Decoding the RNA viromes in rodent lungs to understand rodent-borne pathogens (preprint)

Most human infectious viral diseases – including COVID-19 and Ebola – originated in animals. As the largest group of mammalian species, rodents are natural reservoirs for many diverse zoonotic viruses. Better understanding the core rodent virome will reduce the risk of future emergence or re-emergence of rodent-borne pathogens. A recent study focused on viruses found in the lungs of rodents in Mainland Southeast Asia, a hotspot for zoonotic emerging infectious diseases. Lung samples were collected from 3,284 rodents and insectivores throughout Thailand, Lao PDR, and Cambodia. Using metatranscriptomics, researchers outlined unique characteristics of the rodent viruses identified. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time, and viruses related to known pathogens were found. These results expand our understanding of the core virome in rodent species in Mainland Southeast Asia and suggest that a highly diverse array of viruses remains to be found in these species. Viral surveillance in wildlife hosts will minimize the impact of potential wildlife-originating infectious diseases.

A One Health Approach to Studying the Differences in the Evolutionary Dynamics of MERS and SARS Coronaviruses (preprint)

BackgroundSARS-CoV and MERS-CoV are two coronaviruses that received great attention due to their high pathogenicity and mortality rates in human populations. While SARS was controlled, MERS continues to be a global public health concern. To examine differences in the epidemic patterns of these two viruses, we collected all available sequences to compare the different evolutionary characteristics of SARS-CoV and MERS-CoV. Notably, almost all of the human infection cases occurred in the Middle East, and cases that occurred outside of the Middle East involved travelers from this region, while African infections have so far not been reported. It is not clear that genetic differences between Africans and Arabs lead to differences in susceptibility.ResultsIn this study, we compared their evolutionary dynamics to provide a One Health perspective of their different results of disease control. The phylogenetic network of SARS-CoVs showed that human isolates gathered into a “super-spreader” cluster, and were distinct from civet isolates. In contrast, dromedary camel- and human-isolated MERS-CoVs were clustered together. Thus, most clades of MERS-CoV can infect humans, and MERS-CoVs seem easier to spill over from animal-to-human interface. Although MERS-CoVs are endemic to dromedary camels in both the Middle East and Africa, all human infections are linked to the Middle East. The nucleotide sequences of the MERS-CoV receptor gene--dipeptidyl peptidase 4 (DPP4) from 30 Egyptians, 36 Sudanese, and 34 Saudi Arabians showed little difference.ConclusionsOur study reveals the reason why MERS-CoV is not easily controlled. Analysis of genetic differences between Africans and Arabs suggest that human population differences in DPP4 might not be the reason for their different MERS prevalence, raising the possibility that other reasons, such as poorer disease surveillance in Africa, might explain these observations.

Worldwide tracing of mutations and the evolutionary dynamics of SARS-CoV-2 (preprint)

Understanding the mutational and evolutionary dynamics of SARS-CoV-2 is essential for treating COVID-19 and the development of a vaccine. Here, we analyzed publicly available 15,818 assembled SARS-CoV-2 genome sequences, along with 2,350 raw sequence datasets sampled worldwide. We investigated the distribution of inter-host single nucleotide polymorphisms (inter-host SNPs) and intra-host single nucleotide variations (iSNVs). Mutations have been observed at 35.6% (10,649/29,903) of the bases in the genome. The substitution rate in some protein coding regions is higher than the average in SARS-CoV-2 viruses, and the high substitution rate in some regions might be driven to escape immune recognition by diversifying selection. Both recurrent mutations and human-to-human transmission are mechanisms that generate fitness advantageous mutations. Furthermore, the frequency of three mutations (S protein, F400L; ORF3a protein, T164I; and ORF1a protein, Q6383H) has gradual increased over time on lineages, which provides new clues for the early detection of fitness advantageous mutations. Our study provides theoretical support for vaccine development and the optimization of treatment for COVID-19. We call researchers to submit raw sequence data to public databases.