"Натура", июль (полный текст доступен). Что исходный природный резервуар пока так точно и не установлен - не должно особо удивлять; к примеру, у первого SARS конкретный источник (не просто вид мышек, а пещеру с популяцией) искали более десяти лет, и то вероятность того, что нашли таки именно её, а не человека, похожего на генерального прокурора, хоть и весьма высока, но не 100%.
Интересно, что тут упоминают о том, что у разных животных и в самых разных регионах обнаружено множество коронавирусов, довольно схожих с ковидом, причём многие выделены до пандемии. Так что как бы еще можно гадать, откуда он есть пошёл - можно даже с некоторой гиперболой сказать, кандидатов в предки даже слишком много!
A study reports the detection and characterization of SARS-CoV-2-like viruses in Laotian cave-dwelling bats that are also demonstrated to infect human cells through the ACE2 pathway.
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The animal reservoir of SARS-CoV-2 is unknown despite reports of SARS-CoV-2-related viruses in Asian Rhinolophus bats1,2,3,4, including the closest virus from R. affinis, RaTG13 (refs. 5,6), and pangolins7,8,9. SARS-CoV-2 has a mosaic genome, to which different progenitors contribute. The spike sequence determines the binding affinity and accessibility of its receptor-binding domain to the cellular angiotensin-converting enzyme 2 (ACE2) receptor and is responsible for host range10,11,12. SARS-CoV-2 progenitor bat viruses genetically close to SARS-CoV-2 and able to enter human cells through a human ACE2 (hACE2) pathway have not yet been identified, although they would be key in understanding the origin of the epidemic.
Here we show that such viruses circulate in cave bats living in the limestone karstic terrain in northern Laos, in the Indochinese peninsula.
We found that the receptor-binding domains of these viruses differ from that of SARS-CoV-2 by only one or two residues at the interface with ACE2, bind more efficiently to the hACE2 protein than that of the SARS-CoV-2 strain isolated in Wuhan from early human cases, and mediate hACE2-dependent entry and replication in human cells, which is inhibited by antibodies that neutralize SARS-CoV-2. None of these bat viruses contains a furin cleavage site in the spike protein. Our findings therefore indicate that bat-borne SARS-CoV-2-like viruses that are potentially infectious for humans circulate in Rhinolophus spp. in the Indochinese peninsula.
Main
The origin of SARS-CoV-2, as well as its mode of introduction into the human population, are unknown at present. Since its emergence, numerous animal species have been studied to identify possible reservoirs and/or intermediate hosts of the virus, including a large diversity of insectivorous bats of the genus Rhinolophus. Despite the
recent report of various SARS-CoV-2-related viruses in R. shameli (isolated in Cambodia in 201013), R. pusillus and R. malayanus (China, 2020 and 2019, respectively2), R. acuminatus (Thailand, 2020 3) and R. cornutus (Japan, 2013 4), the closest SARS-CoV-2 bat-borne genome still remains the one from R. affinis, RaTG13 (China, 20135,6), with 96.1% identity at the whole-genome level. Several studies also suggested the involvement of pangolin coronaviruses in the emergence of SARS-CoV-2 (refs. 7,8,9). Since its appearance in humans, SARS-CoV-2 has evolved through sporadic mutations and recombination events14, some of which correspond to gains in fitness allowing the virus to spread more widely, or to escape neutralizing antibodies15.
To decipher the origin of SARS-CoV-2, it is therefore essential to ascertain the diversity of animal coronaviruses, and more specifically, that of bat coronaviruses. Although the identification of SARS-CoV-2 in bats is a main goal, a more realistic objective is to identify the sequences that contribute to its mosaicism. The spike sequence seems essential, as it determines the binding affinity and accessibility of the receptor-binding domain (RBD) to the cellular ACE2 receptor and is therefore responsible for host range10,11,12. The closest related bat strain identified so far (RaTG13) has a low RBD sequence similarity to SARS-CoV-2, and with only 11/17 hACE2 contact amino acid residues conserved with SARS-CoV-2, its affinity for hACE2 is very limited16. Moreover, SARS-CoV-2 poorly infects bats and bat cells tested so far17. In addition, no bat SARS-CoV-2-like virus has been shown to use hACE2 to efficiently enter human cells, and none has the furin cleavage site that is associated with an increased pathogenicity in humans18. The SARS-CoV-2 RBD binds to R. macrotis ACE2 with a lower affinity than to hACE2 (ref. 19). An essential piece of information—finding bat viruses with an RBD motif genetically close to that of SARS-CoV-2 and capable of binding to hACE2 with high affinity—is therefore missing.
