A multiplex reverse transcription PCR and automated electronic microarray assay for detection and differentiation of seven viruses affecting swine

Microarray technology can be useful for pathogen detection as it allows simultaneous interrogation of the presence or absence of a large number of genetic signatures. However, most microarray assays are labour-intensive and time-consuming to perform. This study describes the development and initial evaluation of a multiplex reverse transcription (RT)-PCR and novel accompanying automated electronic microarray assay for simultaneous detection and differentiation of seven important viruses that affect swine (foot-and-mouth disease virus [FMDV], swine vesicular disease virus [SVDV], vesicular exanthema of swine virus [VESV], African swine fever virus [ASFV], classical swine fever virus [CSFV], porcine respiratory and reproductive syndrome virus [PRRSV] and porcine circovirus type 2 [PCV2]). The novel electronic microarray assay utilizes a single, user-friendly instrument that integrates and automates capture probe printing, hybridization, washing and reporting on a disposable electronic microarray cartridge with 400 features. This assay accurately detected and identified a total of 68 isolates of the seven targeted virus species including 23 samples of FMDV, representing all seven serotypes, and 10 CSFV strains, representing all three genotypes. The assay successfully detected viruses in clinical samples from the field, experimentally infected animals (as early as 1 day post-infection (dpi) for FMDV and SVDV, 4 dpi for ASFV, 5 dpi for CSFV), as well as in biological material that were spiked with target viruses. The limit of detection was 10 copies/μl for ASFV, PCV2 and PRRSV, 100 copies/μl for SVDV, CSFV, VESV and 1,000 copies/μl for FMDV. The electronic microarray component had reduced analytical sensitivity for several of the target viruses when compared with the multiplex RT-PCR. The integration of capture probe printing allows custom onsite array printing as needed, while electrophoretically driven hybridization generates results faster than conventional microarrays that rely on passive hybridization. With further refinement, this novel, rapid, highly automated microarray technology has potential applications in multipathogen surveillance of livestock diseases.

Efficacy of accelerated hydrogen peroxide® disinfectant on foot-and-mouth disease virus, swine vesicular disease virus and Senecavirus A

AIMS

In a laboratory, disinfectants used to inactivate pathogens on contaminated surfaces and to prevent spread of diseases often have adverse side effects on personnel and the environment. It is, therefore, essential to find safer, fast-acting and yet effective disinfectants. The objective of this study was to evaluate an accelerated hydrogen peroxide^® (AHP^® )-based disinfectant against high consequence foreign animal disease pathogens such as foot-and-mouth disease virus (FMDV) and swine vesicular disease virus (SVDV), as well as Senecavirus A (SVA), which causes similar lesions as FMDV and SVDV.

METHODS AND RESULTS

We tested varying dilutions and contact times of AHP against FMDV, SVDV and SVA by the standard US EPA and modified methods. AHP was effective against all three viruses, albeit at a higher concentration and double the manufacturer recommended contact time when testing wet films of SVDV.

CONCLUSIONS

AHP is an effective disinfectant against FMDV, SVDV and SVA.

SIGNIFICANCE AND IMPACT OF THE STUDY

AHP-based disinfectant can, therefore, be used in high containment laboratories working with FMDV, SVDV and related pathogens.

Use of Oral Fluids for Detection of Virus and Antibodies in Pigs Infected with Swine Vesicular Disease Virus

The use of swine oral fluid (OF) for the detection of nucleic acids and antibodies is gaining significant popularity. Assays have been developed for this purpose for endemic and foreign animal diseases of swine. Here, we report the use of OF for the detection of virus and antibodies in pigs experimentally infected with swine vesicular disease virus (SVDV), a virus that causes a disease clinically indistinguishable from the economically devastating foot-and-mouth disease. Viral genome was detected in OF by real-time reverse transcription polymerase chain reaction (RRT-PCR) from 1 day post-infection (DPI) to 21 DPI. Virus isolation from OF was also successful at 1-5 DPI. An adapted competitive ELISA based on the monoclonal antibodies 5B7 detected antibodies to SVDV in OF starting at DPI 6. Additionally, using isotype-specific indirect ELISAs, SVDV-specific IgM and IgA were evaluated in OF. IgM response started at DPI 6, peaking at DPI 7 or 14 and declining sharply at DPI 21, while IgA response started at DPI 7, peaked at DPI 14 and remained high until the end of the experiment. These results confirm the potential use of OF for SVD surveillance using both established and partially validated assays in this study.

