The emergence, genomic diversity and global spread of SARS-CoV-2

Abstract

The emergence of SARS-CoV-2 SARS-CoV-2 related coronavirusesMany of the early cases of COVID-19 in Wuhan, China, were associated with the Huanan Seafood Market 2 , which-because of the presence of wildlife at the market-was considered an obvious candidate for the location of the initial zoonotic (that is, cross-species transmission) event. However, none of the animals from the market (including rabbits, snakes, stray cats, badgers and bamboo rats) tested positive for SARS-CoV-2 (ref. 7 ), and viral genome sequences of environmental samples from the market were not considered to occupy basal positions on the viral phylogeny (although the position of the rooting on the tree is uncertain) 8 . In addition, some of the early cases of COVID-19 in Wuhan were not epidemiologically linked to the market 9 , and some were linked to other markets 10,11 . Therefore, although it has not been resolved fully, the current evidence suggests that the Huanan Seafood Market could be the location of an early 'superspreading' event.From the earliest genomic comparisons, it was clear that SARS-CoV-2 had a genomic organization similar to SARS-CoV 2 . The spike proteins of both viruses have similar three-dimensional structures, suggesting that these viruses might use the same cell surface receptor-human angiotensin-converting enzyme 2(ACE2) 2 : this was soon confirmed in vitro 4,12 and using structural biology 12,13 . However, SARS-CoV-2 differs from SARS-CoV in two fundamental ways 14 . First, there are six amino acid positions in the receptor-binding domain (RBD) of the spike protein that mediate the attachment of the SARS-CoV and SARS-CoV-2 spike proteins to the human ACE2 receptor 15 . However, amino acids at five of the six positions differed between SARS-CoV and SARS- 14 ). Notably, such differences caused SARS-CoV-2 to have a higher binding avidity to the human ACE2 receptor 11 , and may have contributed to the higher transmissibility of SARS-CoV-2 compared with SARS-CoV. Second, there is a 12-nucleotide (nt) insertion at the cleavage site of the

Emergence of SARS-CoV-2 Variants in the World: How Could This Happen?

“…The SARS-CoV-2 genomic surveillance has been the largest genomic sequencing project ever conducted for a pathogen, with more than 2.8 million sequences completed by August 2021 [136]. This surveillance has had a significant role in the prevention and control of SARS-CoV-2 since it has allowed: a follow-up of the place and moment of origin of the introductory events of mutations and VOIs/VOCs, the characterization of the dissemination of VOIs/VOCs at a regional and international level, and identification of risk factors for the transmission, infectivity, and pathogenicity of the virus.…”

Effects of a Prolonged Booster Interval on Neutralization of Omicron Variant

“… To the Editor: The coronavirus disease 2019 (Covid-19) pandemic is still ongoing, 1 and the B.1.1.529 (or omicron) variant, first detected in November 2021, has already spread globally. The ability of the omicron variant to escape vaccine-elicited immunity is of great concern.…”

Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic

“…The 2009 swine flu pandemic, caused by the H1N1 influenza A virus, lasted approximately 14 months and was responsible for over 280,000 deaths [42]. SARS-CoV-2 arrived in late 2019 [1,8] and quickly became the second but so far major pandemic of the 21st century [9]. Since the days of the H1N1 influenza virus A virus, responsible for the 1918 Spanish flu [43], no other respiratory virus has been able to have such consequences on global health and the world economy like this new coronavirus [44].…”

“…At that point, it was clear that we were facing another coronavirus outbreak, similar to the zoonotic events caused by SARS-CoV in 2002 and 2003 [2] and MERS-CoV since 2012 [3]. SARS-CoV-2 infections spread rapidly within China, then in early 2020 travel-associated cases were identified in Thailand and Japan, followed by cases in multiple other countries in Asia, Europe and North America [1,[4][5][6][7][8][9], which triggered a massive effort to monitor the global distribution and evolution of the virus [10][11][12][13]. As of 6 January 2022, close to 6.8 million SARS-CoV-2 wholegenome sequences had been shared via GISAID (https://www.gisaid.org/, accessed on 6 January 2022) [10].…”