Impact of seasonal temperature transition, alkalinity and other abiotic factors on the persistence of viruses in swine and dairy manures.

Animal manures are a valued source of nutrients for crop production. They frequently do, however, contain zoonotic pathogens including a wide range of viruses. Ideally, manures would be treated prior to land application, reducing the burden of zoonotic viruses, and thus the potential for transmission to adjacent water resources or crops intended for human or animal consumption. In the present study, manure was obtained from four dairy and three swine farms. The manure was incubated anaerobically in the laboratory for 28 weeks at temperatures ranging from 4 to 25 °C, and multiple physical and chemical parameters were monitored. The abundance of various DNA and RNA viruses was measured throughout the incubation by amplifying virus-specific gene targets. A combination of statistical analyses were applied to identify whether the viruses are significantly impacted by temperature transition or affected by other abiotic factors. Temperature had no effect on the persistence of any of the viruses studied. An increase in pH of the manures during the incubation was significantly (P < 0.05) associated with decreased persistence, suggesting that pH manipulation during storage could reduce the abundance of viruses.

Frequency of hepatitis E virus, rotavirus and porcine enteric calicivirus at various stages of pork carcass processing in two pork processing plants.

Hepatitis E virus (HEV), rotavirus (RV), and porcine enteric calicivirus (PEC) infections are common in swine and raises concerns about the potential for zoonotic transmission through undercooked meat products. Enteric viruses can potentially contaminate carcasses during meat processing operations. There is a lack of information on the prevalence and control of enteric viruses in the pork processing chain. This study compared the incidence and levels of contamination of hog carcasses with HEV, RV and PEC at different stages of the dressing process. A total of 1000 swabs were collected from 2 pork processing plants on 10 separate occasions over the span of a year. The samples were obtained from random sites on hog carcasses at 4 dressing stages (plant A: bleeding, dehairing, pasteurization, and evisceration; plant B: bleeding, skinning, evisceration, and washing) and from meat cuts. Numbers of genome copies (gc) of HEV, RV and PEC were determined by RT-qPCR. RV and PEC were detected in 100%, and 18% of samples, respectively, after bleeding for plant A and in 98%, and 36% of samples, respectively, after bleeding for plant B. After evisceration, RV and PEC were detected in 21% and 3% of samples, respectively, for plant A and in 1%, and 0% of samples, respectively for plant B. RV and PEC were detected on 1%, and 5% of pork cuts, respectively, for plant A and on 0%, and 0% of pork cuts, respectively, for plant B. HEV was not detected in any pork carcass or retail pork samples from plants A or B. The frequency of PEC and RV on pork is progressively reduced along the pork processing chain but the viruses were not completely eliminated. The findings suggest that consumers could be at risk when consuming undercooked meat contaminated with pathogenic enteric viruses.

F-coliphages, porcine adenovirus and porcine teschovirus as potential indicator viruses of fecal contamination for pork carcass processing.

There are concerns about the zoonotic transmission of viruses through undercooked pork products. There is a lack of information on suitable indicator viruses for fecal contamination with pathogenic enteric viruses in the meat processing chain. The study compared the incidence and levels of contamination of hog carcasses with F-coliphages, porcine teschovirus (PTV), and porcine adenovirus (PAdV) at different stages of the dressing process to assess their potential as indicator viruses of fecal contamination. One hundred swab samples (200cm2) were collected from random sites on hog carcasses at 4 different stages of the dressing process and from retail pork over the span of a year from 2 pork processing plants (500/plant). Viable F-coliphages, PAdV DNA and PTV RNA were each detected on ≥99% of the incoming carcasses at both plants and were traceable through the pork processing chain. Significant correlations were observed between viable F-coliphages and PAdV DNA and between F-coliphages and PTV RNA but not between PAdV DNA and PTV RNA at the various stages of pork processing. Detection of viable F-coliphages was more sensitive than genomic copies of PAdV and PTV at low levels of contamination, making F-coliphages a preferred indicator in the pork slaughter process as it also provides an indication of infectivity. For plant A, F-RNA coliphages were detected in 25%, 63%, and 21% of carcass swabs after pasteurization, evisceration, and retail pork products, respectively. For plant B, F-coliphages were detected in 33%, 25%, and 13% of carcass swabs after skinning, evisceration, and retail pork samples, respectively. Viable F-RNA coliphages were genotyped. Viable F-RNA GII and GIII were generally not detected at the earlier stages of the slaughter process but they were detected on 13% of carcasses after evisceration and 2% of retail pork samples at plant A, which raises concerns of potential food handler contamination during pork processing. Consumers could be at risk when consuming undercooked meat contaminated with pathogenic enteric viruses.