Field-Deployable Reverse Transcription-Insulated Isothermal PCR (RT-iiPCR) Assay for Rapid and Sensitive Detection of Foot-and-Mouth Disease Virus

Foot‐and‐mouth disease (FMD) is a highly contagious viral disease of cloven‐hoofed animals, which can decimate the livestock industry and economy of countries previously free of this disease. Rapid detection of foot‐and‐mouth disease virus (FMDV) is critical to containing an FMD outbreak. Availability of a rapid, highly sensitive and specific, yet simple and field‐deployable assay would support local decision‐making during an FMDV outbreak. Here we report validation of a novel reverse transcription‐insulated isothermal PCR (RT‐iiPCR) assay that can be performed on a commercially available, compact and portable POCKIT^™ analyser that automatically analyses data and displays ‘+’ or ‘−’ results. The FMDV RT‐iiPCR assay targets the 3D region of the FMDV genome and was capable of detecting 9 copies of in vitro‐transcribed RNA standard with 95% confidence. It accurately identified 63 FMDV strains belonging to all seven serotypes and showed no cross‐reactivity with viruses causing similar clinical diseases in cloven‐hoofed animals. The assay was able to identify FMDV RNA in multiple sample types including oral, nasal and lesion swabs, epithelial tissue suspensions, vesicular and oral fluid samples, even before the appearance of clinical signs. Clinical sensitivity of the assay was comparable or slightly higher than the laboratory‐based real‐time RT‐PCR assay in use. The assay was able to detect FMDV RNA in vesicular fluid samples without nucleic acid extraction. For RNA extraction from more complex sample types, a commercially available taco^™ mini transportable magnetic bead‐based, automated extraction system was used. This assay provides a potentially useful field‐deployable diagnostic tool for rapid detection of FMDV in an outbreak in FMD‐free countries or for routine diagnostics in endemic countries with less structured laboratory systems.

Plant-derived H7 VLP vaccine elicits protective immune response against H7N9 influenza virus in mice and ferrets

In March 2013, the Chinese Centre for Disease Control and Prevention confirmed the first reported case of human infection with an avian influenza A H7N9 virus. Infection with this virus often caused severe pneumonia and acute respiratory distress syndrome resulting in a case fatality rate >35%. The risk of pandemic highlighted, once again, the need for a more rapid and scalable vaccine response capability. Here, we describe the rapid (19 days) development of a plant-derived VLP vaccine based on the hemagglutinin sequence of influenza H7N9 A/Hangzhou/1/2013. The immunogenicity of the H7 VLP vaccine was assessed in mice and ferrets after one or two intramuscular dose(s) with and without adjuvant (alum or GLA-SE™). In ferrets, we also measured H7-specific cell-mediated immunity. The mice and ferrets were then challenged with H7N9 A/Anhui/1/2013 influenza virus. A single immunization with the adjuvanted vaccine elicited a strong humoral response and protected mice against an otherwise lethal challenge. Two doses of unadjuvanted vaccine significantly increased humoral response and resulted in 100% protection with significant reduction of clinical signs leading to nearly asymptomatic infections. In ferrets, a single immunization with the alum-adjuvanted H7 VLP vaccine induced strong humoral and CMI responses with antigen-specific activation of CD3(+) T cells. Compared to animals injected with placebo, ferrets vaccinated with alum-adjuvanted vaccine displayed no weight loss during the challenge. Moreover, the vaccination significantly reduced the viral load in lungs and nasal washes 3 days after the infection. This candidate plant-made H7 vaccine therefore induced protective responses after either one adjuvanted or two unadjuvanted doses. Studies are currently ongoing to better characterize the immune response elicited by the plant-derived VLP vaccines. Regardless, these data are very promising for the rapid production of an immunogenic and protective vaccine against this potentially pandemic virus.

