Analysis of Swine Movements in a Province in Northern Vietnam and Application in the Design of Surveillance Strategies for Infectious Diseases

Long-Term Epidemiology and Evolution of Swine Influenza Viruses, Vietnam

Influenza A viruses are a One Health threat because they can spill over between host populations, including among humans, swine, and birds. Surveillance of swine influenza virus in Hanoi, Vietnam, during 2013-2019 revealed gene pool enrichment from imported swine from Asia and North America and showed long-term maintenance, persistence, and reassortment of virus lineages. Genome sequencing showed continuous enrichment of H1 and H3 diversity through repeat introduction of human virus variants and swine influenza viruses endemic in other countries. In particular, the North American H1-δ1a strain, which has a triple-reassortant backbone that potentially results in increased human adaptation, emerged as a virus that could pose a zoonotic threat. Co-circulation of H1-δ1a viruses with other swine influenza virus genotypes raises concerns for both human and animal health.

One Health Surveillance Highlights Circulation of Viruses with Zoonotic Potential in Bats, Pigs, and Humans in Viet Nam

A One Health cross-sectoral surveillance approach was implemented to screen biological samples from bats, pigs, and humans at high-risk interfaces for zoonotic viral spillover for five viral families with zoonotic potential in Viet Nam. Over 1600 animal and human samples from bat guano harvesting sites, natural bat roosts, and pig farming operations were tested for coronaviruses (CoVs), paramyxoviruses, influenza viruses, filoviruses and flaviviruses using consensus PCR assays. Human samples were also tested using immunoassays to detect antibodies against eight virus groups. Significant viral diversity, including CoVs closely related to ancestors of pig pathogens, was detected in bats roosting at the human-animal interfaces, illustrating the high risk for CoV spillover from bats to pigs in Viet Nam, where pig density is very high. Season and reproductive period were significantly associated with the detection of bat CoVs, with site-specific effects. Phylogeographic analysis indicated localized viral transmission among pig farms. Our limited human sampling did not detect any known zoonotic bat viruses in human communities living close to the bat cave and harvesting bat guano, but our serological assays showed possible previous exposure to Marburg virus-like (Filoviridae), Crimean-Congo hemorrhagic fever virus-like (Bunyaviridae) viruses and flaviviruses. Targeted and coordinated One Health surveillance helped uncover this viral pathogen emergence hotspot.

Phylogeography as a Proxy for Population Connectivity for Spatial Modeling of Foot-and-Mouth Disease Outbreaks in Vietnam

Bayesian space-time regression models are helpful tools to describe and predict the distribution of infectious disease outbreaks and to delineate high-risk areas for disease control. In these models, structured and unstructured spatial and temporal effects account for various forms of non-independence amongst case counts across spatial units. Structured spatial effects capture correlations in case counts amongst neighboring provinces arising from shared risk factors or population connectivity. For highly mobile populations, spatial adjacency is an imperfect measure of connectivity due to long-distance movement, but we often lack data on host movements. Phylogeographic models inferring routes of viral dissemination across a region could serve as a proxy for patterns of population connectivity. The objective of this study was to investigate whether the effects of population connectivity in space-time regressions of case counts were better captured by spatial adjacency or by inferences from phylogeographic analyses. To compare these two approaches, we used foot-and-mouth disease virus (FMDV) outbreak data from across Vietnam as an example. We identified that accounting for virus movement through phylogeographic analysis serves as a better proxy for population connectivity than spatial adjacency in spatial-temporal risk models. This approach may contribute to design surveillance activities in countries lacking movement data.

