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Bat coronavirus RaTG13 is a SARS-like
betacoronavirus ''Betacoronavirus'' (β-CoVs or Beta-CoVs) is one of four genera (''Alpha''-, ''Beta-'', '' Gamma-'', and '' Delta-'') of coronaviruses. Member viruses are enveloped, positive-strand RNA viruses that infect mammals (of which humans are part ...
that infects the horseshoe bat '' Rhinolophus affinis''. It was discovered in 2013 in bat droppings from a mining cave near the town of Tongguan in
Mojiang Mojiang Hani Autonomous County (; Hani: ) is an autonomous county under the jurisdiction of Pu'er City, in the south of Yunnan Province, China. Administrative divisions In the present, Mojiang Hani Autonomous County has 12 towns, 2 townships an ...
county in
Yunnan Yunnan , () is a landlocked province in the southwest of the People's Republic of China. The province spans approximately and has a population of 48.3 million (as of 2018). The capital of the province is Kunming. The province borders the ...
,
China China, officially the People's Republic of China (PRC), is a country in East Asia. It is the world's List of countries and dependencies by population, most populous country, with a Population of China, population exceeding 1.4 billion, slig ...
. In February 2020, it was identified as the closest known (at the time) relative of
SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus previously had a ...
, the virus that causes
COVID-19 Coronavirus disease 2019 (COVID-19) is a contagious disease caused by a virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The first known case was identified in Wuhan, China, in December 2019. The disease quick ...
, sharing 96.1% nucleotide similarity. However, in 2022, scientists found three closer matches in bats found 530 km south, in Feuang, Laos, designated as BANAL-52 (96.8% similarity), BANAL-103 and BANAL-236.


History

In spring 2012, three miners cleaning bat feces in an abandoned copper mine near the town of Tongguan in
Mojiang Hani Autonomous County Mojiang Hani Autonomous County (; Hani: ) is an autonomous county under the jurisdiction of Pu'er City, in the south of Yunnan Province, China. Administrative divisions In the present, Mojiang Hani Autonomous County has 12 towns, 2 townships an ...
developed fatal
pneumonia Pneumonia is an inflammatory condition of the lung primarily affecting the small air sacs known as alveoli. Symptoms typically include some combination of productive or dry cough, chest pain, fever, and difficulty breathing. The severit ...
. Out of concerns that the miner's cases could represent a novel disease, serum samples collected from the miners were sent to the
Wuhan Institute of Virology The Wuhan Institute of Virology, Chinese Academy of Sciences (WIV; ) is a research institute on virology administered by the Chinese Academy of Sciences (CAS), which reports to the State Council of the People's Republic of China. The institute ...
and tested by Shi Zhengli and her group for
Ebola virus ''Zaire ebolavirus'', more commonly known as Ebola virus (; EBOV), is one of six known species within the genus ''Ebolavirus''. Four of the six known ebolaviruses, including EBOV, cause a severe and often fatal hemorrhagic fever in humans and o ...
,
Nipah virus Nipah virus, scientific name ''Nipah henipavirus'', is a bat-borne virus that causes Nipah virus infection in humans and other animals, a disease with a high mortality rate. Numerous disease outbreaks caused by Nipah virus have occurred in Sou ...
, and bat SARSr-CoV Rp3. The samples tested negative. In order to discover the possible cause of the infection, different animals (including bats, rats, and musk shrews) were sampled in and around the mining cave. Between 2012 and 2015, Shi Zhengli and her group isolated 293 diverse
coronaviruses Coronaviruses are a group of related RNA viruses that cause diseases in mammals and birds. In humans and birds, they cause respiratory tract infections that can range from mild to lethal. Mild illnesses in humans include some cases of the c ...
(284 alphacoronaviruses and 9 betacoronaviruses) from bat feces samples in the cave. One of the samples collected in 2013 from ''Rhinolophus affinis'' bat feces was the bat coronavirus RaTG13. The strain name was derived from the originating bat species, geographic location, and year collected. In 2020, Shi and her group retested the serum samples from the miners for SARS-CoV-2. The samples tested negative. In 2020, the virus was renamed from the original Ra4991 to RatG13, to reflect the species of bat from which the virus was collected (''Rhinolophus affinis''), the location where it was collected (Tongguan) and the year of the sample’s collection (2013). The change of name of the virus has been considered as innuendo by lab leak advocates.


Virology

RaTG13 is a
positive-strand RNA virus Positive-strand RNA viruses (+ssRNA viruses) are a group of related viruses that have positive-sense, single-stranded genomes made of ribonucleic acid. The positive-sense genome can act as messenger RNA (mRNA) and can be directly translated in ...
with an outer membrane. Its genome is approximately 29,800 nucleotides. The genome encodes a replicase (ORF1a/1b) and four structural proteins; including a
spike protein In virology, a spike protein or peplomer protein is a protein that forms a large structure known as a spike or peplomer projecting from the surface of an enveloped virus. as cited in The proteins are usually glycoproteins that form dimers or ...
(S),
membrane protein Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending on their location. Integral membrane proteins are a permanent part of a cell membrane ...
(M), envelope protein (E) and nucleocapsid protein (N); and five viral accessory proteins, including ORF3a (NS3), ORF6 (NS6), ORF7a (NS7a), ORF7b (NS7b) and
ORF8 ORF8 is a gene that encodes a viral accessory protein, Betacoronavirus NS8 protein, in coronaviruses of the subgenus ''Sarbecovirus''. It is one of the least well conserved and most variable parts of the genome. In some viruses, a deletion ...
(NS8). RaTG13 bears strong resemblance to the
SARS-CoV-2 Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) is a strain of coronavirus that causes COVID-19 (coronavirus disease 2019), the respiratory illness responsible for the ongoing COVID-19 pandemic. The virus previously had a ...
virus (it shares 96.1% nucleotide similarity), and its existence is a supporting piece of evidence for SARS-CoV-2's natural origin. The difference between RaTG13 and SARS-CoV-2 is in the receptor-binding domain (RBD) of the spike protein (S), which is the portion that binds to the receptor protein on the surface of the
host cell In biology and medicine, a host is a larger organism that harbours a smaller organism; whether a parasitic, a mutualistic, or a commensalist ''guest'' (symbiont). The guest is typically provided with nourishment and shelter. Examples include a ...
and causes infection, indicating that the RaTG13 virus might not use
angiotensin-converting enzyme 2 Angiotensin-converting enzyme 2 (ACE2) is an enzyme that can be found either attached to the membrane of cells (mACE2) in the intestines, kidney, testis, gallbladder, and heart or in a soluble form (sACE2). Both membrane bound and soluble ACE2 ...
(ACE2) as its entry site into the cell as does SARS-CoV-2. Further, the S protein of RaTG13 virus lacks the
furin Furin is a protease, a proteolytic enzyme that in humans and other animals is encoded by the ''FURIN'' gene. Some proteins are inactive when they are first synthesized, and must have sections removed in order to become active. Furin cleaves thes ...
cleavage motif RRAR↓S. The binding affinity between RATG13 and hACE2 is lower than that between SARS-CoV-2 RBD and hACE2.


Phylogenetics


Phylogenetic tree


See also

* Bat SARS-like coronavirus RsSHC014 * Bat SARS-like coronavirus WIV1 * Mòjiāng virus


References

{{Coronaviridae SARS-CoV-2 Bat virome Coronaviridae Animal virology Sarbecovirus Zoonoses