Genomic characterizations and epidemiology
Printed From: Avian Flu Talk
Category: Main Forums
Forum Name: General Discussion
Forum Description: (General discussion regarding the next pandemic)
URL: http://www.avianflutalk.com/forum_posts.asp?TID=40630
Printed Date: April 30 2024 at 9:37pm
Topic: Genomic characterizations and epidemiology
Posted By: Southeastern
Subject: Genomic characterizations and epidemiology
Date Posted: February 01 2020 at 8:22am
Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding
February 01, 2020
Via The Lancet
The summary:
Background
In late December, 2019, patients presenting with viral pneumonia due to an unidentified microbial agent were reported in Wuhan, China. A novel coronavirus was subsequently identified as the causative pathogen, provisionally named 2019 novel coronavirus (2019-nCoV). As of Jan 26, 2020, more than 2000 cases of 2019-nCoV infection have been confirmed, most of which involved people living in or visiting Wuhan, and human-to-human transmission has been confirmed.
Methods
We did next-generation sequencing of samples from bronchoalveolar lavage fluid and cultured isolates from nine inpatients, eight of whom had visited the Huanan seafood market in Wuhan. Complete and partial 2019-nCoV genome sequences were obtained from these individuals. Viral contigs were connected using Sanger sequencing to obtain the full-length genomes, with the terminal regions determined by rapid amplification of cDNA ends. Phylogenetic analysis of these 2019-nCoV genomes and those of other coronaviruses was used to determine the evolutionary history of the virus and help infer its likely origin. Homology modelling was done to explore the likely receptor-binding properties of the virus.
Findings
The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99ยท98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues.
Interpretation
2019-nCoV is sufficiently divergent from SARS-CoV to be considered a new human-infecting betacoronavirus. Although our phylogenetic analysis suggests that bats might be the original host of this virus, an animal sold at the seafood market in Wuhan might represent an intermediate host facilitating the emergence of the virus in humans. Importantly, structural analysis suggests that 2019-nCoV might be able to bind to the angiotensin-converting enzyme 2 receptor in humans. The future evolution, adaptation, and spread of this virus warrant urgent investigation.
https://crofsblogs.typepad.com/h5n1/" rel="nofollow - https://crofsblogs.typepad.com/h5n1/
-------------
"It had taken, with unconceivable rapidity, the character of a gigantic mantle of rare flame, extending from horizon to horizon."
**Good Night and Good Luck**
|
Replies:
Posted By: Technophobe
Date Posted: February 01 2020 at 8:45am
Thank you, Oakviolet! Wonderful info!!!
-------------
How do you tell if a politician is lying?
His lips or pen are moving.
|
|