Early‐phase risk assessments during the first epidemic year of African swine fever outbreaks in Vietnamese pigs

Background

Objectives

Methods

Results

Conclusions

Genetic Characteristics and Pathogenicity of a Novel Porcine Deltacoronavirus Southeast Asia-Like Strain Found in China

Farmers involved in the lucrative pork trading business between China and Southeast Asian countries should be aware of a recently discovered novel porcine deltacoronavirus (PDCoV) in Guangxi province, China. A PDCoV strain, CHN/GX/1468B/2017, was isolated from the small intestinal contents of piglets with diarrhea from this region, with a titer of 1 × 10^8.0 TCID₅₀/mL on LLC-PK cells. The full-length genome sequence consists of 25,399 nt as determined by next-generation sequencing and this was deposited in the GenBank (accession number MN025260.1). Genomic analysis showed that CHN/GX/1468B/2017 strain had 96.9~99.4% nucleotide homology with other 87 referenced PDCoV strains from different areas, and contained 6 and 9-nt deletions at positions 1,733~1,738 and 2,804~2,812, respectively, in the ORF1a gene. Phylogenetic analyses based on the whole gene sequence as well as S protein and ORF1a/1b protein sequences all showed that this strain was closely related to the Southeast Asia strain. When 7-day-old piglets were inoculated orally with the CHN/GX/1468B/2017 strain, they developed severe diarrhea, with a peak of fecal viral shedding at 4 days post-infection. Although no death or fever were observed, the CHN/GX/1468B/2017 strain produced a wide range of tissue tropism, with the main target being the intestine. Importantly, the VH:CD ratios of the jejunum and ileum in infected piglets were significantly lower than controls. These results indicate that CHN/GX/1468B/2017, isolated in China, is a novel PDCoV Southeast Asia-like strain with distinct genetic characteristics and pathogenicity. This finding enriches the international information on the genetic diversity of PDCoV.

A stochastic simulation model of African swine fever transmission in domestic pig farms in the Red River Delta region in Vietnam

The main objectives of this study were to model various scenarios of African swine fever (ASF) virus transmission among farms in Vietnam and to evaluate the impact of control strategies using North American Animal Disease Spread Model (NAADSM). A total of 7,882 pig farms in the Red River Delta (RRD) region were obtained from the General Statistics Office, and then, random points corresponding to the number of farms in each province were generated as exact farm locations were not available. A total of 10 models were developed, including movement control scenarios. In addition, we conducted sensitivity analysis to assess the impact of indirect contact transmission probability (TP). Overall, the indirect contact exhibited an important role in transmitting the ASF virus. In order to minimize ASF transmission between farms, we found that movement restriction needed to reach a certain level (approximately between 50% and 75%) and that the restriction had to be applied in a timely manner. This study offers valuable insight into how ASF virus can be transmitted via direct and indirect contact and controlled among farms under the various simulation scenarios. Our results suggest that the enforcement of movement restriction was an effective control measure as soon as the outbreaks were reported. In addition, this study provided evidence that high standards of biosecurity can contribute to the reduction of disease spread.

A stochastic network-based model to simulate farm-level transmission of African swine fever virus in Vietnam

African swine fever virus is highly contagious, and mortality rates reach up to 100% depending on the host, virus dose, and the transmission routes. The main objective of this study was to develop a network-based simulation model for the farm-level transmission of ASF virus to evaluate the impact of changes in farm connectivity on ASF spread in Vietnam. A hypothetical population of 1,000 pig farms was created and used for the network-based simulation, where each farm represented a node, and the connection between farms represented an edge. The three scenarios modelled in this way (baseline, low, and high) evaluated the impact of connectivity on disease transmission. The median number of infected farms was higher as the connectivity increased (low: 659, baseline: 968 and high: 993). In addition, we evaluated the impact of the culling strategy on the number of infected farms. A total of four scenarios were simulated depending on the timing of culling after a farm was infected. We found that the timing of culling at 16, 12, 8, and 6 weeks had resulted in a reduction of the number of median infected farms by 81.92%, 91.63%, 100%, and 100%, respectively. Finally, our evaluation of the implication of stability of ties between farms indicated that if the farms were to have the same trading partners for at least six months could significantly reduce the median number of infected farms to two (95th percentile: 413) than in the basic model. Our study showed that pig movements among farms had a significant influence on the transmission dynamics of ASF virus. In addition, we found that the either timing of culling, reduction in the number of trading partners each farm had, or decreased mean contact rate during the outbreaks were essential to prevent or stop further outbreaks.

