Wuhan, Hubei

Researchers in British Columbia have identified a set of gene variants that are likely to influence disease progression from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection to COVID-19 disease. They have identified a rare set of variants in specific amino acid residues on the protein angiotensin-converting enzyme 2 (ACE2) that affect the viral spike protein’s ability to bind to and enter human cells. A spike protein is a key structural protein on the surface of SARS-CoV and SARS-CoV2 (the causative agent in COVID-19) virions that enables interaction with human cell receptors and fusion with the host cell membrane....

 

For their study, the team used the gnomAD database – a resource cataloging genetic coding variants for 141,456 adults. They assessed entries on ACE2 in the database and downloaded files predicting missense variants in the protein. The database cataloged 242 coding missense variants, 15 of which were predicted to be located at or close to the ACE2 binding site for SARS-CoV-2 spike protein. On aggregating the frequency of these variants, the team estimated that they occur in approximately 3.9 per 1,000 males and 8.5 per 1,000 females. However, the distribution of these rare alleles is not even across subpopulations, and the only common one was rs41303171 (thought to encode p.Asn720Asp), which occurred in 1.7% of males and 3.2% of females in the database. 

 

Although the occurrence of this allele was frequent enough to be identified in genome-wide association studies, it does not lie in the ACE2 domain thought to be bound by SARS-CoV-2 and was therefore not considered a worthwhile candidate for this interaction. The second most common variant was rs4646116 (thought to encode p.Lys26Arg), which was predicted to lie next to the ACE2-Spike protein interface.

 

Preprint of the original study available at bioRxiV (April 14, 2020):

https://www.biorxiv.org/content/10.1101/2020.04.05.026633v1

Via Juan Lama

A l'heure où les mesures de confinement de la ville de Wuhan sont levées, je voulais vous dire ma joie de voir revivre la ville, mais aussi exprimer à nouveau mes très sincères condoléances à toutes celles et tous ceux qui pendant cette épreuve ont perdu un parent, un proche, un ami.

Scientists in Shanghai say some recovered patients show no signs of the neutralising proteins.  Researchers in Shanghai hope to determine whether some recovered coronavirus patients  have a higher risk of reinfection after finding surprisingly low levels of Covid-19 antibodies in a number of people discharged from hospital. A team from Fudan University analysed blood samples from 175 patients discharged from the Shanghai Public Health Clinical Centre and found that nearly a third had unexpectedly low levels of antibodies. In some cases, antibodies could not be detected at all. 

Via Juan Lama

Abstract The 2019 novel coronavirus (2019-nCoV) outbreak has caused a large number of deaths with thousands of confirmed cases worldwide, especially in East Asia This study took an immunoinformatics approach to identify significant cytotoxic T lymphocyte (CTL) and B cell epitopes in the 2019-nCoV surface glycoprotein Also, interactions between identified CTL epitopes and their corresponding MHC class I supertype representatives prevalent in China were studied by molecular dynamics simulations We identified five CTL epitopes, three sequential B cell epitopes and five discontinuous B cell epitopes in the viral surface glycoprotein Also, during simulations, the CTL epitopes were observed to be binding MHC class I peptide-binding grooves via multiple contacts, with continuous hydrogen bonds and salt bridge anchors, indicating their potential in generating immune responses Some of these identified epitopes can be potential candidates for development of 2019-nCoV vaccines

Via Krishan Maggon