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1.
BMC Vet Res ; 18(1): 401, 2022 Nov 14.
Article in English | MEDLINE | ID: covidwho-2115817

ABSTRACT

BACKGROUND: African swine fever (ASF) has been present in Lithuania since 2014. The disease affects mainly the wild boar population. Thus, hunters play a key role in the performance of disease surveillance and control measures. We used participatory methods to gain insight into the knowledge of hunters and to include their perceptions in the design and the implementation of surveillance and control measures to increase their effectiveness. RESULTS: The willingness and the interest of hunters to participate was high, but only eight focus group meetings with 33 hunters could be held due to the COVID-19 pandemic. The overall knowledge of Lithuanian hunters regarding ASF, investigated by semi-structured interviews, was sufficient to understand their part in ASF control and surveillance. However, their knowledge did not necessarily lead to an increased acceptance of some ASF control measures, like the targeted hunting of female wild boar. Participating hunters showed a good understanding of the processes of the surveillance system. Their trust in the performance within this system was highest towards the hunters themselves, thus emphasizing the importance of acknowledging their role in the system. Hunters refused measures including the reduction of hunting activities. They feared a complete elimination of the wild boar population, which in turn demonstrates the necessity to increase professional information exchange. CONCLUSIONS: The perceptions of Lithuanian hunters regarding ASF surveillance and control in wild boar resembled those obtained in neighboring countries. It is imperative to communicate the results with decision-makers, to consider the views of hunters, when designing or adapting measures to control ASF in wild boar and to communicate with hunters on these measures and their justification.


Subject(s)
African Swine Fever Virus , African Swine Fever , COVID-19 , Swine Diseases , Female , Swine , Animals , African Swine Fever/epidemiology , African Swine Fever/prevention & control , Lithuania/epidemiology , Pandemics , COVID-19/veterinary , Sus scrofa , Swine Diseases/epidemiology
2.
BMC Vet Res ; 18(1): 392, 2022 Nov 08.
Article in English | MEDLINE | ID: covidwho-2108779

ABSTRACT

BACKGROUND: Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, has become the major causative agent of acute gastroenteritis in piglets since 2010 in China. RESULTS: In the current study, 91 complete spike (S) gene sequences were obtained from PEDV positive samples collected from 17 provinces in China from March 2020 to March 2021. A phylogenetic analysis showed that 92.3% (84 out of 91) of the identified strains belonged to GII subtype, while 7.7% (7 out of 91) were categorized as S-INDEL like strains and grouped within GI-c clade. Based on a recombination analysis, six of S-INDEL like strains were recombinant strains originated from S-INDEL strain FR/001/2014 and virulent strain AJ1102. In addition, PEDV variant strains (CH/GDMM/202012, CH/GXDX/202010 et al) carrying novel insertions (360QGRKS364 and 1278VDVF1281) in the S protein were observed. Furthermore, the deduced amino acid sequences for the S protein showed that multiple amino acid substitutions in the antigenic epitopes in comparison with the vaccine strains. CONCLUSIONS: In conclusion, these data provide novel molecular evidence on the epidemiology and molecular diversity of PEDV in 2020-2021. This information may help design a strategy for controlling and preventing the prevalence of PEDV variant strains in China.


Subject(s)
Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Swine , Phylogeny , Swine Diseases/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Amino Acid Sequence , China/epidemiology , Spike Glycoprotein, Coronavirus/genetics
3.
Transbound Emerg Dis ; 69(5): e2443-e2455, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-2053020

