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| Rhinolophus affinis from Thailand. Photo by Charles Francis. |
Based on virus genome sequencing, bats have been mentioned in connection to the origin of SARS-CoV2
from the very beginning. This early picture then became more
complicated as in depth-analyses revealed a key part of the viral genome that enables entry into host cells —the
receptor binding domain (RBD) of the
spike protein— is more closely
related to similar domains from viruses found
in pangolins. But the close evolutionary relatedness between the human pathogen
(SARS-CoV2) and a virus not known to cause disease in humans (RatG2013,
sampled in 2013 from the Intermediate horseshoe bat
Rhinolophus affinis) is
undisputed. Yet it's difficult to parse out the wildlife source of SARS-CoV2 because despite its close relatedness (see below) to other wildlife viruses, it is not the direct result of
recombination of any of the wildlife viruses known to date. A
preprint by Boni et al. (2020) provides the evolutionary context for better understanding the wildlife origin of SARS-CoV.
Phylogenies, the evolutionary representation of relatedness among species can be hard to read. Below, is the phylogeny that
Boni et al. (2020)
estimated using the genomes of many different viruses sampled from
wildlife. How closely related the different viruses are depends on
how recently they share a common ancestor so that the
red human (SARS-CoV2) and the bat virus (RatG2013) in the figure are
sister lineages–as
close as any two separate branches can get. But this phylogeny provides
even more information: the length of the branches is proportional to
time, so it can actually tell us
when the bat virus and the human
pathogen went their separate ways or diverged. This is why the inset
shows several different sets of dates depending on what viruses are
compared; however SARS-CoV2 and the bat virus RatG2013 are separated by
40-70 years! In other words, there is no way the human pathogen came
directly from the virus that was circulating among intermediate
horseshoe bats in 2013. Thanks to these genomic analyses we know that to
figure out where SARS-CoV2 really came from in 2019, we have to keep
looking at other possible hosts,
and in the wild.
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| Timetree of sarbecovirus lineages. The boxplots represent the divergence time estimates for SARS-CoV-2 (red boxplot) and the 2002-2003 SARS-CoV virus (blue boxplot) from their most closely related bat virus. Green
boxplots show the time to most recent common ancestor estimate for the
RaTG13/SARS-CoV-2 lineage and its most closely related pangolin lineage
(from Guangdong 2020). Grey tips correspond to bat viruses, green to pangolin, blue to the SARS-CoV virus, and red
to SARS-CoV-2. The size of the black internal node circles are
proportional to the posterior node support. 95% credible intervals bars
are shown for all internal node ages. Legend modified from Boni et al.
2020.
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Source: Boni, M. F., P. Lemey, X. Jiang, T. T.-Y. Lam, B. Perry, T. Castoe, A. Rambaut et al. 2020.
Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. bioRxiv:2020.2003.2030.015008.
