A strategy to estimate unknown viral diversity in mammals

mBio

Volumn 4, Issue 5, 2013, Pages

  Anthony, Simon J ^a,b   Epstein, Jonathan H ^b   Murray, Kris A ^b   Navarrete Macias, Isamara ^a   Zambrana Torrelio, Carlos M ^b   Solovyov, Alexander ^a   Ojeda Flores, Rafael ^c   Arrigo, Nicole C ^a   Islam, Ariful ^b   Khan, Shahneaz Ali ^d   Hosseini, Parviez ^b   Bogich, Tiffany L ^e,f   Olival, Kevin J ^b   Sanchez Leon, Maria D ^a,b   Karesh, William B ^b   Goldstein, Tracey ^g   Luby, Stephen P ^h   Morse, Stephen S ^a,g   Mazet, Jonna A K ^g   Daszak, Peter ^b   Lipkin, W Ian ^a   more..

^a Department of Medicine   (United States)

^b ECOHEALTH ALLIANCE   (United States)

^c UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

^d Chittagong Government Veterinary College   (Bangladesh)

^e PRINCETON UNIVERSITY   (United States)

^f NATIONAL INSTITUTES OF HEALTH   (United States)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h INTERNATIONAL CENTRE FOR DIARRHOEAL DISEASE RESEARCH   (Bangladesh)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOVIRUS; ADENOVIRUS INFECTION; ARTICLE; ASTROVIRUS; BOCAVIRUS; CORONAVIRUS; COST BENEFIT ANALYSIS; FOX; HERPES VIRUS; HERPES VIRUS INFECTION; HOST PATHOGEN INTERACTION; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MIXED INFECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PARAMYXOVIRUS; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; POLYOMA VIRUS; PRIORITY JOURNAL; PTEROPUS GIGANTEUS; SPECIES DIVERSITY; SPECIES RICHNESS; UNINDEXED SEQUENCE; VIRUS DETECTION; VIRUS IDENTIFICATION; ZOONOSIS;

ANIMALS; ANIMALS, WILD; BIODIVERSITY; CHIROPTERA; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; VIRUSES; ZOONOSES;

EID: 84885410330     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00598-13     Document Type: Article

References (64)

