COVID-19 Pandemic Information - PDF

The pandemic Pneumonia: opacities in lungs Clusters of patients with pneumonia first publicly reported in late Dec 2019 in Wuhan. Hospitals in Wuhan were overwhelmed in the initial days of the outbreak. First pu...

The pandemic Pneumonia: opacities in lungs Clusters of patients with pneumonia first publicly reported in late Dec 2019 in Wuhan. Hospitals in Wuhan were overwhelmed in the initial days of the outbreak. First public confirmation on person-to-person spread on Jan 22, 2020, by a group of top Chinese 2d health experts. Wuhan City was sealed off on Jan 22 until Apr 8. WHO confirmed Covid-19 as pandemic on Mar 11. 8d  The Wuhan seafood market Poor hygiene condition in wet market The suspected origin of the virus due to a cluster of cases related to this market. The game meat, sold at the market, has been a suspected source. However, we now know the market is not the origin and the meats of wild animals are not likely the source of the virus.  Viral particles from patient showing classic crown-like particles with spikes protruding from their surface _ https://www.nejm.org/doi/full/10.1056/nejmoa2001017 Name and sequences of this novel coronavirus The disease name: Coronavirus Disease 2019 (COVID-19) Official virus name: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – previously “2019-nCoV” First viral genome sequences: – Molecular diagnostic companies in Wuhan sequenced clinical samples from the hospitals and by using metagenomic approach, they identified new SARS-like sequences. – China publicly shared the genetic sequence of COVID-19 on Jan 12.  Genome structure ssRNA (+) virus 」 containing multiple open reading frames in a single RNA genome of ~30 kilobases (kb) -terminal cap structure (required for efficient protein -end (likely produced by viral polymerase or cytoplasmic poly(A) polymerase) 4 looke lihe mRNA ( ar.aolyAfll ) https://www.nejm.org/doi/full/10.1056/nejmoa2001017  Phylogenetic tree shows similarity to known bat coronaviruses: 86.9% nucleotide sequence identity to bat SARS-like CoV (bat-SL- CoVZC45). https://www.nejm.org/doi/full/10.1056/nejmoa2001017  Unique features of SARS-CoV-2: 1. similarity to bat and pangolin coronaviruses A novel bat coronavirus shows very high similarities (96%) to SARS-CoV-2: Bat CoV RaTG13, previously detected in Rhinolophus affinis from a bat cave in Yunnan province Rhinolophus affinis ~ m Intermediate Horseshoe Bat contaicning only one a sRAS staln , https://www.nature.com/articles/s41586-020-2012-7  SARS-CoV-2-related coronaviruses in Malayan pangolins have 85.5% to 92.4% sequence similarity to SARS-CoV-2. However the S protein of SARS-CoV-2 exhibits very high sequence similarity (97.4%) to the Guangdong pangolin coronaviruses in the receptor-binding domain (RBD). Jimin Lai/Agence France-Presse — Getty Images https://www.nature.com/articles/s41586-020-2169-0  2. Polybasic amino acids in the receptor binding domain ‘Polybasic sequence’ is unique to SARS-CoV-2: R (Arg, Arginine) has a positively charged side group Cut here SARS-CoV-2 Figure 2: Multiple alignment at the amino acid level of PRRA insertion region and flanking areas across three coronavirus genomes relative to the outbreak strain (SARS-CoV-2). Box show the PRRA insertion present in SARS-CoV-2 and missing in the other three CoV genomes. RRAR: Polybasic sequence is a furin cleavage motif. Cut here Furin protease could cleave protein at the sequence: Arg-X-X-Arg Further reading on potential origin and sequence property of SARS-CoV-2: Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019 https://www.biorxiv.org/content/10.1101/2020.02.07.939207v1 The Proximal Origin of SARS-CoV-2 http://virological.org/t/the-proximal-origin-of-sars-cov-2/398  Origin? Mostly liked, SARS-CoV-2 is originated from the bat coronavirus (RaTG13) and has been incubated in an intermediate mammalian host (?), before jumping to human. Bat CoV RaTG13 strain ??? (unlikely) Maintaining in Adaptation to Jump to human wild bats mammalian species and adaptation