Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients
| Autor: | Athari Alotaibi, Asif Naeem, Maaweya E. Hamed, Lilian Okdah, Majed F. Alghoribi, Bandar Alosaimi, Ahmad S. AlYami, Mushira Enani |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Adult
Male 0301 basic medicine Influenza vaccine viruses lcsh:QR1-502 Biology Article Protein Structure Secondary DNA sequencing Virus lcsh:Microbiology Viroporin Proteins silent transmission NGS influenza like illness COVID-19 influenza vaccine 03 medical and health sciences 0302 clinical medicine Virology Pandemic Disease Transmission Infectious Humans 030212 general & internal medicine Clade Gene Influenza-like illness SARS-CoV-2 Transmission (medicine) virus diseases RNA-Dependent RNA Polymerase respiratory tract diseases 030104 developmental biology Infectious Diseases Epidemiological Monitoring Spike Glycoprotein Coronavirus RNA Viral Female |
| Zdroj: | Viruses, Vol 13, Iss 136, p 136 (2021) Viruses; Volume 13; Issue 1; Pages: 136 Viruses |
| ISSN: | 1999-4915 |
| Popis: | In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019–2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation. |
| Databáze: | OpenAIRE |
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