 |
| DOI: | 10.1371/journal.pone.0255691 |
| Popis: | Accurate and timely diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-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. |
| Databáze: | OpenAIRE |
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