Mapping the pork value chain in Vietnam: a systematic review

In Vietnam, pork is the most commonly consumed type of meat, and the demand is expected to rise even further. Nevertheless, food safety is a major concern, as the country bears a high burden of food-borne diseases, including these caused by pork products. Knowledge of the flows of pigs and pork from producers up to the consumers is important; however, up to now, a comprehensive overview is lacking. We addressed this by conducting a systematic review on the pork value chain (PVC) mapping for the country. Four international and three Vietnamese databases were searched for data on the pork value chain in Vietnam, and the results were reported according to the PRISMA guidelines. Data obtained from the retained records showed that 10 main PVC types are present in Vietnam, comprising of five main actors including: producers, middlemen, slaughter men, retailers and consumers. Among the identified chains, the one involving producers, slaughter men, retailers and consumers is the most common one, with up to 75% of pork following this route. In cities or export routes to other countries, middlemen and/or traders are important additional actors in the PVCs. The small scale of PVC linkages is prominent. The presence of middlemen, pig traders and pork traders is contributing to further distribution of pork products in geographical terms. Transactions between actors in the traditional PVCs in Vietnam are characterized by the absence of official contracts; therefore, the linkages in the chains are loose and the origin of pork is not traceable. More industrial forms of PVCs are slowly developing; however, the traditional PVCs are still prevailing in Vietnam. The weak linkages between actors and poor hygienic practices in these chains form a risk to pork safety.

Exploring the Socioeconomic Importance of Antimicrobial Use in the Small-Scale Pig Sector in Vietnam

Antimicrobial resistance (AMR) is influenced by antimicrobial use in human and animal health. This use exerts selection pressure on pathogen populations with the development of resistance and the exchange of resistance genes. While the exact scale of AMR in Vietnam remains uncertain, recent studies suggest that it is a major issue in both human and animal health. This study explored antimicrobial use behaviors in 36 pig farms in the Nam Dinh Province (North) and the Dong Nai Province (South) of Vietnam (with a median of 5.5 breeding sows and 41 fattening pigs). It also estimated the economic costs and benefits of use for the producer. Data were collected through a structured face-to-face interview with additional productivity data collected by farmers during a six-week period following the initial interview. Overall, antimicrobial use was high across the farms; however, in-feed antimicrobial use is likely to be under-reported due to misleading and imprecise labelling on premixed commercial feeds. An economic analysis found that the cost of antimicrobials was low relative to other farm inputs (~2% of total costs), and that farm profitability was precariously balanced, with high disease and poor prices leading to negative and low profits. Future policies for smallholder farms need to consider farm-level economics and livestock food supply issues when developing further antimicrobial use interventions in the region.

Surveillance of swine influenza viruses in sentinel familial farms in Hung Yen province in Northern Vietnam in 2013-2014

From May 2013 to April 2014, 15 swine family-run farms (17 pig litters) in two districts in Hung Yen province, near Hanoi, were virologically and epizootiologically monitored for swine influenza viruses (SIV) monthly. No SIV was isolated from nasal swabs. Maternal antibodies were detected in 10 litters, and seroconversion against SIV was detected in six litters. There was a marked difference in patterns of SIV transmission in the two districts. Van Lam district which has low density of swine with mainly smallholder farms had low intensity of SIV, with much of the infection caused by H1N1 2009 pandemic-like viruses A(H1N1)pdm09, likely originated from humans. In contrast, Van Giang district, which has high swine density and larger farms, had high levels of typical SIV (triple reassortants H3N2 and H3N2 Binh Duong lineage viruses) circulating within swine. With one exception, the SIV lineages detected were those we concurrently isolated from studies in a large central abattoir in Hanoi. Influenza-like illness symptoms reported by farmers were poorly correlated with serological evidence of SIV infection.