1. Morse SS. 1995. Factors in the emergence of infectious diseases. Emerg. Infect. Dis. 1:7-15.
2. Woolhouse ME, Gowtage-Sequeria S. 2005. Host range and emerging and reemerging pathogens. Emerg. Infect. Dis. 11:1842-1847.
3. Jones KE, Patel NG, Levy MA, Storeygard A, Balk D, Gittleman JL, Daszak P. 2008. Global trends in emerging infectious diseases. Nature 451:990-993.
4. Rondinini C, Di Marco M, Chiozza F, Santulli G, Baisero D, Visconti P, Hoffmann M, Schipper J, Stuart SN, Tognelli MF, Amori G, Falcucci A, Maiorano L, Boitani L. 2011. Global habitat suitability models of terrestrial mammals. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366: 2633-2641.
5. Lipkin WI. 2013. The changing faces of pathogen discovery and surveillance. Nat. Rev. Microbiol. 11:133-141.
6. Sumibcay L, Kadjo B, Gu SH, Kang HJ, Lim BK, Cook JA, Song JW, Yanagihara R. 2012. Divergent lineage of a novel hantavirus in the banana pipistrelle (Neoromicia nanus) in Côte d'Ivoire. Virol. J. 9:1-6.
7. Tong S, Li Y, Rivailler P, Conrardy C, Castillo DA, Chen LM, Recuenco S, Ellison JA, Davis CT, York IA, Turmelle AS, Moran D, Rogers S, Shi M, Tao Y, Weil MR, Tang K, Rowe LA, Sammons S, Xu X, Frace M, Lindblade KA, Cox NJ, Anderson LJ, Rupprecht CE, Donis RO. 2012. A distinct lineage of influenza A virus from bats. Proc. Natl. Acad. Sci. U.S.A. 109:4269-4274.
8. Weiss S, Witkowski PT, Auste B, Nowak K, Weber N, Fahr J, Mombouli JV, Wolfe ND, Drexler JF, Drosten C, Klempa B, Leendertz FH, Kruger DH. 2012. Hantavirus in bat, Sierra Leone. Emerg. Infect. Dis. 18:159-161.
9. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (ed). 2012. Virus taxonomy: classification and nomenclature of viruses. Ninth report of the International Committee on Taxonomy of Viruses. Academic Press, San Diego, CA.
10. Chao A, Colwell RK, Lin CW, Gotelli NJ. 2009. Sufficient sampling for asymptotic minimum species richness estimators. Ecology 90:1125-1133.
11. Ulrich W. 2008. Pairs-a FORTRAN program for studying pair-wise species associations in ecological matrices. http://www.uni.torun.pl/*ulrichw.
12. Gotelli NJ, Ulrich W. 2010. The empirical Bayes approach as a tool to identify non-random species associations. Oecologica 162:463-477.
13. Woolhouse ME, Howey R, Gaunt E, Reilly L, Chase-Topping M, Savill N. 2008. Temporal trends in the discovery of human viruses. Proc. Biol. Sci. 275:2111-2115.
14. Woolhouse M, Scott F, Hudson Z, Howey R, Chase-Topping M. 2012. Human viruses: discovery and emergence. Philos. Trans. R. Soc. Lond. B Biol. Sci. 367:2864-2871.
15. Chao A. 2005. Species estimation and applications. In Balakrishnan N, Read CB, Vidakovic B (ed), Encyclopedia of statistical sciences. Wiley, New York, NY.
16. Mora C, Tittensor DP, Myers RA. 2008. The completeness of taxonomic inventories for describing the global diversity and distribution of marine fishes. Proc. Biol. Sci. 275:149-155.
17. Magurran AE, McGill BJ. 2011. Biological diversity: frontiers in measurement and assessment. Oxford University Press, Oxford, United Kingdom.
18. Morse SS, Mazet JA, Woolhouse M, Parrish CR, Carroll D, Karesh WB, Zambrana-Torrelio C, Lipkin WI, Daszak P. 2012. Prediction and prevention of the next pandemic zoonosis. Lancet 380:1956-1965.
19. Wilson DE, Reeder DM. 2005. Mammal species of the world. Johns Hopkins University Press, Baltimore, MD.
20. Ge X-Y, Li J-L, Yang X-L, Chmura AA, Zhu G, Epstein JH, Mazet JK, Hu B, Zhang W, Peng C, Zhang Y-J, Luo C-M, Tan B, Wang N, Zhu Y, Crameri G, Zhang S-Y, Wang L-F, Daszak P, Shi Z-L. First isolation and characterization of bat SARS-like coronaviruses that use the ACE2 receptor. Nature, in press.
21. Epstein JH, Prakash V, Smith CS, Daszak P, McLaughlin AB, Meehan G, Field HE, Cunningham AA. 2008. Henipavirus infection in fruit bats (Pteropus giganteus), India. Emerg. Infect. Dis. 14:1309-1311.
22. Epstein JH, Quan PL, Briese T, Street C, Jabado O, Conlan S, Ali Khan S, Verdugo D, Hossain MJ, Hutchison SK, Egholm M, Luby SP, Daszak P, Lipkin WI. 2010. Identification of GBV-D, a novel GB-like flavivirus from old world frugivorous bats (Pteropus giganteus) in Bangladesh. PLoS Pathog. 6:e1000972. doi:10.1371/journal.ppat.1000972.
