Viral diversity in wild and urban rodents of Yunnan Province, China

References

• Mammal Diversity Database. Mammal Diversity Database. 2023. Available from: doi:10.5281/ZENODO.4139722
   Google Scholar
• Armien B, Pascale J, Bayard V, et al. High seroprevalence of hantavirus infection on the Azuero peninsula of Panama. Am J Trop Med Hyg. 2004;70:682–687. doi:10.4269/ajtmh.2004.70.682
   PubMed Web of Science ®Google Scholar
• Brisse ME, Ly H. Hemorrhagic fever-causing arenaviruses: lethal pathogens and potent immune suppressors. Front Immunol. 2019;10:4–5. doi:10.3389/fimmu.2019.00372
   PubMed Web of Science ®Google Scholar
• Wu Z, Lu L, Du J, et al. Comparative analysis of rodent and small mammal viromes to better understand the wildlife origin of emerging infectious diseases. Microbiome. 2018;6:178. doi:10.1186/s40168-018-0554-9
   PubMed Web of Science ®Google Scholar
• Li X, Wang L, Liu P, et al. A novel potentially recombinant rodent coronavirus with a polybasic cleavage site in the spike protein. J Virol. 2021;95:e0117321.
   PubMed Web of Science ®Google Scholar
• Xiong Y-Q, You F-F, Chen X-J, et al. Detection and phylogenetic analysis of porcine bocaviruses carried by murine rodents and house shrews in China. Transbound Emerg Dis. 2019;66:259–267. doi:10.1111/tbed.13011
   PubMed Web of Science ®Google Scholar
• Morcatty TQ, Pereyra PER, Ardiansyah A, et al. Risk of viral infectious diseases from live bats, primates, rodents and carnivores for sale in indonesian wildlife markets. Viruses. 2022;14:2756. doi:10.3390/v14122756
   PubMed Web of Science ®Google Scholar
• Motro Y, Ghendler Y, Muller Y, et al. A comparison of trapping efficacy of 11 rodent traps in agriculture. Mammal Res. 2019;64:435–443. doi:10.1007/s13364-019-00424-7
   Web of Science ®Google Scholar
• Francis C. Field guide to the mammals of south-east Asia. 2nd ed. San Francisco, CA: Bloomsbury Publishing, 2019.
   Google Scholar
• Twist Pan Viral Panel. Twist Bioscience. [accessed August 2023 29]. Available from https://www.twistbioscience.com/resources/product-sheet/twist-pan-viral-panel.
   Google Scholar
• Mastriani E, Bienes KM, Wong G, et al. PIMGAVir and Vir-MinION: Two viral metagenomic pipelines for complete baseline analysis of 2nd and 3rd generation data. Viruses. 2022;14:1260. doi:10.3390/v14061260
   PubMed Web of Science ®Google Scholar
• Li D, Liu C-M, Luo R, et al. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinforma Oxf Engl. 2015;31:1674–1676. doi:10.1093/bioinformatics/btv033
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol J Comput Mol Cell Biol. 2012;19:455–477. doi:10.1089/cmb.2012.0021
   PubMed Web of Science ®Google Scholar
• Rognes T, Flouri T, Nichols B, et al. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. doi:10.7717/peerj.2584
   PubMed Web of Science ®Google Scholar
• Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60. doi:10.1038/nmeth.3176
   PubMed Web of Science ®Google Scholar
• Shen W, Ren H. TaxonKit: a practical and efficient NCBI taxonomy toolkit. J Genet Genomics Yi Chuan Xue Bao. 2021;48:844–850. doi:10.1016/j.jgg.2021.03.006
   PubMed Web of Science ®Google Scholar
• Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–359. doi:10.1038/nmeth.1923
   PubMed Web of Science ®Google Scholar
• Li H, Handsaker B, Wysoker A, et al. The sequence alignment/map format and SAMtools. Bioinforma Oxf Engl. 2009;25:2078–2079. doi:10.1093/bioinformatics/btp352
   PubMed Web of Science ®Google Scholar
• Bedre R. bioinfokit: bioinformatics data analysis and visualization toolkit; 2020.. doi:10.5281/zenodo.3747737
   Google Scholar
• Shannon CE. A mathematical theory of communication. Bell Syst Tech J. 1948;27(3):379–423. doi:10.1002/j.1538-7305.1948.tb01338.x
   Google Scholar
• Magurran AE. Measuring biological diversity. Malden (Ma): Blackwell Pub; 2004.