A dynamic model of transmission and elimination of peste des petits ruminants in Ethiopia

Peste des petits ruminants (PPR), a devastating viral disease of sheep and goats, has been targeted by the global community for eradication within the next 15 years. Although an efficacious attenuated live vaccine is available, the lack of knowledge about the transmission potential of PPR virus (PPRV) may compromise eradication efforts. By fitting a metapopulation model simulating PPRV spread to the results of a nationwide serological survey in Ethiopia, we estimated the level of viral transmission in an endemic setting and the vaccination coverage required for elimination. Results suggest that the pastoral production system as a whole acts as a viral reservoir, from which PPRV spills over into the sedentary production system, where viral persistence is uncertain. Estimated levels of PPRV transmission indicate that viral spread could be prevented if the proportion of immune small ruminants is kept permanently above 37% in at least 71% of pastoral village populations. However, due to the high turnover of these populations, maintaining the fraction of immune animals above this threshold would require high vaccine coverage within villages, and vaccination campaigns to be conducted annually. Adapting vaccination strategies to the specific characteristics of the local epidemiological context and small ruminant population dynamics would result in optimized allocation of limited resources and increase the likelihood of PPR eradication.

Swine influenza viruses in Northern Vietnam in 2013-2014

Swine are an important intermediate host for emergence of pandemic influenza. Vietnam is the largest swine producer in South East Asia. Systematic virological and serological surveillance of swine influenza viruses was carried out in Northern Vietnam from May 2013 to June 2014 with monthly sampling of pigs in local and large collective slaughterhouses and in a live pig market. Influenza A seroprevalence in the local slaughterhouses and in the large collective slaughterhouse was 48.7% and 29.1%, respectively. Seventy-seven influenza A viruses were isolated, all from the large collective slaughterhouse. Genetic analysis revealed six virus genotypes including H1N1 2009 pandemic (H1N1pdm09) viruses, H1N2 with H1 of human origin, H3N2 and H1N1pdm09 reassortants, and triple-reassortant H3N2 viruses. Phylogenetic analysis of swine and human H1N1pdm09 viruses showed evidence of repeated spill-over from humans to swine rather than the establishment of H1N1pdm09 as long-term distinct lineage in swine. Surveillance at the large collective slaughterhouse proved to be the most efficient, cost-effective, and sustainable method of surveillance for swine influenza viruses in Vietnam.

Network, cluster and risk factor analyses for porcine reproductive and respiratory syndrome using data from swine sites participating in a disease control program

The objectives of this study were to describe networks of Ontario swine sites and their service providers (including trucking, feed, semen, gilt and boar companies); to categorize swine sites into clusters based on site-level centrality measures, and to investigate risk factors for porcine reproductive and respiratory syndrome (PRRS) using information gathered from the above-mentioned analyses. All 816 sites included in the current study were enrolled in the PRRS area regional control and elimination projects in Ontario. Demographics, biosecurity and network data were collected using a standardized questionnaire and PRRS status was determined on the basis of available diagnostic tests and assessment by site veterinarians. Two-mode networks were transformed into one-mode dichotomized networks. Cluster and risk factor analyses were conducted separately for breeding and growing pig sites. In addition to the clusters obtained from cluster analyses, other explanatory variables of interest included: production type, type of animal flow, use of a shower facility, and number of neighboring swine sites within 3km. Unadjusted univariable analyses were followed by two types of adjusted models (adjusted for production systems): a generalizing estimation equation model (GEE) and a generalized linear mixed model (GLMM). Results showed that the gilt network was the most fragmented network, followed by the boar and truck networks. Considering all networks simultaneously, approximately 94% of all swine sites were indirectly connected. Unadjusted risk factor analyses showed significant associations between almost all predictors of interest and PRRS positivity, but these disappeared once production system was taken into consideration. Finally, the vast majority of the variation on PRRS status was explained by production system according to GLMM, which shows the highly correlated nature of the data, and raises the point that interventions at this level could potentially have high impact in PRRS status change and/or maintenance.