Molecular Epidemiology Questions Transmission Pathways Identified During the Year 2000 Outbreak of Classical Swine Fever in the UK

The last outbreak of classical swine fever (CSF) in the UK occurred in 2000. A total of 16 domestic pig holdings in the East Anglia region were confirmed as infected over a 3-month period. Obtaining viral genome sequences has since become easier and more cost-effective and has accordingly been applied to trace viral transmission events for a variety of viruses. The rate of genetic evolution varies for different viruses and is influenced by different transmission events, which will vary according to the epidemiology of an outbreak. To examine if genetic changes over the course of any future CSF outbreak would occur to supplement epidemiological investigations and help to track virus movements, the E2 gene and full genome of the virus present in archived tonsil samples from 14 of these infected premises were sequenced. Insufficient changes occurred in the full E2 gene to discriminate between the viruses from the different premises. In contrast, between 5 and 14 nucleotide changes were detected between the genome sequence of the virus from the presumed index case and the sequences from the other 13 infected premises. Phylogenetic analysis of these full CSFV genome sequences identified clusters of closely related viruses that allowed to corroborate some of the transmission pathways inferred by epidemiological investigations at the time. However, other sequences were more distinct and raised questions about the virus transmission routes previously implicated. We are thus confident that in future outbreaks, real-time monitoring of the outbreak via full genome sequencing will be beneficial.

Costs of multidrug-resistant TB treatment in Finland and Estonia affected by the 2019 WHO guidelines

BACKGROUND:

Multidrug-resistant TB (MDR-TB) is a growing problem in the effort to end the global TB epidemic. In 2019, the WHO adopted a new standardised regiment for MDR-TB, consisting of only oral medications.

METHODS:

We estimated the impact of the new guidelines on the costs of TB treatment in Estonia and Finland. For both countries, the costs of the two most common new drug regimens were calculated, including drug costs, as well as care- and monitoring-related costs.

RESULTS:

In Turku, Finland, treatment costs with the old regimen were €178,714; this could either increase by 10% or decrease by 18%, depending on the duration of bedaquiline use (6 months vs. 20 months). In Estonia, treatment costs with the old regimen were €33,664, whereas the new regimens were associated with a 40% increase in overall costs.

CONCLUSIONS:

The 2019 WHO guidelines have led to significant changes in the costs of MDR-TB treatment in Finland and Estonia. These changes depend mostly on the drug regimen administered and on care-related practices, with important differences between countries and even within the same country due to local practices.

First detection of Hepatitis E virus (Orthohepevirus C) in wild brown rats (Rattus norvegicus) from Great Britain

In the United Kingdom, there has been an increase in the number of hepatitis E virus (HEV) infections in people annually since 2010. Most of these are thought to be indigenously acquired Orthohepevirus A genotype 3 (HEV G3), which has been linked to pork production and consumption. However, the dominant subgroup circulating in British pigs differs from that which is found in people; therefore, an alternative, potentially zoonotic, source is suspected as a possible cause of these infections. Rodents, brown rats (Rattus norvegicus) in particular, have been shown to carry HEV, both the swine HEV G3 genotype and Orthohepevirus C, genotype C1 (rat HEV). To investigate the prevalence of HEV in British rodents, liver tissue was taken from 307 rodents collected from pig farms (n = 12) and other locations (n = 10). The RNA from these samples was extracted and tested using a pan‐HEV nested RT‐PCR. Limited histopathology was also performed. In this study, 8/61 (13%, 95% CI, 5–21) of brown rat livers were positive for HEV RNA. Sequencing of amplicons demonstrated all infections to be rat HEV with 87%–92% nucleotide identity to other rat HEV sequences circulating within Europe and China (224 nt ORF‐1). Lesions and necrosis were observed histologically in 2/3 samples examined. No rat HEV RNA was detected in any other species, and no HEV G3 RNA was detected in any rodent in this study. This is the first reported detection of rat HEV in Great Britain. A human case of rat HEV infection has recently been reported in Asia, suggesting that rat HEV could pose a risk to public health.