ABSTRACT

The porcine deltacoronavirus (PDCoV) is a newly discovered pig enteric coronavirus that can infect cells from various species. In Haiti, PDCoV infections in children with acute undifferentiated febrile fever were recently reported. Considering the great potential of inter-species transmission of PDCoV, we performed a comprehensive analysis of codon usage patterns and host adaptation profiles of 54 representative PDCoV strains with the spike (S) gene. Phylogenetic analysis of the PDCoV S gene indicates that the PDCoV strains can be divided into five genogroups. We found a certain codon usage bias existed in the S gene, in which the synonymous codons are often ended with U or A. Heat map analysis revealed that all the PDCoV strains shared a similar codon usage trend. The PDCoV S gene with a dN/dS ratio lower than 1 reveals a negative selection on the PDCoV S gene. Neutrality analysis showed that natural selection is the dominant force in shaping the codon usage bias of the PDCoV S gene. Unexpectedly, host adaptation analysis reveals a higher adaptation level of PDCoV to Homo sapiens and Gallus gallus than to Sus scrofa. Compared to the USA lineage, the PDCoV strains in the Early China lineage and Thailand lineage were less adapted to their hosts, which indicates that the evolutionary process plays an important role in the adaptation ability of PDCoV. These findings of this study add to our understanding of PDCoV's evolution, adaptability, and inter-species transmission.


Subject(s)
Coronavirus Infections , Swine Diseases , Animals , Codon/genetics , Codon Usage , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Deltacoronavirus , Genome, Viral/genetics , Phylogeny , Swine , Swine Diseases/epidemiology
4.
Viruses ; 14(8)2022 08 17.
Article in English | MEDLINE | ID: covidwho-2010307

ABSTRACT

A safe and efficacious live-attenuated vaccine for porcine epidemic diarrhea virus (PEDV) is not commercially available in the United States yet. Two major PEDV strains are currently circulating in US swine: highly virulent non-S-INDEL strain and milder virulent S-INDEL strain. In this study, the safety and protective efficacy of a plaque-purified S-INDEL PEDV isolate formulated as a vaccine candidate was evaluated. Ten pregnant gilts were divided into three groups and orally inoculated at 79 days of gestation and then boosted at 100 days gestation (T01: n = 4, vaccination/challenge; T02: n = 4, non-vaccination/challenge; T03: n = 2, non-vaccination/non-challenge). None of the gilts had adverse clinical signs after vaccination. Only one T01 gilt (#5026) had viral replication and detectible viral RNA in feces. The same gilt had consistent levels of PEDV-specific IgG and IgA antibodies in serum and colostrum/milk. Farrowed piglets at 3 to 5 days of age from T01 and T02 gilts were orally challenged with 103 TCID50/pig of the virulent non-S-INDEL PEDV while T03 piglets were orally inoculated with virus-negative medium. T01 litters had overall lower mortality than T02 (T01 36.4% vs. T02 74.4%). Specifically, there was 0% litter mortality from T01 gilt 5026. Overall, it appears that vaccination of pregnant gilts with S-INDEL PEDV can passively protect piglets if there is virus replication and immune response induction in the pregnant gilts.


Subject(s)
Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Viral Vaccines , Animals , Animals, Newborn , Antibodies, Viral , Coronavirus Infections/prevention & control , Coronavirus Infections/veterinary , Female , Porcine epidemic diarrhea virus/genetics , Pregnancy , Sus scrofa , Swine , Swine Diseases/epidemiology , United States , Vaccines, Attenuated
5.
Int J Mol Sci ; 23(17)2022 Aug 29.
Article in English | MEDLINE | ID: covidwho-2006045

