Plowright RK, Parrish CR, McCallum H, Hudson PJ, Ko AI, Graham AL, Lloyd-Smith JO (2017) Pathways to zoonotic spillover. Nat Rev Microbiol 15:502–510

CAS  Article  Google Scholar 

World Health Organization (2004) Report of the WHO/FAO/OIE joint consultation on emerging zoonotic diseases / in collaboration with the Health Council of the Netherlands. World Health Organization. https://apps.who.int/iris/handle/10665/68899

Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P (2008) Global trends in emerging infectious diseases. Nature 451(7181):990–993

CAS  Article  Google Scholar 

Sánchez CA, Venkatachalam-Vaz J, Drake JM (2021) Spillover of zoonotic pathogens: a review of reviews. Zoonoses Public Health 68(6):563–577

Article  Google Scholar 

International Monetary Fund (IMF), World Economic Outlook (2020) A long and difficult ascent. International Monetary Fund, Washington, DC, p 2020

Google Scholar 

Näpflin K, O’Connor EA, Becks L et al (2019) Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales. PeerJ 7:e8013

Article  Google Scholar 

Wolfe ND, Dunavan CP, Diamond J (2007) Origins of major human infectious diseases. Nature 447(7142):279–283

CAS  Article  Google Scholar 

Young PR (2018) Arboviruses: a family on the move. Adv Exp Med Biol 1062:1–10. https://doi.org/10.1007/978-981-10-8727-1_1

CAS  Article  Google Scholar 

Sharp PM, Hahn BH (2011) Origins of HIV and the AIDS pandemic. Cold Spring Harb Perspect Med 1(1):a006841

Article  CAS  Google Scholar 

Leroy EM, Kumulungui B, Pourrut X et al (2005) Fruit bats as reservoirs of Ebola virus. Nature 438(7068):575–576

CAS  Article  Google Scholar 

Heeney JL, Dalgleish AG, Weiss RA (2006) Origins of HIV and the evolution of resistance to AIDS. Science 313(5786):462–466

CAS  Article  Google Scholar 

Gire SK, Goba A, Andersen KG et al (2014) Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345(6202):1369–1372

CAS  Article  Google Scholar 

Centers for Disease Control and Prevention (2012) Principles of epidemiology. Centers for Disease Control and Prevention. https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section10.html. Accessed 20 January 2022

Luis AD, Hayman DT, O’Shea TJ et al (2013) A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc Bol Sci 280(1756):20122753

Google Scholar 

Patterson JE, Ruckstuhl KE (2013) Parasite infection and host group size: a meta-analytical review. Parasitology 140(7):803–813

Article  Google Scholar 

Rohr JR, Barrett CB, Civitello DJ et al (2019) Emerging human infectious diseases and the links to global food production. Nat Sustain 2(6):445–456

Article  Google Scholar 

Aggarwal R, Jameel S (2011) Hepatitis E. Hepatology 54(6):2218–2226

Article  Google Scholar 

Leland DS, Ginocchio CC (2007) Role of cell culture for virus detection in the age of technology. Clin Microbiol Rev 20(1):49–78

CAS  Article  Google Scholar 

Halpin K, Hyatt AD, Fogarty R et al (2011) Pteropid bats are confirmed as the reservoir hosts of henipaviruses: a comprehensive experimental study of virus transmission. Am J Trop Med Hyg 85(5):946–951

Article  Google Scholar 

Wittmann G, Rziha HJ (1989) Aujeszky’s disease (pseudorabies) in pigs. In: Wittmann G (ed) Herpesvirus diseases of cattle, horses, and pigs. Springer, Boston, MA, pp 230–325

Chapter  Google Scholar 

Gilbert AT, Fooks AR, Hayman DT et al (2013) Deciphering serology to understand the ecology of infectious diseases in wildlife. EcoHealth 10(3):298–313

Article  Google Scholar 

Banerjee A, Misra V, Schountz T, Baker ML (2018) Tools to study pathogen–host interactions in bats. Virus Res 248:5–12

CAS  Article  Google Scholar 

Michel AL, Lane EP, de Klerk-Lorist LM, Hofmeyr M, van der Heijden EMDL, Botha L, van Helden P, Miller M, Buss P (2017) Experimental Mycobacterium bovis infection in three white rhinoceroses (Ceratotherium simum): susceptibility, clinical and anatomical pathology. PLoS ONE 12(7):e0179943

Article  CAS  Google Scholar 

Dickens MJ, Delehanty DJ, Romero LM (2009) Stress and translocation: alterations in the stress physiology of translocated birds. Proc Biol Sci 276(1664):2051–2056

Google Scholar 

Wade W (2002) Unculturable bacteria—the uncharacterized organisms that cause oral infections. J R Soc Med 95(2):81–83

Google Scholar 

Mokili JL, Rohwer F, Dutilh BE (2012) Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2(1):63–77

CAS  Article  Google Scholar 

Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685

CAS  Article  Google Scholar 

Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, Wolber PK, Relman DA, Brown PA (2006) Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res 34(1):e5

Article  CAS  Google Scholar 

Van Brussel K, Holmes EC (2021) Zoonotic disease and virome diversity in bats. Curr Opin Virol 52:192–202