We speculated that this type of virus could be identified in bats living in the limestone karstic terrain common to China, Laos and Vietnam in the Indochinese peninsula. Here we report the presence of sarbecoviruses close to SARS-CoV-2 whose RBDs differ from that of SARS-CoV-2 by only one or two contact residues, strongly bind to the hACE2 protein and mediate hACE2-dependent entry and replication into human cells. Despite the absence of the furin cleavage site, these viruses may have contributed to the origin of SARS-CoV-2 and may intrinsically pose a future risk of direct transmission to humans.
Diversity of bat and coronavirus species
A total of 645 bats belonging to 6 families and 46 species were captured (Supplementary Table 1). Two hundred and forty-seven blood samples, 608 saliva, 539 anal/faecal and 157 urine swabs were collected from bats in the northern part of Laos (Supplementary Table 2). We first screened all 539 faecal samples through a pan-coronavirus nested RT-PCR analysis20. Overall, 24 individuals of 10 species were positive, and 1 individual (BANAL-27) was concomitantly infected by an alphacoronavirus and a betacoronavirus (Supplementary Table 3). BLAST analysis of amplicons identified alphacoronavirus sequences of the Decacovirus, Pedacovirus and Rhinacovirus subgenera and betacoronavirus sequences of the Nobecovirus and Sarbecovirus subgenera. Sequences of the Sarbecovirus subgenus were all identified from Rhinolophus individuals belonging to three different species (R. malayanus, R. marshalli and R. pusillus). Positive individuals were trapped in three different districts, and those infected with a sarbecovirus were all from the Fueng district in Vientiane province (Fig. 1a, site 1).
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Our results therefore support the hypothesis that SARS-CoV-2 could originally result from a recombination of sequences pre-existing in Rhinolophus bats living in the extensive limestone cave systems of Southeast Asia and South China41,42. Many species forage in the same cave areas, including R. malayanus and R. pusillus43. In addition, the distributions of R. marshalli, R. malayanus and R. pusillus overlap in the Indochinese subregion (Supplementary Fig. 5), which means that they may share caves as roost sites and foraging habitats44. With the new viruses described here, understanding the emergence of SARS-CoV-2 does not require speculation of recombination or natural selection for increased RBD affinity for hACE2 in an intermediate host such as the pangolin before spillover45, nor natural selection in humans following spillover46. However, we found no furin cleavage site in any of these viruses on sequences determined directly from original faecal swab samples, which prevent from any risk of counterselection of the furin site by amplification in Vero cells18. The lack of the furin cleavage site may be explained by insufficient sampling in bats. On the basis of comparison of the sequences around the cleavage site between S1 and S2 (Extended Data Fig. 3), it has been suggested that the furin cleavage site in SARS-CoV-2 could originate from recombination events between SARS-CoV-2-related coronaviruses co-circulating in bats2,47, meaning that BANAL-116, BANAL-247, bat RmYN02 (ref. 2) and bat RacCS203 (ref. 3) coronaviruses may share a common history with SARS-CoV-2. Alternatively, the furin cleavage site could have been acquired through passages of the virus in an alternative host or during an early poorly symptomatic unreported circulation in humans. Finally, the epidemiological link between these bat viruses and the first human cases remains to be established.
As expected from the high affinity for hACE2 of the S ectodomain of BANAL-236, pseudoviruses expressing it were able to efficiently enter human cells expressing endogenous hACE2 using an ACE2-dependent pathway. However, alternative routes of entry may still exist, especially in cells that do not express ACE2 (ref. 48). Entry was blocked by a serum neutralizing SARS-CoV-2. The RaTG13 strain, the closest to SARS-CoV-2 known previously, had never been isolated. By contrast, preliminary studies show that BANAL-236 replicated in primate VeroE6 cells with a small plaque phenotype compared to that of SARS-CoV-2. Further analysis may indicate more clearly which steps shape infectivity.
To conclude,
our results pinpoint the presence of new bat sarbecoviruses that seem to have the same potential for infecting humans as early strains of SARS-CoV-2. Guano collectors, certain ascetic religious communities who spend time in or very close to caves and tourists visiting caves are particularly at risk of being exposed. Further investigations are needed to assess whether such exposed populations have been infected, symptomatically or not, by one of these viruses, and whether infection could confer protection against subsequent SARS-CoV-2 infections. In this context, it is noteworthy that SARS-CoV-2 with the furin site deleted replicates in hamsters and in transgenic mice expressing hACE2, but leads to less severe disease and protects from rechallenge with wild-type SARS-CoV-2 (ref. 18).