23. Stapleton JT, Williams CF, Xiang J. 2004. GB virus type C: a beneficial infection? J. Clin. Microbiol. 42:3915-3919.
24. Lawn SD, Bekker LG, Middelkoop K, Myer L, Wood R. 2006. Impact of HIV infection on the epidemiology of tuberculosis in a peri-urban community in South Africa: the need for age-specific interventions. Clin. Infect. Dis. 42:1040-1047.
25. Joseph SB, Hanley KA, Chao L, Burch CL. 2009. Coinfection rates in 6 bacteriophage are enhanced by virus-induced changes in host cells. Evol. Appl. 2:24-31.
26. Techasaensiri B, Techasaensiri C, Mejías A, McCracken GH, Jr, Ramilo O. 2010. Viral coinfections in children with invasive pneumococcal disease. Pediatr. Infect. Dis. J. 29:519-523.
27. Telfer S, Lambin X, Birtles R, Beldomenico P, Burthe S, Paterson S, Begon M. 2010. Species interactions in a parasite community drive infection risk in a wildlife population. Science 330:243-246.
28. Newman CM, Cerutti F, Anderson TK, Hamer GL, Walker ED, Kitron UD, Ruiz MO, Brawn JD, Goldberg TL. 2011. Culex flavivirus and West Nile virus mosquito coinfection and positive ecological association in Chicago, United States. Vector Borne Zoonotic Dis. 11:1099-1105.
29. Mühldorfer K, Speck S, Kurth A, Lesnik R, Freuling C, Müller T, Kramer-Schadt S, Wibbelt G. 2011. Diseases and causes of death in European bats: dynamics in disease susceptibility and infection Rates. PLoS One 6:e29773. doi:10.1371/journal.pone.0029773.
30. Meyer-König U, Ebert K, Schrage B, Pollak S, Hufert FT. 1998. Simultaneous infection of healthy people with multiple human cytomegalovirus strains. Lancet 352:1280-1281.
31. Haberland M, Meyer-König U, Hufert FT. 1999. Variation within the glycoprotein B gene of human cytomegalovirus is due to homologous recombination. J. Gen. Virol. 80:1495-1500.
32. Thiry E, Meurens F, Muylkens B, McVoy M, Gogev S, Thiry J, Vanderplasschen A, Epstein A, Keil G, Schynts F. 2005. Recombination in alphaherpesviruses. Rev. Med. Virol. 15:89-103.
33. Norberg P, Kasubi MJ, Haarr L, Bergström T, Liljeqvist JA. 2007. Divergence and recombination of clinical herpes simplex virus type 2 isolates. J. Virol. 81:13158-13167.
34. Greenwood AD, Tsangaras K, Ho SY, Szentiks CA, Nikolin VM, Ma G, Damiani A, East ML, Lawrenz A, Hofer H, Osterrieder N. 2012. A potentially fatal mix of herpes in zoos. Curr. Biol. 22:1727-1731.
35. Roycroft E, Rose L, Scallan MF, Crowley B. 2012. Molecular characterization of varicella-zoster virus clinical isolates from 2006 to 2008 in a tertiary care hospital, Dublin, Ireland, using different genotyping methods. J. Med. Virol. 84:1672-1679.
36. Smith LM, McWhorter AR, Shellam GR, Redwood AJ. 2012. The genome of murine cytomegalovirus is shaped by purifying selection and extensive recombination. Virology 435:258-268.
37. Boppana SB, Rivera LB, Fowler KB, Mach M, Britt WJ. 2001. Intrauterine transmission of cytomegalovirus to infants of women with preconceptional immunity. N. Engl. J. Med. 344:1366-1371.
38. Anthony SJ, St Leger JA, Pugliares K, Ip HS, Chan JM, Carpenter ZW, Navarrete-Macias I, Sanchez-Leon M, Saliki JT, Pedersen J, Karesh W, Daszak P, Rabadan R, Rowles T, Lipkin WI. 2012. Emergence of fatal avian influenza in New England harbor seals. mBio 3(4):e00166-12. doi: 10.1128/mBio.00166-12.
39. Chadha MS, Comer JA, Lowe L, Rota PA, Rollin PE, Bellini WJ, Ksiazek TG, Mishra A. 2006. Nipah virus-associated encephalitis outbreak, Siliguri, India. Emerg. Infect. Dis. 12:235-240.
40. ICDDRB. 2008. Outbreaks of Nipah virus in Rajbari and Manikgonj. Health Sci. Bull. 6:12-13.
41. Luby SP, Hossain MJ, Gurley ES, Ahmed BN, Banu S, Khan SU, Homaira N, Rota PA, Rollin PE, Comer JA, Kenah E, Ksiazek TG, Rahman M. 2009. Recurrent zoonotic transmission of Nipah virus into humans, Bangladesh, 2001-2007. Emerg. Infect. Dis. 15:1229-1235.
42. ICDDRB. 2010. Nipah outbreak in Faridpur District, Bangladesh, 2010. Health Sci. Bull. 8:6-11.
43. Arankalle VA, Bandyopadhyay BT, Ramdasi AY, Jadi R, Patil DR, Rahman M, Majumdar M, Banerjee PS, Hati AK, Goswami RP, Neogi DK, Mishra AC. 2011. Genomic characterization of Nipah virus, West Bengal, India. Emerg. Infect. Dis. 17:907-909.
