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Article

Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients

1
Department of Research labs, Research Center, King Fahad Medical City, Riyadh 11525, Saudi Arabia
2
College of Medicine, King Fahad Medical City, Riyadh 11525, Saudi Arabia
3
King Abdullah International Medical Research Center, Riyadh 11211, Saudi Arabia
4
College of Science, King Saud University, Riyadh 11451, Saudi Arabia
5
Pathology and Clinical Laboratory Medicine Administration, King Fahad Medical City, Riyadh 11525, Saudi Arabia
6
General Administration for Research and Studies, Ministry of Health, Riyadh 11176, Saudi Arabia
7
Medical Specialties Department, King Fahad Medical City, Riyadh 11525, Saudi Arabia
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editors: Luis Martinez-Sobrido and Fernando Almazan Toral
Received: 8 November 2020 / Revised: 24 December 2020 / Accepted: 5 January 2021 / Published: 19 January 2021
(This article belongs to the Collection Coronaviruses)
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. View Full-Text
Keywords: silent transmission; NGS; influenza like illness; COVID-19; influenza vaccine silent transmission; NGS; influenza like illness; COVID-19; influenza vaccine
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MDPI and ACS Style

Alosaimi, B.; Naeem, A.; Alghoribi, M.F.; Okdah, L.; Hamed, M.E.; AlYami, A.S.; Alotaibi, A.; Enani, M. Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Viruses 2021, 13, 136. https://0-doi-org.brum.beds.ac.uk/10.3390/v13010136

AMA Style

Alosaimi B, Naeem A, Alghoribi MF, Okdah L, Hamed ME, AlYami AS, Alotaibi A, Enani M. Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients. Viruses. 2021; 13(1):136. https://0-doi-org.brum.beds.ac.uk/10.3390/v13010136

Chicago/Turabian Style

Alosaimi, Bandar; Naeem, Asif; Alghoribi, Majed F.; Okdah, Lilian; Hamed, Maaweya E.; AlYami, Ahmad S.; Alotaibi, Athari; Enani, Mushira. 2021. "Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients" Viruses 13, no. 1: 136. https://0-doi-org.brum.beds.ac.uk/10.3390/v13010136

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