High-throughput sequencing revealed the presence of an unforeseen parvovirus species in Canadian swine: the porcine partetravirus.

摘要: During the course of a research project on full viral genome sequencing porcine reproductive and respiratory syndrome (PRRS) virus, 62 samples swine sera were collected from piglets various Canadian farms that experiencing PRRS outbreaks. In order to lower contamination serum by host (i.e., genome) for high-throughput (HTS) procedure, particles purified ultracentrifugation (113 000 × g 20% sucrose cushion) followed nuclease treatment (1 h at 37°C with 500 μg/mL DNase 250 RNase A). The was then extracted Trizol reagent (Invitrogen, Burlington, Ontario) according manufacturer’s recommended procedure. Genomic material subjected random polymerase chain reaction (PCR) amplification as previously described (1). Qualitative quantitative evaluations products respectively assessed agarose gel electrophoresis real-time PCR (EZ-PRRSVTM MPX 4.0 Real Time RT-PCR Target-Specific Reagents Rapid Identification Differentiation North American European Viral RNA, Tetracore, Rockville, Maryland, USA). Based those results, total 11 samples, comprised 6 Quebec, 4 Ontario, 1 Alberta, selected sent “Institut de biologie integrative et des systemes” (IBIS) HTS (Table 1). For each sample, GS-FLX rapid library produced amplified genomic using instructions provided kit (Roche/454 Sequencing, Brandford, Connecticut, Emulsion titanium performed Sequencing) Plateforme d’Analyses Genomiques IBIS (Laval University, Quebec City, Quebec). Raw reads assembled gsAssembler module Newbler v.2.5.3. Table 1 Description virus positive tested their partetravirus status In addition sequences, results revealed presence parvovirus highly similar (a also known hokovirus, PARV4-like 3) in one Ontario Parvoviruses are small non-enveloped icosahedral viruses linear single-stranded DNA about 6.3 kb (2,3). this result, prevalence herds established be 9.09% However, estimate Canada may biased because: i) regards status, ii) number low, iii) geographical origins did not accurately represent overall industry. To our knowledge, has never been isolated cell culture, although isolation attempted Lau al (2008) Streck (2013)(4,5). Currently, 5 parvoviruses (PPV) have identified swine: par-vovirus (PPV1), PPV2, (PPV3), PPV4, PPV5, which recently reported United States (2). When compared another, PPV1 through PPV5 substantial genetic divergence. is genomically related human (60% 65% nucleotide homology). Human 2005 plasma sample homeless drug user who had an acute infection (6). first time China 2008 (4). Since then, other countries, including States, Great Britain, Romania, Hungary, Germany (4,7–10). Canada. The strain, named FMV10-1437266, possesses length 5402 nucleotides (nt) (GenBank accession {"type":"entrez-nucleotide","attrs":{"text":"KC992732","term_id":"530452842","term_text":"KC992732"}}KC992732) GC content 51.29%. After FMV10-1437266 sequence 938 reads, mean coverage 48 per nt (minimum 8 maximum 85 reads). strain nearly 300 larger than longest 2009 {"type":"entrez-nucleotide","attrs":{"text":"EU200677","term_id":"164710113","term_text":"EU200677"}}EU200677). This increased gives better insight into inverted terminal repeats (ITR) found both 5′ 3′ ends genome. ITR involved replication (3). comparison sequences gathered GenBank database identities varying between 95.4% 99.3% (data shown), accordance previous reports (5,8,10,11). A phylogenetic tree (Figure 1) constructed neighbor-joining method 1000 bootstrap replicates Geneious Pro (version 5.6.6) software. done common all (which correspond positions 292 5074 FMV10-1437266). Phylogenetic analysis USA detected Iowa 2011 {"type":"entrez-nucleotide","attrs":{"text":"JQ425257","term_id":"394987188","term_text":"JQ425257"}}JQ425257). USA, Carolina (7). Figure 1 Phylogenetic strains. generated V5.6.6 software resampling (1000 replications) ... The classical (PPV1) important pathogen associated disorders sows widely distributed around world, (10). identification novel (such partetravirus, PPV5) raises concerns potential involvement health manifestations clinical signs or disease. At present, data sparse unknown (12). Porcine etiological agent disease currently considered non-pathogenic. Nonetheless, Dr. Opriessnig’s team pigs diseases, systemic/central nervous system enteric diseases 14.4%, 11.6%, 2.7%, (7). These suggest these systems but still needs proven. blood pharmaceutical by-products such Factor VIII (FVIII). Porcine-derived FVIII being used treat autoimmune hemophilia patients possess antibodies against FVIII. Thus, subsequently threat (11). swine, adult nursery pigs, fetuses suckling near future, experiments will conducted establish precision population. Moreover, further needed ascertain diseases.