Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing

Biologicals

Volumn 43, Issue 1, 2015, Pages 31-36

  Dumarest, Marine ^a   Muth, Erika ^b   Cheval, Justine ^b   Gratigny, Marlène ^b   Hébert, Charles ^b   Gagnieur, Léa ^a   Eloit, Marc ^a,b,c  

^a INSTITUT PASTEUR   (France)

^b PathoQuest   (France)

^c ECOLE NATIONALE VÉTÉRINAIRE D ALFORT   (France)

Author keywords

Gut; Heparin; High throughput sequencing; Metagenomics; Pig; Virus

Indexed keywords

HEPARIN; PRIMER DNA;

ADENOVIRIDAE; ANELLOVIRIDAE; ARTICLE; ASTROVIRUS; BIRNAVIRIDAE; CALICIVIRUS; CIRCOVIRIDAE; DRUG CONTAMINATION; DRUG MANUFACTURE; HIGH THROUGHPUT SEQUENCING; INTESTINAL MUCUS; MICROBIAL DIVERSITY; MUCUS; NONHUMAN; PARVOVIRIDAE; PICORNAVIRIDAE; POLYMERASE CHAIN REACTION; REOVIRIDAE; SWINE; VIRUS; VIRUS LOAD; ANIMAL; BIOSYNTHESIS; CLASSIFICATION; HIGH THROUGHPUT SCREENING; INTESTINE; NUCLEOTIDE SEQUENCE; PIG; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; VIROLOGY;

ADENOVIRIDAE; ANIMALIA; ASTROVIRIDAE; BIRNAVIRIDAE; CALICIVIRIDAE; CIRCOVIRIDAE; PARVOVIRIDAE; PICORNAVIRIDAE; REOVIRIDAE; SUIDAE;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; HEPARIN; HIGH-THROUGHPUT SCREENING ASSAYS; INTESTINES; MUCUS; REAL-TIME POLYMERASE CHAIN REACTION; SWINE; VIRUSES;

EID: 84921498214     PISSN: 10451056     EISSN: 10958320     Source Type: Journal    
DOI: 10.1016/j.biologicals.2014.10.004     Document Type: Article

References (37)

