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

Abstract

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.

Confusion and Hallucination: A Case Report of an Unusual Presentation of COVID-19

“…This case report lay emphasis on the importance of interdisciplinary teamwork, allowing clinicians to collaboratively recognize the real prevalence and clinical significance of any atypical presentations in COVID-19 patients. Narrowing the criteria for COVID-19 testing to only typical symptoms may lead to unreported community spread of the disease and silent transmission of the infection in hospitals [ 10 ]. On the other hand, the balance between utilizing resources and infection control is crucial since widespread testing without clear clinical indications is relatively waste of resources.…”

Influenza co-infection associated with severity and mortality in COVID-19 patients

“…RT-PCR assay targeting the E gene and RdRp (ORF1ab) of SARS-CoV-2 was carried out in 7500 Fast Real-Time PCR instrument (Thermo Fisher scientific, USA) with the Superscript III one-step RT-PCR kit (Invitrogen, Darmstadt, Germany) and performed as previously described [ 23 , 24 ]. Thermal cycling conditions were 55 °C for 10 min, then 95 °C for 3 min, followed by 45 cycles of 95 °C for 15 s, and lastly 58 °C for 30 s.…”

Moderately Low Effectiveness of the Influenza Quadrivalent Vaccine: Potential Mismatch between Circulating Strains and Vaccine Strains

“…For full haemagglutinin (HA) and neuraminidase (NA) gene sequencing, all H3N2 and H1N1positive cases with high viral load (cycle threshold (Ct) ≤ 25) were selected and subjected to a specific one-step RT-PCR amplification protocol using (HA) and (NA) gene-specific primers according to the WHO information for the molecular detection of influenza viruses Global Influenza Programme [ 18 ]. The resulting amplicon of each (HA) and (NA) gene fragment were sequenced by the Sanger method [ 19 ] with the BigDye Direct Cycle Sequencing Kit in an ABI 3730xl DNA Sequencer (Applied Biosystems, Life Technologies, Foster City, CA, USA) at the Research laboratories, biomedical administration, Research Center, King Fahad Medical City, Saudi Arabia. Using Genius Tool, the collected sequences were subjected to quality control, including primer trimming and eliminating low-quality sequences.…”