   Google Scholar
• Leray M, Knowlton N, Machida RJ. MIDORI2: a collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences. Environ DNA. 2022;4:894–907. doi:10.1002/edn3.303
   Google Scholar
• Katoh K, Rozewicki J, Yamada KD. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief Bioinform. 2019;20:1160–1166. doi:10.1093/bib/bbx108
   PubMed Web of Science ®Google Scholar
• Nguyen L-T, Schmidt HA, von Haeseler A, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–274. doi:10.1093/molbev/msu300
   PubMed Web of Science ®Google Scholar
• Kalyaanamoorthy S, Minh BQ, Wong TKF, et al. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–589. doi:10.1038/nmeth.4285
   PubMed Web of Science ®Google Scholar
• Samson S, Lord É, Makarenkov V. SimPlot++: a Python application for representing sequence similarity and detecting recombination. Bioinforma Oxf Engl. 2022;38:3118–3120. doi:10.1093/bioinformatics/btac287
   PubMed Web of Science ®Google Scholar
• Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111–120. doi:10.1007/BF01731581
   PubMed Web of Science ®Google Scholar
• KASSAMBARA A. rstatix. (2023). [accessed 2023 April 28]. Available from: https://github.com/kassambara/rstatix.
   Google Scholar
• Wickham H. ggplot2: Elegant graphics for data analysis. New York (NY): Springer; 2009.
   Google Scholar
• Rongen MC, van M. Chapter 1 Overview | Core Statistics in R. [accessed 2023 April 28]. Available from: https://cambiotraining.github.io/corestats-in-r/.
   Google Scholar
• Pearson K. (1857–1936). On the theory of contingency and its relation to association and normal correlation.
   Google Scholar
• Jones MS, Lukashov VV, Ganac RD, et al. Discovery of a novel human picornavirus in a stool sample from a pediatric patient presenting with fever of unknown origin. J Clin Microbiol. 2007;45:2144–2150. doi:10.1128/JCM.00174-07
   PubMed Web of Science ®Google Scholar
• Nasar F, Palacios G, Gorchakov RV, et al. Eilat virus, a unique alphavirus with host range restricted to insects by RNA replication. Proc Natl Acad Sci U S A. 2012;109:14622–14627. doi:10.1073/pnas.1204787109
   PubMed Web of Science ®Google Scholar
• Jones KE, Patel NG, Levy MA, et al. Global trends in emerging infectious diseases. Nature. 2008;451:990–993. doi:10.1038/nature06536
   PubMed Web of Science ®Google Scholar
• Wu Z, Han Y, Liu B, et al. Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia. Microbiome. 2021;9:18. doi:10.1186/s40168-020-00965-z
   PubMed Web of Science ®Google Scholar
• van der Walt AJ, van Goethem MW, Ramond J-B, et al. Assembling metagenomes, one community at a time. BMC Genomics. 2017;18:521. doi:10.1186/s12864-017-3918-9
   PubMed Web of Science ®Google Scholar
• Wu Z, Han Y, Liu B, et al. Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia. Microbiome. 2021;9:7–9. doi:10.1186/s40168-020-00965-z
   PubMed Web of Science ®Google Scholar
• Du H, Zhang L, Zhang X, et al. Metagenome-assembled viral genomes analysis reveals diversity and infectivity of the RNA virome of gerbillinae species. Viruses. 2022;14:356. doi:10.3390/v14020356
   PubMed Web of Science ®Google Scholar
• Hassell JM, Begon M, Ward MJ, et al. Urbanization and disease emergence: dynamics at the wildlife–livestock–human interface. Trends Ecol Evol. 2017;32:55–67. doi:10.1016/j.tree.2016.09.012
   PubMed Web of Science ®Google Scholar
• Mull N, Schexnayder A, Stolt A, et al. Effects of habitat management on rodent diversity, abundance, and virus infection dynamics. Ecol Evol. 2023;13:e10039. doi:10.1002/ece3.10039
   PubMed Web of Science ®Google Scholar
• Ecke F, Han BA, Hörnfeldt B, et al. Population fluctuations and synanthropy explain transmission risk in rodent-borne zoonoses. Nat Commun. 2022;13:7532. doi:10.1038/s41467-022-35273-7
   PubMed Web of Science ®Google Scholar
• Magnusson M, Ecke F, Khalil H, et al. Spatial and temporal variation of Hantavirus bank vole infection in managed forest landscapes. Ecosphere. 2015;6:art163. doi:10.1890/ES15-00039.1