ABSTRACT

Since the beginning of the 21st century, humans have experienced three coronavirus pandemics, all of which were transmitted to humans via animals. Recent studies have found that porcine deltacoronavirus (PDCoV) can infect humans, so swine enteric coronavirus (SeCoV) may cause harm through cross-species transmission. Transmissible gastroenteritis virus (TGEV) and PDCoV have caused tremendous damage and loss to the pig industry around the world. Therefore, we analyzed the genome sequence data of these two SeCoVs by evolutionary dynamics and phylogeography, revealing the genetic diversity and spatiotemporal distribution characteristics. Maximum likelihood and Bayesian inference analysis showed that TGEV could be divided into two different genotypes, and PDCoV could be divided into four main lineages. Based on the analysis results inferred by phylogeography, we inferred that TGEV might originate from America, PDCoV might originate from Asia, and different migration events had different migration rates. In addition, we also identified positive selection sites of spike protein in TGEV and PDCoV, indicating that the above sites play an essential role in promoting membrane fusion to achieve adaptive evolution. In a word, TGEV and PDCoV are the past and future of SeCoV, and the relatively smooth transmission rate of TGEV and the increasing transmission events of PDCoV are their respective transmission characteristics. Our results provide new insights into the evolutionary characteristics and transmission diversity of these SeCoVs, highlighting the potential for cross-species transmission of SeCoV and the importance of enhanced surveillance and biosecurity measures for SeCoV in the context of the COVID-19 epidemic.


Subject(s)
COVID-19 , Swine Diseases , Transmissible gastroenteritis virus , Animals , Bayes Theorem , Deltacoronavirus , Humans , Phylogeography , Swine , Swine Diseases/epidemiology , Transmissible gastroenteritis virus/genetics
6.
J Vet Diagn Invest ; 34(4): 602-611, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1986641

ABSTRACT

Porcine circovirus 3 (PCV3) is widespread in pigs worldwide. Diverse clinical signs and lesions have been associated with PCV3, but the role of PCV3 as a cause of disease in swine remains unclear. We investigated the association of PCV3 with clinical signs and histologic lesions in 730 diagnostic swine cases between February 2016 and January 2018. The cases contained 2,177 samples submitted from 474 sites located in 21 states in the United States. PCR assay results were positive for PCV3 for 577 of 2,177 (27%) samples, 255 of 730 (35%) cases, 181 of 474 (38%) sites, and 17 of 21 (81%) states. We detected PCV3 in 19 of 28 specimen types and in pigs of all ages and clinical presentations, including healthy pigs, with the highest detection rate in adult pigs. PCV3 detection was not associated with respiratory, gastrointestinal, or CNS signs, weight loss, or sudden death. Of 58 types of histologic lesions evaluated, PCV3 detection was associated with myocarditis, cardiac vasculitis, and interstitial pneumonia in growing pigs. A high PCV3 detection rate was observed in aborted fetuses.


Subject(s)
Circoviridae Infections , Circovirus , Swine Diseases , Animals , Circoviridae Infections/diagnosis , Circoviridae Infections/epidemiology , Circoviridae Infections/veterinary , Circovirus/genetics , Phylogeny , Polymerase Chain Reaction/veterinary , Swine , Swine Diseases/diagnosis , Swine Diseases/epidemiology , Swine Diseases/pathology , United States/epidemiology
7.
Viruses ; 14(7)2022 Jun 28.
Article in English | MEDLINE | ID: covidwho-1964115

ABSTRACT

Swine enteric viruses are a major cause of piglet diarrhea, causing a devastating impact on the pork industry. To further understand the molecular epidemiology and evolutionary diversity of swine enteric viruses, we carried out a molecular epidemiological investigation of swine enteric viruses (PEDV, PDCoV, PoRVA, and TGEV) on 7107 samples collected from pig farms in south-central China. The results demonstrated that PEDV is the predominant pathogen causing piglet diarrhea, and its infection occurs mainly in relatively cold winter and spring in Hunan and Hubei provinces. The positive rate of PEDV showed an abnormal increase from 2020 to 2021, and that of PoRVA and PDCoV exhibited gradual increases from 2018 to 2021. PEDV-PoRVA and PEDV-PDCoV were the dominant co-infection modes. A genetic evolution analysis based on the PEDV S1 gene and ORF3 gene revealed that the PEDV GII-a is currently epidemic genotype, and the ORF3 gene of DY2020 belongs to a different clade relative to other GII-a strains isolated in this study. Overall, our results indicated that the variant PEDV GII-a is the main pathogen of piglet diarrhea with a trend of outbreak. G9 is the dominant PoRVA genotype and has the possibility of outbreak as well. It is therefore critical to strengthen the surveillance of PEDV and PoRVA, and to provide technical reserves for the prevention and control of piglet diarrhea.