Review of Ebola virus infections in domestic animals

Ebola viruses (EBOV; genus Ebolavirus, family Filoviridae) cause often fatal, hemorrhagic fever in several species of simian primates including human. While fruit bats are considered a natural reservoir, the involvement of other species in the EBOV transmission cycle is unclear, especially for domesticated animals. Dogs and pigs are so far the only domestic animals identified as species that can be infected with EBOV. In 2009 Reston-EBOV was the first EBOV reported to infect swine with indicated transmission to humans; and a survey in Gabon found over 30% seroprevalence for EBOV in dogs during the Ebola outbreak in 2001-2002. While infections in dogs appear to be asymptomatic, pigs experimentally infected with EBOV can develop clinical disease, depending on the virus species and possibly the age of the infected animals. In the experimental settings, pigs can transmit Zaire-Ebola virus to naive pigs and macaques; however, their role during Ebola outbreaks in Africa needs to be clarified. Attempts at virus and antibody detection require as a prerequisite validation of viral RNA and antibody detection methods especially for pigs, as well as the development of a sampling strategy. Significant issues about disease development remain to be resolved for EBOV. Evaluation of current human vaccine candidates or development of veterinary vaccines de novo for EBOV might need to be considered, especially if pigs or dogs are implicated in the transmission of an African species of EBOV to humans.

Molecular and antigenic characterization of triple-reassortant H3N2 swine influenza viruses isolated from pigs, turkey and quail in Canada

In 2005, triple-reassortant H3N2 (trH3N2) influenza A viruses were isolated from swine and turkeys in Canada. Subsequently, these viruses were isolated from humans and mink in 2006 and 2007, respectively. Following full genome sequencing, H3N2 viruses isolated from turkeys (2005), quail (2008) and swine (2009) in Canada, were characterized as trH3N2. The 2005 turkey isolate was found to be almost identical to other viruses isolated in that year, with quail and pig isolates related very closely to the 2005 trH3N2. Minimal antigenic evolution of the swine isolates relative to the reference 2005 virus was observed. These results suggest the establishment of a stable lineage of trH3N2 in Canadian pigs, with evidence for interspecies transmission to turkeys and quails.

Geographical and age-stratified distributions of foot-and-mouth disease virus-seropositive and probang-positive cattle herds in the Adamawa province of Cameroon

Six of the seven known serotypes of foot-and-mouth disease (FMD) virus occur in Africa. This paper describes the results of a population-based cross-sectional study of the seroprevalence of FMD and the persistence of the virus in cattle herds and associated sheep flocks in the Adamawa province of Cameroon. Antibody titres measured by the virus neutralising test indicated that serotypes O, A and SAT2 viruses had been circulating in the province. The estimates of apparent seroprevalence in cattle herds, based on five juvenile animals (eight to 24 months old) per herd, were 74.8 per cent for serotype SAT2, 30.8 per cent for serotype A and 11.2 per cent for serotype O, indicating recent exposure; the estimates based on animals more than 24 months of age were 91.1 per cent for SAT2, 83.6 per cent for A and 34.2 per cent for serotype O. Epithelial and oropharyngeal samples were collected from cattle and small ruminants, cultured and typed by ELISA; serotypes A and SAT2 were isolated from both types of sample. The herd-level estimate of apparent prevalence of probang-positive herds was 19.5 per cent and the animal-level estimate of apparent prevalence was 3.4 per cent. The geographical distribution of the seropositive herds based on juveniles suggested that recent SAT2 exposure was widespread and particularly high in the more northern and western parts of the province, whereas recent exposure to serotype A was patchy and more concentrated in the south and east. This distribution corresponded very closely with the distribution of herds from which virus was recovered by probang, indicating recent exposure or infection. No serotype O viruses were recovered from cattle, and the distribution of seropositive herds suggested very localised recent exposure. The apparent prevalence of probang-positive animals declined with the age of the animal and the period since the last recorded outbreak in the herd.

