Omicron genetics and early transmission patterns are characterized in
new study
Date:
January 26, 2022
Source:
Penn State
Summary:
The Omicron variant of SARS-CoV-2 diverged from previous SARS-CoV-
2 variants as a result of adaptive evolution, in which beneficial
mutations are passed on to future generations through natural
selection, rather than through recombination between previous
variants, according to researchers.
FULL STORY ==========================================================================
The Omicron variant of SARS-CoV-2 diverged from previous SARS-CoV-2
variants as a result of adaptive evolution, in which beneficial mutations
are passed on to future generations through natural selection, rather
than through recombination between previous variants, according to a
large international team of researchers. The study, which published
recently in Nature, is the first to describe the genomic profile of
Omicron and explore the origins of the variant.
==========================================================================
"We have seen SARS-CoV-2 generate three major variants -- Alpha, Delta
and Omicron -- in about 16 months, which is very surprising because
other viruses do not make such repeated big evolutionary leaps," said
Maciej Boni, associate professor of biology, Penn State, who led the recombination analysis for this global collaboration. "The latest variant
-- Omicron -- is extraordinary because of the even bigger jump it made
in the evolution of its spike protein." Boni noted that compared to
previous variants, Omicron's spike protein has more than 30 mutations,
many of which are known to influence host antibody neutralization.
"Given that Omicron made such a big leap forward evolutionarily speaking,
we wanted to investigate why and how this may have happened," he said.
To do that, the team -- which was led by the Centre for Epidemic Response
and Innovation in South Africa -- analyzed all 686 Omicron sequences
that were available by Dec. 7, 2021. They found that Omicron falls within
the B.1.1 lineage, which also includes the Alpha variant. Interestingly,
the team found that Omicron is genetically distinct from Alpha, as well
as any other known variants of interest.
"What this means is that although Omicron belongs to the same lineage
as the Alpha variant, it has changed to such a great extent that it is
largely unrecognizable as a cousin or nephew of the Alpha variant," said
Boni. "When the Omicron genome was first sequenced, it became clear that
this virus had the potential to be phenotypically very different from
previous SARS-CoV-2 variants that we were familiar with." To determine
when the Omicron variant first emerged, the team used a technique, called time-calibrated Bayesian phylogenetic analysis. They estimated that the
date when the most recent common ancestor of all Omicrons existed was
early October 2021.
========================================================================== Next, the team applied a selection analysis to the 686 Omicron sequences
and found evidence of positive natural selection in many genes since
the variant split from other B.1.1 lineages. "This finding led to our conclusion that adaptive evolution played a significant role in the
early emergence and establishment of Omicron," said Boni. "This finding suggests that Omicron is likely the result of an evolutionary process
that created a highly transmissible virus that partially evades our
antibody responses." Additionally, the finding ruled out recombination
of previous variants in the origin of Omicron.
"We found no convincing evidence of Omicron being a recombinant of
previous SARS-CoV-2 variants," said Boni.
The team did find that some samples of Omicron displayed weak evidence
of having inherited genetic material from a Delta virus, but statistical analyses could not rule out random chance or small sequencing errors as
causes of this curious recombination signal.
"Given the recent misinformation suggesting that the Omicron and
Delta variants have recombined to create a 'Deltacron' super variant,
it is important to note that such recombination is in fact possible,
but there is currently no evidence that this has occurred," said
Boni. "Additionally, if it does occur, there's no telling what the
properties of such a virus would be in terms of its ability to transmit
and/or cause severe disease, among other factors." Regarding Omicron's transmissibility, the team concluded that partial immune evasion was
likely a major driver of the rapid spread of omicron in South Africa
given that the proportion of the South African population that was immune (either from infection, vaccination or both) was above 60%.
========================================================================== "This idea that Omicron can partially evade the immune system is
supported by other recent findings showing an increased risk of SARS-CoV-2 reinfection associated with the emergence of Omicron," said Boni. "We
also know now that the viral load of Omicron is higher in people who are infected, which also contributes substantially to its high transmission
rate." Boni noted that the current Omicron wave is a reminder to all
Americans to keep our COVID-19 vaccinations as current as possible.
"We can't afford to endure another calendar year with half a million
deaths," he said.
Other institutions represented on the paper include Lancet Laboratories,
the Botswana Harvard HIV Reference Laboratory, the Harvard T.H. Chan
School of Public Health, the Botswana Presidential COVID-19 Taskforce,
the National Health Laboratory Service of South Africa, the University
of KwaZulu-Natal, the University of the Witwatersrand, the University of
Bern, the University of the Free State, Diagnofirm Medical Laboratories,
the University of Edinburgh, the University of Pretoria, Emweb bv,
the University of Cape Town, Stellenbosch University, Fundacao Oswaldo
Cruz, the Universidade Federal de Minas Gerais, the NHLS Groote Schuur Laboratory, the Wellcome Centre for Infectious Diseases Research in
Africa, Temple University, the University of Oxford, the Ministry of
Health and Wellness of Botswana, the NHLS Port Elizabeth Laboratory,
Walter Sisulu University, the NHLS Tygerberg Laboratory, the Charlotte
Maxeke Johannesburg Academic Hospital, Botswana-Baylor Children's Clinical Centre of Excellence, Baylor College of Medicine, Centre for the AIDS
Programme of Research in South Africa, the University of Botswana,
PathCare Vermaak, and the University of Washington.
========================================================================== Story Source: Materials provided by Penn_State. Original written by Sara LaJeunesse. Note: Content may be edited for style and length.
========================================================================== Journal Reference:
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Cathrine Scheepers, Christian L. Althaus, Ugochukwu J. Anyaneji,
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Anele Mnguni, Thabo Mohale, Monika Moir, Kgomotso Moruisi, Mosepele
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Noxolo Ntuli, Martin Nyaga, Lucier Olubayo, Sureshnee Pillay,
Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, James E. San,
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Wendy Stevens, Amy Strydom, Kathleen Subramoney, Naume Tebeila,
Derek Tshiabuila, Joseph Tsui, Stephanie van Wyk, Steven Weaver,
Constantinos K. Wibmer, Eduan Wilkinson, Nicole Wolter, Alexander E.
Zarebski, Boitumelo Zuze, Dominique Goedhals, Wolfgang Preiser,
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Oliveira. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant
in southern Africa. Nature, 2022; DOI: 10.1038/s41586-022-04411-y ==========================================================================
Link to news story:
https://www.sciencedaily.com/releases/2022/01/220126165537.htm
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