   Web of Science ®Google Scholar
• Williams EP, Spruill-Harrell BM, Taylor MK, et al. Common themes in zoonotic spillover and disease emergence: lessons learned from bat- and rodent-borne RNA viruses. Viruses. 2021;13:1509. doi:10.3390/v13081509
   PubMed Web of Science ®Google Scholar
• Gibb R, Redding DW, Chin KQ, et al. Zoonotic host diversity increases in human-dominated ecosystems. Nature. 2020;584:398–402. doi:10.1038/s41586-020-2562-8
   PubMed Web of Science ®Google Scholar
• García-Peña GE, Rubio AV, Mendoza H, et al. Land-use change and rodent-borne diseases: hazards on the shared socioeconomic pathways. Philos Trans R Soc B Biol Sci. 2021;376:20200362. doi:10.1098/rstb.2020.0362
   PubMed Web of Science ®Google Scholar
• Muylaert RL, Sabino-Santos G, Prist PR, et al. Spatiotemporal dynamics of Hantavirus cardiopulmonary syndrome transmission risk in Brazil. Viruses. 2019;11:1008. doi:10.3390/v11111008
   PubMed Web of Science ®Google Scholar
• Prist PR, Uriarte M, Fernandes K, et al. Climate change and sugarcane expansion increase Hantavirus infection risk. PLoS Negl Trop Dis. 2017;11:e0005705. doi:10.1371/journal.pntd.0005705
   PubMed Web of Science ®Google Scholar
• Prist PR, D´Andrea PS, Metzger JP. Landscape, climate and hantavirus cardiopulmonary syndrome outbreaks. EcoHealth. 2017;14:614–629. doi:10.1007/s10393-017-1255-8
   PubMed Web of Science ®Google Scholar
• Levine RS, Peterson AT, Yorita KL, et al. Ecological niche and geographic distribution of human Monkeypox in Africa. PLoS One. 2007;2:e176. doi:10.1371/journal.pone.0000176
   PubMed Web of Science ®Google Scholar
• Kenmoe S, Tchatchouang S, Ebogo-Belobo JT, et al. Systematic review and meta-analysis of the epidemiology of Lassa virus in humans, rodents and other mammals in sub-Saharan Africa. PLoS Negl Trop Dis. 2020;14:e0008589. doi:10.1371/journal.pntd.0008589
   PubMed Web of Science ®Google Scholar
• Wang J, Cheng S, Yi L, et al. Evidence for natural recombination between mink enteritis virus and canine parvovirus. Virol J. 2012;9:252. doi:10.1186/1743-422X-9-252
   PubMed Web of Science ®Google Scholar
• Kemenesi G, Dallos B, Görföl T, et al. Genetic diversity and recombination within bufaviruses: detection of a novel strain in Hungarian bats. Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis. 2015;33:288–292.
   PubMed Web of Science ®Google Scholar
• Summa M, Henttonen H, Maunula L. Human noroviruses in the faeces of wild birds and rodents-new potential transmission routes. Zoonoses Public Health. 2018;65:3–6. doi:10.1111/zph.12461
   Web of Science ®Google Scholar
• Tan SZK, Tan MZY, Prabakaran M. Saffold virus, an emerging human cardiovirus. Rev Med Virol. 2017;27:e1908. doi:10.1002/rmv.1908
   PubMed Web of Science ®Google Scholar
• Blinkova O, Kapoor A, Victoria J, et al. Cardioviruses are genetically diverse and cause common enteric infections in South Asian children. J Virol. 2009;83:4631–4641. doi:10.1128/JVI.02085-08
   PubMed Web of Science ®Google Scholar
• Naeem A, Hosomi T, Nishimura Y, et al. Genetic diversity of circulating Saffold viruses in Pakistan and Afghanistan. J Gen Virol. 2014;95:1945–1957. doi:10.1099/vir.0.066498-0
   PubMed Web of Science ®Google Scholar
• Wang L, Tang Q, Liang G. Rabies and rabies virus in wildlife in mainland China, 1990–2013. Int J Infect Dis. 2014;25:122–129. doi:10.1016/j.ijid.2014.04.016
   PubMed Web of Science ®Google Scholar
• Zhao Y, Qian A, Li Y, et al. Sequencing and analysis of G–gene of rabies virus strain from wild mous. Jilin Nong Ye Xue Xue Bao Acta Agric Univ Jilinensis. 2004;26:210–212, 216.
   Google Scholar
• Lei Y, Wang X, Li H, et al. New animal hosts of rabies virus in mountain areas in Zhejiang province. Zhonghua Liu Xing Bing Xue Za Zhi Zhonghua Liuxingbingxue Zazhi. 2009;30:344–347.
   PubMedGoogle Scholar
• Chernomor O, von Haeseler A, Minh BQ. Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol. 2016;65:997–1008. doi:10.1093/sysbio/syw037
   PubMed Web of Science ®Google Scholar