UK Pigs at the Time of Slaughter: Investigation into the Correlation of Infection with PRRSV and HEV

Hepatitis E virus (HEV) and porcine reproductive and respiratory syndrome virus (PRRSV) and are both globally prevalent in the pig population. While HEV does not cause clinical disease in pigs, its zoonotic potential has raised concerns in the food safety sector. PRRS has become endemic in the United Kingdom (UK) since its introduction in 1991, and continues to cause considerable economic losses to the swine industry. A better understanding of the current prevalence and diversity of PRRSV and HEV in the UK, and their potential association, is needed to assess risks and target control measures appropriately. This study used plasma, tonsil, and cecal content samples previously collected from pigs in 14 abattoirs in England and Northern Ireland to study the prevalence of several pathogens including PRRSV and HEV. The diversity of PRRSV strains detected in these samples was analyzed by sequencing open reading frame 5 (ORF5), revealing no substantial difference in PRRSV strains from these clinically unaffected pigs relative to those from clinical cases of disease in the UK. Despite the potential immuno-modulatory effect of PRRSV infection, previously demonstrated to affect Salmonella and HEV shedding profiles, no significant association was found between positive PRRSV status and positive HEV status.

Prevalence of Hepatitis E Virus Infection in Pigs at the Time of Slaughter, United Kingdom, 2013

Pigs raised in the United Kingdom are unlikely to be the source of UK human infections.

Since 2010, reports of infection with hepatitis E virus (HEV) have increased in England and Wales. Despite mounting evidence regarding the zoonotic potential of porcine HEV, there are limited data on its prevalence in pigs in the United Kingdom. We investigated antibody prevalence, active infection, and virus variation in serum and cecal content samples from 629 pigs at slaughter. Prevalence of antibodies to HEV was 92.8% (584/629), and HEV RNA was detected in 15% of cecal contents (93/629), 3% of plasma samples (22/629), and 2% of both (14/629). However, although HEV is prevalent in pigs in the United Kingdom and viremic pigs are entering the food chain, most (22/23) viral sequences clustered separately from the dominant type seen in humans. Thus, pigs raised in the United Kingdom are unlikely to be the main source of human HEV infections in the United Kingdom. Further research is needed to identify the source of these infections.

Discovery of a polyomavirus in European badgers (Meles meles) and the evolution of host range in the family Polyomaviridae

Polyomaviruses infect a diverse range of mammalian and avian hosts, and are associated with a variety of symptoms. However, it is unknown whether the viruses are found in all mammalian families and the evolutionary history of the polyomaviruses is still unclear. Here, we report the discovery of a novel polyomavirus in the European badger (Meles meles), which to our knowledge represents the first polyomavirus to be characterized in the family Mustelidae, and within a European carnivoran. Although the virus was discovered serendipitously in the supernatant of a cell culture inoculated with badger material, we subsequently confirmed its presence in wild badgers. The European badger polyomavirus was tentatively named Meles meles polyomavirus 1 (MmelPyV1). The genome is 5187 bp long and encodes proteins typical of polyomaviruses. Phylogenetic analyses including all known polyomavirus genomes consistently group MmelPyV1 with California sea lion polyomavirus 1 across all regions of the genome. Further evolutionary analyses revealed phylogenetic discordance amongst polyomavirus genome regions, possibly arising from evolutionary rate heterogeneity, and a complex association between polyomavirus phylogeny and host taxonomic groups.

Global gene expression profiling of myeloid immune cell subsets in response to in vitro challenge with porcine circovirus 2b

Compelling evidence suggests that the early interaction between porcine circovirus 2 (PCV-2) and the innate immune system is the key event in the pathogenesis of Post-Weaning Multisystemic Wasting Syndrome (PMWS). Furthermore, PCV2 has been detected in bone-marrow samples, potentially enabling an easy spread and reservoir for the virus. To assess the gene-expression differences induced by an in-vitro PCV2b infection in different three different myeloid innate immune cell subsets generated from the same animal, we used the Agilent Porcine Gene Expression Microarray (V2). Alveolar macrophages (AMØs), monocyte-derived dendritic cells (MoDCs) and bone-marrow cells (BMCs) were generated from each animal, and challenged with a UK-isolate of a PCV2 genotype b-strain at a MOI of 0.5. Remarkably, analysis showed a highly distinct and cell-type dependent response to PCV2b challenge. Overall, MoDCs showed the most marked response to PCV2b challenge in vitro and revealed a key role for TNF in the interaction with PCV2b, whereas only few genes were affected in BMCs and AMØs. These observations were further supported by an enrichment of genes in the downstream NF-κB Signalling pathway as well as an up regulation of genes with pro-apoptotic functions post-challenge. PCV2b challenge increases the expression of a large number of immune-related and pro-apoptotic genes mainly in MoDC, which possibly explain the increased inflammation, granulomatous inflammation and lymphocyte depletion seen in PMWS-affected pigs.