44. Rahman MA, Hossain MJ, Sultana S, Homaira N, Khan SU, Rahman M, Gurley ES, Rollin PE, Lo MK, Comer JA, Lowe L, Rota PA, Ksiazek TG, Kenah E, Sharker Y, Luby SP. 2012. Date palm sap linked to Nipah virus outbreak in Bangladesh, 2008. Vector Borne Zoonotic Dis. 12:65-72.
45. Chua KB, Wang LF, Lam SK, Crameri G, Yu M, Wise T, Boyle D, Hyatt AD, Eaton BT. 2001. Tioman virus, a novel paramyxovirus isolated from fruit bats in Malaysia. Virology 283:215-229.
46. Yaiw KC, Crameri G, Wang L, Chong HT, Chua KB, Tan CT, Goh KJ, Shamala D, Wong KT. 2007. Serological evidence of possible human infection with Tioman virus, a newly described paramyxovirus of bat origin. J. Infect. Dis. 196:884-886.
47. Brahmbhatt M, Dutta A. 2008. On SARS type economic effects during infectious disease outbreaks. Policy research working paper WPS 4466. World Bank, East Asia and Pacific Region, Chief Economist's Office.
48. Newman SH, Field H, de Jong CE, Epstein JH (ed). 2011. Investigating the role of bats in emerging zoonoses: balancing ecology, conservation and public health interests. FAO Animal production and health manual no. 12. FAO, Rome, Italy.
49. Quan PL, Firth C, Street C, Henriquez JA, Petrosov A, Tashmukhamedova A, Hutchison SK, Egholm M, Osinubi MOV, Niezgoda M, Ogunkoya AB, Briese T, Rupprecht CE, Lipkin WI. 2010. Identification of a severe acute respiratory syndrome coronavirus-like virus in a leafnosed bat in Nigeria. mBio 1(4):e00208-10. doi: 10.1128/mBio.00208-10.
50. Tong S, Chern SW, Li Y, Pallansch MA, Anderson LJ. 2008. Sensitive and broadly reactive reverse transcription-PCR assays to detect novel paramyxoviruses. J. Clin. Microbiol. 46:2652-2658.
51. Atkins A, Wellehan JF, Jr, Childress AL, Archer LL, Fraser WA, Citino SB. 2009. Characterization of an outbreak of astroviral diarrhea in a group of cheetahs (Acinonyx jubatus). Vet. Microbiol. 136:160-165.
52. Wellehan JF, Johnson AJ, Harrach B, Benkö M, Pessier AP, Johnson CM, Garner MM, Childress A, Jacobson ER. 2004. Detection and analysis of six lizard adenoviruses by consensus primer PCR provides further evidence of a reptilian origin for the atadenoviruses. J. Virol. 78: 13366-13369.
53. Johne R, Enderlein D, Nieper H, Müller H. 2005. Novel polyomavirus detected in the feces of a chimpanzee by nested broad-spectrum PCR. J. Virol. 79:3883-3887.
54. Kapoor A, Mehta N, Esper F, Poljsak-Prijatelj M, Quan PL, Qaisar N, Delwart E, Lipkin WI. 2010. Identification and characterization of a new bocavirus species in gorillas. PLoS One 5:e11948. doi:10.1371/ journal.pone.0011948.
55. VanDevanter DR, Warrener P, Bennett L, Schultz ER, Coulter S, Garber RL, Rose TM. 1996. Detection and analysis of diverse herpesviral species by consensus primer PCR. J. Clin. Microbiol. 34:1666-1671.
56. Aitichou M, Saleh SS, McElroy AK, Schmaljohn C, Ibrahim MS. 2005. Identification of Dobrava, Hantaan, Seoul, and Puumala viruses by onestep real-time RT-PCR. J. Virol. Methods 124:21-26.
57. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
58. Maes P, Klempa B, Clement J, Matthijnssens J, Gajdusek DC, Krüger DH, Van Ranst M. 2009. A proposal for new criteria for the classification of hantaviruses, based on S and M segment protein sequences. Infect. Genet. Evol. 9:813-820.
59. Jones E, Oliphant T, Peterson P. 2001. SciPy: open source scientific tools for Python. http://www.scipy.org.
60. Gotelli NJ, Colwell RK. 2001. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol. Lett. 4:379-391.
61. Gotelli NJ, Colwell RK. 2011. Estimating species richness, p. 39-54. In Magurran AE, McGill BJ (ed), Biological diversity: Frontiers in measuring biodiversity. Oxford University Press, Oxford, United Kingdom.
62. Vavrek MJ. 2012. Package "fossil." In Palaeoecological and palaeogeographical analysis tools.
63. R Development Core Team. 2012. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
64. The World Bank. 2012. People, pathogens and our planet. Volume 2: The economics of One Health. The World Bank, Washington, DC.