Article  CAS  Google Scholar 

Rota PA, Oberste MS, Monroe SS et al (2003) Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science 300(5624):1394–1399

CAS  Article  Google Scholar 

Lam TTY, Jia N, Zhang YW, Shum MHH et al (2020) Identifying SARS-CoV-2-related coronaviruses in Malayan pangolins. Nature 583(7815):282–285

CAS  Article  Google Scholar 

Cobbin JC, Charon J, Harvey E, Holmes EC, Mahar JE (2021) Current challenges to virus discovery by meta-transcriptomics. Curr Opin Virol 51:48–55

CAS  Article  Google Scholar 

New FN, Brito IL (2020) What is metagenomics teaching us, and what is missed? Annu Rev Microbiol 74:117–135

CAS  Article  Google Scholar 

Chiu CY, Miller SA (2019) Clinical metagenomics. Nat Rev Genet 20(6):341–355

CAS  Article  Google Scholar 

Barr J, Smith C, Smith I, de Jong C, Todd S, Melville D, Broos A, Crameri S, Haining J, Marsh G, Crameri G (2015) Isolation of multiple novel paramyxoviruses from pteropid bat urine. J Gen Virol 96(1):24–29

CAS  Article  Google Scholar 

Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, Mazet JK, Hu B, Zhang W, Peng C, Zhang YJ et al (2013) Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 503(7477):535–538

CAS  Article  Google Scholar 

Nshimyimana JP, Cruz MC, Wuertz S, Thompson JR (2019) Variably improved microbial source tracking with digital droplet PCR. Water Res 159:192–202

CAS  Article  Google Scholar 

Li H, Bai R, Zhao Z et al (2018) Application of droplet digital PCR to detect the pathogens of infectious diseases. Biosci Rep 38(6):BSR20181170

Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO et al (2018) Field-deployable viral diagnostics using CRISPR-Cas13. Science 360(6387):444–448

CAS  Article  Google Scholar 

Gootenberg JS, Abudayyeh OO, Lee JW et al (2017) Nucleic acid detection with CRISPR-Cas13a/C2c2. Science 356(6336):438–442

CAS  Article  Google Scholar 

Barnes KG, Lachenauer AE, Nitido A et al (2020) Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in real-time. Nat Commun 11(1):1–10

Article  CAS  Google Scholar 

Broughton JP, Deng X, Yu G et al (2020) CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol 38(7):870–874

CAS  Article  Google Scholar 

Cardozo KHM, Lebkuchen A, Okai GG, Schuch RA, Viana LG, Olive AN, Lazari CDS, Fraga AM, Granato CFH, Pintão MCT, Carvalho VM (2020) Establishing a mass spectrometry-based system for rapid detection of SARS-CoV-2 in large clinical sample cohorts. Nat Commun 11(1):6201

CAS  Article  Google Scholar 

Jiang L, Luo J, Dong W, Wang C, Jin W, Xia Y, Wang H, Ding H, Jiang L, He H (2015) Development and evaluation of a polydiacetylene based biosensor for the detection of H5 influenza virus. J Virol Methods 219:38–45

CAS  Article  Google Scholar 

Ostrov N, Jimenez M, Billerbeck S, Brisbois J, Matragrano J, Ager A, Cornish VW (2017) A modular yeast biosensor for low-cost point-of-care pathogen detection. Sci Adv 3(6):e1603221

Article  CAS  Google Scholar 

Lee SE, Lee DY, Lee WG, Kang B, Jang YS, Ryu B, Lee S, Bahk H, Lee E (2020) Detection of novel coronavirus on the surface of environmental materials contaminated by COVID-19 patients in the Republic of Korea. Osong Public Health Res Perspect 11(3):128–132

Article  Google Scholar 

Thomsen PF, Willerslev E (2015) Environmental DNA—an emerging tool in conservation for monitoring past and present biodiversity. Biol Conserv 183:4–18

Article  Google Scholar 

Aylward ML, Sullivan AP, Perry GH, Johnson SE, Louis EE Jr (2018) An environmental DNA sampling method for aye-ayes from their feeding traces. Ecol Evol 8(18):9229–9240

Article  Google Scholar 

Mengüllüoğlu D, Fickel J, Hofer H, Förster DW (2019) Non-invasive faecal sampling reveals spatial organization and improves measures of genetic diversity for the conservation assessment of territorial species: Caucasian lynx as a case species. PLoS ONE 14(5):e0216549

Article  Google Scholar 

Dib LV, Palmer JP, de Souza Carvalho Class C, Pinheiro JL, Ramos RC, Dos Santos CR, Fonseca AB, Rodríguez-Castro KG, Gonçalves CF, Galetti PM, Bastos OM (2020) Non-invasive sampling in Itatiaia National Park, Brazil: wild mammal parasite detection. BMC Vet Res 16:295

CAS  Article  Google Scholar 

Kitajima M, Ahmed W, Bibby K, Carducci A, Gerba CP, Hamilton KA, Haramoto E, Rose JB (2020) SARS-CoV-2 in wastewater: state of the knowledge and research needs. Sci Total Environ 739:139076

CAS  Article  Google Scholar 

Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA et al (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE 7(8):e41781

CAS  Article  Google Scholar