Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
is one of the most serious pandemics that has invaded the world in recent
years. The virus responsible for this pandemic was isolated for the first time
in China in 2019, and then it spread throughout the world, where it caused up
today about over 7 million deaths and about 800 million confirmed cases.
Therefore, several efforts have been made to study this virus. In about one
year, has been sequenced the whole genome of SARS-CoV-2 and has been elucidated
its mechanism of infection and duplication in host cells and its physiological
effect on humans. Furthermore, the S spike glycoprotein has been identified as the main protein involved in
the viral infection mechanism and it has been used as an antigen to develop
several vaccines, including new generation mRNA-based ones. The data from World
Health Organization (WHO) indicated that approximately 14 billion doses of
vaccines have been dispensed far.
Since the beginning of the pandemic, SARS-CoV-2 has evolved
by accumulating mutations in the genome, resulting in new virus versions
showing different characteristics, and which have replaced the pre-existing
variants. To date, hundreds of variants of the virus have been isolated. As a
general trend, the SARS-CoV-2 variants identified so far have increased their
spread and reduced their danger and mortality. More than 15 million viral
sequences have been carried out to monitor the virus spreading and its
variability.
Among all new variants, a new group of variants was isolated
in early 2022.They were named omicron, and in a few months replaced all the
variants present up to then, because they were characterized by high
transmissibility. We study the omicron variants (BA.1, BA.2, BA.2.12.1, BA.4
and BA.5) and their derivative variants (BQ.1, BQ.1.18 (CH.1.1), XBF, XBB,
XBB.1.5, XBB.1.9 and XBB.1.16), from a
phylogenetic point of view. We generate a multiple alignment of the spike
sequences and analyzed the mutations exhibited by these variants. Based on these
results, we proposed a new phylogenetic tree of omicron variants, which
includes several possible unidentified intermediate variants, proving insight
into the origin of omicron variants.
SARS-CoV-2 has been characterized as a virus that has
accumulated a high number of mutations in the genome that have drastically
modified the infection mechanism by increasing the spread of the virus and
reducing its mortality, transforming the pandemic form of SARS-CoV-2 into an
endemic infection.
Author(s) Details:
Emilia Caputo,
Institute of Genetics and Biophysics-IGB-CNR, “A. Buzzati-Traverso”,
Via Pietro Castellino 111, 80131 Naples, Italy.
Luigi Mandrich,
Research
Institute on Terrestrial Ecosystems-IRET-CNR, Via Pietro Castellino 111, 80131
Naples, Italy.
Please see the link here: https://stm.bookpi.org/IBS-V3/article/view/14251
Keywords: Phylogenetic analysis, infection, SARS-CoV-2
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