Survey of Canadian retail pork chops and pork livers for detection of hepatitis E virus, norovirus, and rotavirus using real time RT-PCR.

Over the past 15 years, hepatitis E virus (HEV), norovirus (NoV), and rotavirus (RV) have been hypothesized to be potentially zoonotic; swine and pork have been suggested as possible human infection sources for all 3 viruses. Our objective was to estimate HEV, NoV, and RV prevalence and load on Canadian retail pork chops and livers. Using the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) sampling platform, pork livers (n=283) and chops (n=599) were collected, processed, and assayed for the 3 viruses by four collaborating federal laboratories using validated real time reverse transcriptase polymerase chain reactions (qRT-PCR). Follow-up qRT-PCR estimating viral load in genomic copies/g was followed by nested classical RT-PCR and isolate sequencing of a partial segment of the ORF2 gene. Local alignments were performed using MUSCLE (Multiple Sequence Comparison by Log-Expectation); a phylogenetic tree was created. Twenty-five livers and 6 chops were classified 'positive' (thresholds for viral RNA detected in both replicates of the assay) or 'suspect' (thresholds detected in one of two replicates) for HEV. Follow-up qRT-PCR detected HEV on 16 livers, 0 chops, and nested classical RT-PCR, on 14 livers and 0 chops. Initial qRT-PCR classified 12 chops 'suspect' for NoV. Follow-up qRT-PCR detected viral RNA on only one sample with thresholds greater than 40 in both replicates. No amplicon was yielded, and therefore no isolate was sequenced from this sample. Partial ORF2 genes from 14 HEV isolates were sequenced, and compared via sequence identity and phylogenetic analysis with selected human case isolates listed in NCBI-GenBank. Overall, HEV prevalence on retail pork was comparable with other published reports.

Presence, viral load and characterization of Torque teno sus viruses in liver and pork chop samples at retail.

Torque teno viruses (TTV) are widespread in humans, swine as well as in several other animal species. In market ready swine, the reported prevalence ranges between 11% and 100%. Through a national retail sampling plan from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) program, 283 and 599 liver and pork chop samples, respectively, were collected over a 12-month period from commercial establishments in 5 selected geographical regions of Canada to assess the presence of Torque teno sus viruses (TTSuVs) in these products. TTSuVs were detected in 97.9% of pork chops with viral loads ranging between 1×10(4) and 9.9×10(5) genomic copies (gc)/g and 98.6% of liver samples with viral loads ranging from 1×10(5) to 9.9×10(6) gc/g. A selection of 20 positive samples (10 pork chop and 10 liver) from the 5 geographical regions were further tested for the production, of a 305bp fragment for TTSuV1 and a 253bp fragment for TTSuV2 in the non-coding region. TTSuV1 was present in all 10 liver and 10 pork chops samples while TTSuV2 was detected in 10 liver and 9 pork chop samples. Two different TTSuV1 sequences were simultaneously detected from 5 of 20 samples and 2 different TTSuV2 sequences were detected from 6 of 19 samples. The omnipresence of TTSuVs in commercial pork samples may allow its use as a viral indicator to monitor the effectiveness of cleaning and disinfecting process in slaughtering, cutting, slicing and packaging facilities.