1. Linhardt R.J., Gunay N.S. Production and chemical processing of low molecular weight heparins. Semin Thromb Hemost 1999, 25(Suppl.3):5-16.
2. Liu H., Zhang Z., Linhardt R.J. Lessons learned from the contamination of heparin. Nat Prod Rep 2009, 26:313-321. 10.1039/b819896a.
3. Sauvage V., Ar Gouilh M., Cheval J., Muth E., Pariente K., Burguiere A., et al. Amember of a new picornaviridae genus is shed in pig feces. JVirol 2012, 86:10036-10046. 10.1128/JVI.00046-12.
4. Cheung A.K., Ng T.F., Lager K.M., Bayles D.O., Alt D.P., Delwart E.L., et al. Adivergent clade of circular single-stranded DNA viruses from pig feces. Arch Virol 2013, 158:2157-2162. 10.1007/s00705-013-1701-z.
5. Lager K.M., Ng T.F., Bayles D.O., Alt D.P., Delwart E.L., Cheung A.K. Diversity of viruses detected by deep sequencing in pigs from a common background. JVet Diagn Invest 2012, 24:1177-1179. 10.1177/1040638712463212.
6. Shan T., Li L., Simmonds P., Wang C., Moeser A., Delwart E. The fecal virome of pigs on a high-density farm. JVirol 2011, 85:11697-11708. 10.1128/JVI.05217-11.
7. Li L., Kapoor A., Slikas B., Bamidele O.S., Wang C., Shaukat S., et al. Multiple diverse circoviruses infect farm animals and are commonly found in human and chimpanzee feces. JVirol 2010, 84:1674-1682. 10.1128/JVI.02109-09.
8. Mokili J.L., Rohwer F., Dutilh B.E. Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2012, 2:63-77. 10.1016/j.coviro.2011.12.004.
9. Lecuit M., Eloit M. The diagnosis of infectious diseases by whole genome next generation sequencing: a new era is opening. Front Cell Infect Microbiol 2014, 4:25. 10.3389/fcimb.2014.00025.
10. Bodemer C., Sauvage V., Mahlaoui N., Cheval J., Couderc T., Leclerc-Mercier S., et al. Live rubella virus vaccine long-term persistence as an antigenic trigger of cutaneous granulomas in patients with primary immunodeficiency. Clin Microbiol Infect 2014, 10.1111/1469-0691.12573.
11. Capobianchi M.R., Giombini E., Rozera G. Next-generation sequencing technology in clinical virology. Clin Microbiol Infect 2013, 19:15-22. 10.1111/1469-0691.12056.
12. McClenahan S.D., Uhlenhaut C., Krause P.R. Optimization of virus detection in cells using massively parallel sequencing. Biologicals 2014, 42:34-41. 10.1016/j.biologicals.2013.11.002.
13. Cheval J., Sauvage V., Frangeul L., Dacheux L., Guigon G., Dumey N., et al. Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples. JClin Microbiol 2011, 49:3268-3275. 10.1128/JCM.00850-11.
14. Sauvage V., Foulongne V., Cheval J., Ar Gouilh M., Pariente K., Dereure O., et al. Human polyomavirus related to African green monkey lymphotropic polyomavirus. Emerg Infect Dis 2011, 17:1364-1370. 10.3201/eid1708.110278.
15. Sauvage V., Cheval J., Foulongne V., Gouilh M.A., Pariente K., Manuguerra J.C., et al. Identification of the first human gyrovirus, a virus related to chicken anemia virus. JVirol 2011, 85:7948-7950. 10.1128/JVI.00639-11.
16. Gagnieur L, Cheval J, Gratigny M, Hébert C, Muth E, Dumarest M, etal. Unbiased analysis by high throughput sequencing of the viral diversity in fetal bovine serum and trypsin used in cell culture. Biologicals. 10.1016/j.biologicals.2014.02.002.
17. Phan T.G., Kapusinszky B., Wang C., Rose R.K., Lipton H.L., Delwart E.L. The fecal viral Flora of Wild Rodents. PLoS Pathog 2011, 7:e1002218. 10.1371/journal.ppat.1002218.
18. Berthet N., Reinhardt A.K., Leclercq I., van Ooyen S., Batéjat C., Dickinson P., et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Mol Biol 2008, 9:77. 10.1186/1471-2199-9-77.
19. Naccache S.N., Greninger A.L., Lee D., Coffey L.L., Phan T., Rein-Weston A., et al. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. JVirol 2013, 87:11966-11977. 10.1128/JVI.02323-13.
20. Smuts H., Kew M., Khan A., Korsman S. Novel hybrid parvovirus-like virus, NIH-CQV/PHV, contaminants in silica column-based nucleic acid extraction kits. JVirol 2014, 88:1398. 10.1128/JVI.03206-13.
21. Baker K.S., Leggett R.M., Bexfield N.H., Alston M., Daly G., Todd S., et al. Metagenomic study of the viruses of African straw-coloured fruit bats: detection of a chiropteran poxvirus and isolation of a novel adenovirus. Virology 2013, 441:95-106. 10.1016/j.virol.2013.03.014.
22. Cheung A.K., Ng T.F.-F., Lager K.M., Alt D.P., Delwart E.L., Pogranichniy R.M. Unique circovirus-like genome detected in pig feces. Genome Announc 2014, 2. 10.1128/genomeA.00251-14.
23. Allan G.M., McNeilly F., Kennedy S., Daft B., Clarke E.G., Ellis J.A., et al. Isolation of porcine circovirus-like viruses from pigs with a wasting disease in the USA and Europe. JVet Diagn Invest 1998, 10:3-10.
24. Shan T., Lan D., Li L., Wang C., Cui L., Zhang W., et al. Genomic characterization and high prevalence of bocaviruses in swine. PLoS One 2011, 6:e17292. 10.1371/journal.pone.0017292.
25. Jiang Y.-H., Xiao C.-T., Yin S.-H., Gerber P.F., Halbur P.G., Opriessnig T. High prevalence and genetic diversity of porcine bocaviruses in pigs in the USA, and identification of multiple novel porcine bocaviruses. JGen Virol 2014, 95:453-465. 10.1099/vir.0.057042-0.
26. Zell R., Scholtissek C., Ludwig S. Genetics, evolution, and the zoonotic capacity of European Swine influenza viruses. Curr Top Microbiol Immunol 2013, 370:29-55. 10.1007/82_2012_267.
27. Christou L., Kosmidou M. Hepatitis E virus in the Western world-a pork-related zoonosis. Clin Microbiol Infect 2013, 19:600-604. 10.1111/1469-0691.12214.
28. Rivera-Benitez J.F., Rosas-Estrada K., Pulido-Camarillo E., de la Peña-Moctezuma A., Castillo-Juárez H., Ramírez-Mendoza H. Serological survey of veterinarians to assess the zoonotic potential of three emerging swine diseases in Mexico. Zoonoses Public Health 2014, 61:131-137. 10.1111/zph.12055.
29. Midgley S.E., Bányai K., Buesa J., Halaihel N., Hjulsager C.K., Jakab F., et al. Diversity and zoonotic potential of rotaviruses in swine and cattle across Europe. Vet Microbiol 2012, 156:238-245. 10.1016/j.vetmic.2011.10.027.
30. Bank-Wolf B.R., König M., Thiel H.-J. Zoonotic aspects of infections with noroviruses and sapoviruses. Vet Microbiol 2010, 140:204-212. 10.1016/j.vetmic.2009.08.021.
31. Cabannes E., Hebert C., Eloit M. Whole genome- next generation sequencing as a virus safety test for biotechnological products 2014, Proceedings from the 2013 PDA/FDA advanced technologies for virus detection Conference - Special Issue of the PDA Journal, [In Press].
32. Ben Salem A.N., Chupin Sergei A., Bjadovskaya Olga P., Andreeva Olga G., Mahjoub A., Prokhvatilova Larissa B. Multiplex nested RT-PCR for the detection of porcine enteric viruses. JVirol Methods 2010, 165:283-293. 10.1016/j.jviromet.2010.02.010.
33. Halaihel N., Masía R.M., Fernández-Jiménez M., Ribes J.M., Montava R., De Blas I., et al. Enteric calicivirus and rotavirus infections in domestic pigs. Epidemiol Infect 2010, 138:542-548. 10.1017/S0950268809990872.
34. Puvanendiran S., Stone S., Yu W., Johnson C.R., Abrahante J., Jimenez L.G., et al. Absence of porcine circovirus type 1 (PCV1) and high prevalence of PCV 2 exposure and infection in swine finisher herds. Virus Res 2011, 157:92-98. 10.1016/j.virusres.2011.02.012.
35. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8:275-282.
36. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739. 10.1093/molbev/msr121.
37. Cotmore S.F., Agbandje-McKenna M., Chiorini J.A., Mukha D.V., Pintel D.J., Qiu J., et al. The family parvoviridae. Arch Virol 2014, 159:1239-1247. 10.1007/s00705-013-1914-1.