Anderson’s White-bellied Rat, Niviventer andersoni (Thomas, 1911) (Muridae, Niviventer) is an species endemic to China. In the present study, we have sequenced the first complete mitochondrial genome of N. andersoni using next-generation sequencing. The 16,291 bp mitochondrial genome consists of 22 transfer RNA genes, 13 protein-coding genes (PCGs), two ribosomal RNA genes, and one non-coding control region (D-Loop). Phylogenetic analyses of the nucleotide sequences of all 13 PCGs, PCGs minus ND6 and the entire mitogenome sequence except for the D-loop, produce nearly identical, well-resolved topologies. Our results support that N. andersoni clustered with N. excelsior and form a sister group with N. confucianus, and they statistically reject the hypothesis from one cytochrome b (cytb) gene tree that N. confucianus is sister to N. fulvescens. Our research may be helpful to further reconsideration of clearer taxonomy and improve our understanding of mitogenomic evolution in the genus Niviventer.

The variety and widespread of coronavirus in natural reservoir animals is likely to cause epidemics via interspecific transmission, which has attracted much attention due to frequent coronavirus epidemics in recent decades. Birds are natural reservoir of various viruses, but the existence of coronaviruses in birds, especially in central China, has been barely studied. The majority of bird coronaviruses belongs to the genus of Deltacoronavirus. To explore the diversity of bird deltacoronaviruses in central China, we tested fecal samples from 415 birds in Hunan Province, China. As the result, we have identified four novel deltacoronavirus stains (HNU1-1, HNU1-2, HNU2 and HNU3) with divergent S genes abounding in common magpies in mainland China. Comparative genomic analysis on the four complete viral genomic sequences showed that these novel magpie deltacoronaviruses containing three different S genes homologous to those of deltacoronaviruses discovered in swine and sparrows. The S genes of HNU1-1 and HNU1-2 showed 93.8% amino acid sequence identities to that of thrush coronavirus HKU12, and the S genes of HNU2 and HNU3 showed 71.1% amino acid sequence identities to White-eye coronavirus HKU16 and sparrow coronavirus HKU17, respectively. Recombination analysis showed that frequent recombination events of the S genes occurred among different deltacoronavirus strains. Two novel putative cleavage sites at the junctions between nonstructural proteins in the HNU CoVs were found. Bayesian phylogeographic analysis showed that the south coast of China might have played a key role in seeding the bird deltacoronavirus epidemics. The results demonstrated that common magpie in China carries diverse deltacoronaviruses with novel genomic features, which indicate an important source of environmental coronaviruses in the biosphere closed to human communities. These findings may contribute to prevention and control the potential coronavirus epidemics.

Coronavirus (CoV) pandemics have become a huge threat to the public health worldwide in the recent decades. Typically, severe acute respiratory syndrome CoV (SARS-CoV) caused SARS pandemic in 2003 and SARS-CoV-2 caused the ongoing COVID-19 pandemic. Both viruses have been reported to originate from bats. Thus, direct or indirect interspecies transmission from bats to humans is required for the viruses to cause pandemics. Receptor utilization is a key factor determining the host range of viruses which is critical to the interspecies transmission. Angiotensin converting enzyme 2 (ACE2) is the receptor of both SARS-CoV and SARS-CoV-2, but only ACE2s of certain animals can be utilized by the viruses. Here, we employed pseudovirus cell-entry assay to evaluate the receptor-utilizing capability of ACE2s of 20 animals by the two viruses and found that SARS-CoV-2 utilized less ACE2s than SARS-CoV, indicating a narrower host range of SARS-CoV-2. Especially, SARS-CoV-2 tended not to use murine or non-mammal ACE2s. Meanwhile, pangolin CoV, another SARS-related coronavirus highly homologous to SARS-CoV-2 in its genome, yet showed similar ACE2 utilization profile with SARS-CoV rather than SARS-CoV-2. To clarify the mechanism underlying the receptor utilization, we compared the amino acid sequences of the 20 ACE2s and found 5 amino acid residues potentially critical for ACE2 utilization, including the N-terminal 20th and 42nd amino acids that may determine the different receptor utilization of SARS-CoV, SARS-CoV-2 and pangolin CoV. Our studies promote the understanding of receptor utilization of pandemic coronaviruses, potentially contributing to the virus tracing, intermediate host screening and epidemic prevention for pathogenic coronaviruses.