Risk factors for herdsman-reported foot-and-mouth disease in the Adamawa Province of Cameroon

We analysed responses from 147 Fulani herdsmen to a questionnaire about cattle herd-level risk factors for foot-and-mouth disease (FMD) in the previous year. The study used a cross-sectional design with a stratified, two-stage random sample of cattle herds in the Adamawa Province of Cameroon. The questionnaire was pre-tested at a local cattle market before a final version was translated into Foulfoulde (the local Fulani dialect). Variables were screened using a univariable analysis and logistic multiple-regression models were developed in a forward-selection process. Fifty-eight percent (50-65; 90% CIs) of herdsmen reported FMD in their herd in the previous 12 months. Important risk factors for FMD in the previous 12 months included going on transhumance (OR=2.6), buying cattle from markets (OR=2.2), mixing of herds at watering points (OR=2.4), feeding cotton-seed cake (OR=3.3), buffalo near the herd (OR=2.2) and administrative division. For the subset of herds that went on transhumance, coming in contact with an FMDV-diseased herd while on transhumance was the strongest factor (OR=16).

Molecular epidemiology of foot-and-mouth disease viruses in the Adamawa province of Cameroon

Foot-and-mouth disease virus (FMDV) causes a highly contagious viral disease of even-toed ungulates and is one of the most important economic diseases of livestock. Most studies of FMDV are done in countries where control measures are being implemented. In contrast, in areas such as sub-Saharan Africa, where FMDV is endemic and new strains are likely to emerge, there are only sporadic submissions to the World Reference Laboratory, Pirbright, United Kingdom. This paper describes the molecular epidemiology of FMDV in the Adamawa province of Cameroon based on a population sample of cattle herds. Serotypes SAT2 and A were isolated in the cross-sectional study. SAT2 isolates were all similar, with phylogenetic distances of <6%, and were most closely related to published sequences of isolates from Eritrea and Saudi Arabia. Serotype A isolates were more variable, with phylogenetic distances of 0 to 11%, and were most closely related to historic isolates from Cameroon. Use of a population-based sample gives a representative sample of virus diversity and will improve our understanding of the evolution of FMDV and its epidemiology. A supplementary study of pigs passing through the railhead collection yard at Ngaoundere detected a serotype O virus. A third pilot longitudinal study monitored viral persistence in three cattle herds over 12 months, and serotype O and A viruses were recovered from a herd 12 months after it was first recorded as being infected with SAT2 virus. The pig type O isolate was not closely related to that recovered from the cattle, suggesting that the pigs had not introduced the O virus into the cattle herds.

Foot and mouth disease and livestock husbandry practices in the Adamawa Province of Cameroon

Foot and mouth disease (FMD) is a highly contagious viral disease of even-toed ungulates and is endemic in most of the tropics. A cross-sectional study using a stratified, two-stage random sample design was undertaken in the Adamawa Province of Cameroon. The objectives were to measure the reported herd-level prevalence of FMD and a range of husbandry practices important for its transmission. The owner-reported prevalence for the previous 12 months was 57.9% (50.4-65.4%), although there was a significant variation across the Province. During the previous dry season, 46.5% (38.6-54.4%) of herds had gone on transhumance. Herds had high numbers of contacts with other herds while on transhumance (98.6%), at pasture (95.8%) and at night (74.4%), with medians of 7-10, 4-6 and 1-3 daily contacts, respectively. The high level of endemic FMD and potential for disease spread presents a significant challenge for control and eradication. Locally sustainable methods need to be developed upon which larger regional control programmes could be built in the future.