Zhou et al. reported the discovery of RmYN02, a strain closely related to SARS-CoV-2, which is claimed to contain a natural PAA amino acid insertion at the S1/S2 junction of the spike protein at the same position of the PRRA insertion that has created a polybasic furin cleavage site in SARS-CoV-2. The authors support with their findings the theory that the furin cleavage site insertion present in SARS-CoV-2 is natural. Because no nucleotide alignment with closely related strains of the region coding for the supposed insertion is provided by Zhou et al., we have applied several alignment algorithms to search for the most parsimonious alignments. We conclude that RmYN02 does not contain an insertion at the S1/S2 junction when compared to its closest relatives at the nucleotide level, but rather a 6-nucleotide deletion and that the claimed PAA insertion is more likely to be the result of mutations. A close examination of RmYN02 sequencing records and assembly methods is wishful. In conclusion, SARS-CoV-2, with its 12-nucleotide insertion at the S1/S2 junction remains unique among its sarbecovirus relatives. Recently, Zhou et al. [1] reported the discovery of a novel coronavirus strain RmYN02, which the authors claim to contain a natural PAA amino acid insertion at the S1/S2 junction of the spike protein at the same position of the PRRA insertion that has created a polybasic furin cleavage site in severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2).

Despite the discovery of animal coronaviruses related to SARS-CoV-2, the evolutionary origins of this virus are elusive. We describe a meta-transcriptomic study of 411 bat samples collected from a small geographical region in Yunnan province, China, between May 2019 and November 2020. We identified 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related viruses. Rhinolophus pusillus virus RpYN06 was the closest relative of SARS-CoV-2 in most of the genome, although it possessed a more divergent spike gene. The other three SARS-CoV-2 related coronaviruses carried a genetically distinct spike gene that could weakly bind to the hACE2 receptor in vitro . Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species, with the largest contiguous hotspots extending from South Laos and Vietnam to southern China. Our study highlights the remarkable diversity of bat coronaviruses at the local scale, including close relatives of both SARS-CoV-2 and SARS-CoV.

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Abstract. Southeast Asia (SE Asia) is a known global hotspot of biodiversity and endemism, yet the region is also one of the most biotically threatened. Ecosystems across the region are threatened by an array of drivers, each of which increases the probability of extinction of species in a variety of ecosystems. These issues are symptomatic of the issues that face the global tropics; however, with around 4 billion people in the wider region and the associated pressures on biodiversity, this region may be under some of the greatest levels of biotic threat. Deforestation rates in SE Asia are some of the highest globally, additionally it has the highest rate of mining in the tropics, around the greatest number of hydropower dams under construction, and a consumption of species for traditional medicines which is a threat to biodiversity globally. In this review, the greatest threats to regional biodiversity in the SE Asian region are discussed. Tree-plantations and deforestation represent one of the most imminent threats, and some countries have already lost over half their original forest cover (i.e., the Philippines, parts of Indonesia), with projections of as much as 98% loss for some regions in the coming decade. Hunting and trade represent a significant threat as demand stems not only for food, but also for medicine, for ornamentation, and as a status symbol. Mining represents a frequently overlooked threat, as the Asian region is one of the greatest exporters of limestone and various minerals globally, and the cost of this to biodiversity is not only through the direct loss of areas for mines, but also through the development of roads that further fragment the landscape, the leakage of heavy metals, and the destruction of limestone karsts, which represent global endemicity hotspots. Reservoir construction, wetland drainage, fires, pollution, invasive species, disease, and finally climate change are also considered. Once each issue has been discussed, the overall prognosis of regional biodiversity and priority actions to protect SE Asian biodiversity in the future is discussed.