OmniVira

Virome characterization of field-collected rodents in suburban city.

Zhen-Yu Hu1,2,3 Fang Tang4 Mei-Qi Zhang2 Jing-Tao Zhang2 Yun-Fa Zhang2 Guang-Qian Si2,5 Bo-Kang Fu1,2 Gang Wang2 Shuang Li2 Lei Zhang2 Cong Peng2 Xiao-Fang Ma6 Yan-Tao Liu6 Hong Su1 Peng-Tao Bao7 Xiao-Ai Zhang8,9 Wei Liu10,11,12
Affiliations 12 institutions
  1. School of Public Health, Anhui Medical University, Hefei, China.
  2. State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, China.
  3. The First Affiliated Hospital of Anhui Medical University, Hefei, China.
  4. Institute of Medical Prevention and Control of Public Health Emergencies, Characteristic Medical Center of the Chinese People's Armed Police Force, Beijing, China.
  5. The Eighth Medical Center of Chinese PLA General Hospital, Beijing, China.
  6. Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China.
  7. The Eighth Medical Center of Chinese PLA General Hospital, Beijing, China. [email protected].
  8. School of Public Health, Anhui Medical University, Hefei, China. [email protected].
  9. State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, China. [email protected].
  10. School of Public Health, Anhui Medical University, Hefei, China. [email protected].
  11. State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing, China. [email protected].
  12. The First Affiliated Hospital of Anhui Medical University, Hefei, China. [email protected].
PMID40500267 DOI10.1038/s41522-025-00740-8 Year2025 Journal NPJ biofilms and microbiomes NPJ Biofilms Microbiomes Languageeng Statusepublish

Abstract

Rodents serve as natural reservoirs and vectors for a multitude of zoonotic viruses. Analyzing the viral diversity in rodents is crucial for predicting the emergence of infectious diseases. Through high-throughput sequencing, we characterized the RNA virome of nine rodent species from the families Cricetidae and Muridae, collected from suburban Beijing (n = 432). The composition of the virome exhibited significant variation at the virus family level across the nine rodent species and three types of natural habitats. A total of 142 viral species were identified, including 133 associated with vertebrates and 9 associated with invertebrates, spanning 26 families. Notably, 75 of these viruses were novel while 67 were known viruses. Twenty-five viruses were classified as high-risk, including eight zoonotic viruses and 17 spillover-risk viruses. Additionally, nine known viruses were identified for the first time in China. Thirty-three viruses demonstrated potential for cross-species transmission. Understanding the virome characterization of field-collected rodent might provide valuable insights into the potential risk of zoonotic spillover to humans.

Supporting text Virus Host Location
Rodentia 51 Virome 33 Viruses 49 Animals 1948 Beijing 1 China 229 Disease Reservoirs 149 High-Throughput Nucleotide Sequencing 39 Humans 1440 Phylogeny 805 Zoonoses 397

Evidence records

3 total
Zoonotic Surveillance
3 records · 1 evidence types
Evidence type Viral Detection
3 records
OVE9395 Viral Detection
Key finding

High-throughput sequencing detected and characterized 142 viral species in nine field-collected rodent species from suburban Beijing.

Virus
142 viral species
Host
rodents Rodentia Natural host Cricetidae Natural host Muridae Natural host
Location
China
Supporting text

Through high-throughput sequencing, we characterized the RNA virome of nine rodent species from the families Cricetidae and Muridae, collected from suburban Beijing (n = 432). A total of 142 viral species were identified.

Method
high-throughput sequencing
Sample type
field-collected rodents
Geographic raw
suburban Beijing
Country inferred
CHN
OVE9396 Viral Detection
Key finding

Nine known viruses were detected in rodents and reported for the first time in China.

Virus
nine known viruses
Host
rodents Rodentia Natural host
Location
China
Supporting text

Additionally, nine known viruses were identified for the first time in China.

Method
high-throughput sequencing
Sample type
rodent samples
Geographic raw
China
Country inferred
CHN
OVE9398 Viral Detection
Key finding

Thirty-three viruses demonstrated potential for cross-species transmission among rodent species collected from suburban Beijing.

Virus
thirty-three viruses
Host
rodents Rodentia Natural host
Location
China
Supporting text

Through high-throughput sequencing, we characterized the RNA virome of nine rodent species from the families Cricetidae and Muridae, collected from suburban Beijing (n = 432). Thirty-three viruses demonstrated potential for cross-species transmission.

Method
high-throughput sequencing
Geographic raw
suburban Beijing