#17,889
Eleven years ago, in mBio: A Strategy To Estimate The Number Of Undiscovered Viruses, we saw an early attempt to estimate the number of undiscovered mammalian viruses in the world. Researchers at Columbia University's Mailman School of Public Health, EcoHealth Alliance, the NIH, et al. came up with `. . . minimum of 320,000 mammalian viruses awaiting discovery.'
Of course, this is a low-end estimate. Some researchers put that number well over 1 million.
Like it or not, we live in a pathogen-rich environment. Every few months we learn about some new or expanding disease threat in the wild (see UK HAIRS Timeline below), and there are no signs that this trend is slowing down.
Three months ago, in V. Sinica: Diversity and Independent Evolutionary Profiling of Rodent-borne Viruses in Hainan, China, we looked at a report, published by Chinese scientists that describes the discovery of 8 previously unknown pathogens with zoonotic potential circulating in rodents on Hainan Island, China.
Today, in a similar vein, we have a preprint detailing the virodiversity among wild rodents collected from suburban Beijing. Samples were collected between May 2017 and October 2018, from three different habitat types: grassland, bushland and woodland).
Due to its length I've only posted the Abstract and a few excerpts from the main body of the report. Those wishing a deeper dive will want to follow the link to read it in its entirety.Researchers, identified 75 novel viruses and 67 known viruses from from 432 wild rodents tested; 25 viruses were classified as high-risk, including 8 zoonotic viruses and 17 spillover-risk viruses.
Virome characterization of field-collected rodents in suburban Beijing reveals a spectrum of emerging pathogens
Zhen-Yu Hu, Fang Tang, Jing-Tao Zhang, Yun-Fa Zhang, Guang-Qian Si, and 11 more
This is a preprint; it has not been peer reviewed by a journal.
https://doi.org/10.21203/rs.3.rs-3901407/v1
This work is licensed under a CC BY 4.0 License
Abstract
Background
Rodents serve as natural reservoirs and transmission hosts for numerous zoonotic viruses, which can cause a range of animal and human diseases, posing significant public health concerns. Analyzing the viral diversity harbored by rodents is crucial for early warnings of emerging infectious diseases.
Results
By conducting meta-transcriptomic sequencing on spleen samples obtained from 432 wild rodents across three habitats, we characterized the high-depth RNA virome of wild rodents representing 9 species of two prominent mammalian families (Cricetidae and Muridae) in suburban Beijing. The composition of virome varied significantly at the virus family level among the nine rodent species and three types of natural habitats. A total of 142 viral species associated with vertebrates (n = 133) and invertebrates (n = 9) were identified from 26 families, including 75 novel viruses and 67 known viruses, thereby substantially expanding our knowledge about the diversity of rodent virome. Among these, twenty-five viruses were classified as high-risk, including 8 zoonotic viruses and 17 spillover-risk viruses. Additionally, nine previously unreported viruses were discovered for the first time in China. Furthermore, thirty-three viruses exhibited species transmission potential and some had evolutionary significance.
Conclusions
These findings enhance our understanding of rodent virome in Suburban Beijing and suggest that there is vast array of undiscovered viruses within these rodent species in China. Understanding the composition of rodent virome might provide insights into the potential risk of zoonotic spillover to humans.
(D) Associations between high-risk viruses and rodent species hosts. The size of the colored circles indicates the number of zoonotic and spillover-risk viruses carried by each rodent species.
(SNIP)
The emergence of novel infectious diseases in humans often occurs as a result of the spillover or cross-species transmission of zoonotic agents from their natural reservoir hosts. An in-depth understanding of the viruses – host interface could contribute to identification of future emergence events, particularly for those viruses that have pathogenic potential in humans. Our data provide compelling evidence for frequent interspecies transmission of rodent borne viruses, that occurred at various levels of the host, including species, genus, and even family.
Approximately 23% of the identified viruses were found in more than two rodent species, accounting for nearly half of the total cross-species transmission events observed in our study, indicating a high level of viral sharing among rodent species. Notably, all the five species identified from the Hantaviridae family are of cross-species viruses and exhibit a higher propensity of cross species transmission compared to other viral families. Successful interspecies transmission depends on a multitude of biological, ecological, and epidemiological factors. While the current cross-species analysis does not allow conclusions regarding competent transmissibility, these discoveries might help to locate the high-priority viruses for further investigation on their emergence risks in human beings.
Our study has inherent limitations that need to be acknowledged. The current surveys have primarily been cross-sectional, capturing a single snapshot of each population at a given time point. Since that viral communities in rodents may be influenced by environmental and meteorological factors, some low-abundance pathogens or even high-risk viruses may have been overlooked due to low sampling frequency, or insufficient sequence data. Therefore, an adequate disclosure of complete virome within the region need warrant temporally dynamic analysis of rodent virome investigation. Second, the current surveillance efforts primarily rely on metagenomic sequencing and epidemiological investigation. The potential pathogenicity of the newly identified viruses toward humans remains unclear, which warrant further studies towards virus isolation and experimental infection in animal models. Additionally, the accurate assessment of zoonotic risk for certain identified viruses is challenging due to a scarcity of sequence data, for instance, only two complete genomes are available for Mossman virus, hindering understanding of crucial aspects such as host range and virus epidemiology.
As peridomestic creatures, rodents rank high on our list of `usual suspects' when it come to the transmission of zoonotic diseases to humans. A few (of many) zoonotic diseases that can be carried by rodents include:
- Lassa Fever
- Monkeypox (Mpox virus)
- A wide range of Hantaviruses (Sin Nombre, Puumala, HFRS)
- Rat Hepatitis E Virus
- Tularemia
- lymphocytic choriomeningitis virus
- Leptospirosis
- Salmonellosis, pathogenic E. coli infections, campylobacterosis, and giardiasis
- Lyme disease
- Tick-borne encephalitis
- Angiostrongyliasis (rat lungworm)
- And quite possibly avian influenza, SARS-COV-2, and many more . . .
Should those trends continue, they suggest `. . . these pathogens to cause four times the number of spillover events and 12 times the number of deaths in 2050, compared with 2020.'
Studies, like today's, suggest where some of those future spillovers may come from.