Hepatitis E virus in pork liver sausage, France

We investigated viability of hepatitis E virus (HEV) identified in contaminated pork liver sausages obtained from France. HEV replication was demonstrated in 1 of 4 samples by using a 3-dimensional cell culture system. The risk for human infection with HEV by consumption of these sausages should be considered to be high.

Hepatitis E virus in pork food chain, United Kingdom, 2009-2010

We investigated contamination by hepatitis E virus (HEV) in the pork production chain in the United Kingdom. We detected HEV in pig liver samples in a slaughterhouse, in surface samples from a processing plant, and in pork sausages and surface samples at point of sale. Our findings provide evidence for possible foodborne transmission of HEV during pork production.

Porcine circovirus type 2 infection before and during an outbreak of postweaning multisystemic wasting syndrome on a pig farm in the UK

The presence of porcine circovirus type 2 (PCV-2) and other pathogens before and during an outbreak of postweaning multisystemic wasting syndrome (PWMS) in pigs is evaluated in this study. At the time of the outbreak on a large commercial pig farm in the UK, serum samples and data were collected in two independent on-going research projects, one in weaned pigs and the other in sows. Serum samples of growing pigs and sows were PCV-2-antibody and PCR positive before and during the PMWS outbreak. Upon sequencing, PCV-2 isolates collected before the outbreak were identified as PCV-2a, and isolates collected during the outbreak were identified as PCV-2b, suggesting a shift of PCV-2 genotypes present on the farm. Pigs in the weaner study were from sows originating from different breeders and an association of sow origin and PCV-2 serostatus in offspring was found. Further, pigs had higher odds to be PCV-2 antigen positive if the sow was PCV-2 antibody positive around farrowing, the sow was of higher parity, and were less likely to test antigen positive if the sow was sourced from a particular breeder. The findings of this study highlight the potential role of the immune status of the sow on the occurrence of PMWS.

Excretion of hepatitis E virus by pigs of different ages and its presence in slurry stores in the United Kingdom

Five faecal samples were collected from four different stages of production at each of 10 pig farms in the Yorkshire Humberside area of the UK, and samples of slurry were collected from nine of the farms. All the samples were tested for hepatitis E virus (HEV) RNA by a nested reverse transcriptase PCR. At least one sample from the pigs on each of the farms tested positive for hev; its prevalence in the 10 herds varied from 5 per cent to 35 per cent and its mean prevalence was 21.5 per cent. The mean prevalence in pigs aged three to five weeks was 26.0 per cent, in pigs aged 10 to 12 weeks 44.0 per cent, in pigs aged 22 to 24 weeks 8.9 per cent, and in adult dry sows 6.0 per cent. Two of the nine slurry lagoons tested positive for HEV RNA. Phylogenetic analysis of the sequence data indicated that the strains of the virus were of genotype 3 and closely related to strains detected in other pigs and in human beings in the UK.

Swine and circovirus

In the 1990s Post-weaning, multi-systemic wasting syndrome (PMWS) emerged in N. America and Europe as a major disease problem with significant welfare and economic consequences for pig producers. The disease, characterised by wasting, respiratory, enteric and lymphoid system problems in pigs of 4-16 weeks of age, has since spread so that today it has a global distribution. PCV-2 is consistently associated with PMWS, is more abundant in association with PMWS and is considered by many to be the causative agent of the syndrome. However, several lines of evidence indicate that PCV-2 is necessary but not sufficient to cause the full range of clinical signs associated with PMWS, suggesting the involvement of an as yet unidentified factor or factors. The process of identifying unknown agents and their respective roles in the pathogenesis of complex syndromes now has an ever broadening spectrum of analytical techniques available. Immune phenotyping, cytokine responses, micro-array profiling, and proteomics are just some of the techniques available. This paper describes the philosophy and the application of these and classical techniques in an integrated, holistic manner to the problem of PMWS and circoviruses, by examination of samples collected from a prospective, clinical case-control study, and discusses some of the preliminary findings in relation to the efforts to understand the aetiopathogenesis of PMWS.

Human and porcine hepatitis E virus strains, United Kingdom

We describe a case of acquired infection of a strain of hepatitis E virus (HEV)with a 100% amino acid identity to the analogous region in strains of HEV circulating in a United Kingdom pig herd. This case further supports the theory that autochthonous HEV infection in industrialized countries is zoonotic.