Subject(s)
Coronavirus Infections , Enteroviruses, Porcine , Porcine epidemic diarrhea virus , Swine Diseases , Animals , China/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Diarrhea/epidemiology , Diarrhea/veterinary , Phylogeny , Swine , Swine Diseases/epidemiology
8.
Viruses ; 14(6)2022 06 16.
Article in English | MEDLINE | ID: covidwho-1911641

ABSTRACT

Porcine epidemic diarrhea (PED), causing up to 100% mortality in neonatal pigs, is a highly contagious enteric disease caused by PED virus (PEDV). The highly virulent genogroup 2 (G2) PEDV emerged in 2010 and has caused huge economic losses to the pork industry globally. It was first reported in the US in 2013, caused country-wide outbreaks, and posed tremendous hardship for many pork producers in 2013-2014. Vaccination of pregnant sows/gilts with live attenuated vaccines (LAVs) is the most effective strategy to induce lactogenic immunity in the sows/gilts and provide a passive protection via the colostrum and milk to suckling piglets against PED. However, there are still no safe and effective vaccines available after about one decade of endeavor. One of the biggest concerns is the potential reversion to virulence of an LAV in the field. In this review, we summarize the status and the major obstacles in PEDV LAV development. We also discuss the function of the transcriptional regulatory sequences in PEDV transcription, contributing to recombination, and possible strategies to prevent the reversion of LAVs. This article provides insights into the rational design of a promising LAV without safety issues.


Subject(s)
Coronavirus Infections , Dysentery , Porcine epidemic diarrhea virus , Swine Diseases , Viral Vaccines , Animals , Coronavirus Infections/prevention & control , Coronavirus Infections/veterinary , Diarrhea/prevention & control , Diarrhea/veterinary , Female , Pregnancy , Recombination, Genetic , Sus scrofa , Swine , Swine Diseases/epidemiology , Vaccines, Attenuated
9.
Vet Q ; 42(1): 125-147, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1852679

ABSTRACT

Swine coronaviruses (SCoVs) are one of the most devastating pathogens affecting the livelihoods of farmers and swine industry across the world. These include transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), porcine respiratory coronavirus (PRCV), porcine hemagglutinating encephalomyelitis virus (PHEV), swine acute diarrhea syndrome coronavirus (SADS-CoV), and porcine delta coronavirus (PDCoV). Coronaviruses infect a wide variety of animal species and humans because these are having single stranded-RNA that accounts for high mutation rates and thus could break the species barrier. The gastrointestinal, cardiovascular, and nervous systems are the primary organ systems affected by SCoVs. Infection is very common in piglets compared to adult swine causing high mortality in the former. Bat is implicated to be the origin of all CoVs affecting animals and humans. Since pig is the only domestic animal in which CoVs cause a wide range of diseases; new coronaviruses with high zoonotic potential could likely emerge in the future as observed in the past. The recently emerged severe acute respiratory syndrome coronavirus virus-2 (SARS-CoV-2), causing COVID-19 pandemic in humans, has been implicated to have animal origin, also reported from few animal species, though its zoonotic concerns are still under investigation. This review discusses SCoVs and their epidemiology, virology, evolution, pathology, wildlife reservoirs, interspecies transmission, spill-over events and highlighting their emerging threats to swine population. The role of pigs amid ongoing SARS-CoV-2 pandemic will also be discussed. A thorough investigation should be conducted to rule out zoonotic potential of SCoVs and to design appropriate strategies for their prevention and control.


Subject(s)
COVID-19 , Porcine epidemic diarrhea virus , Swine Diseases , Alphacoronavirus , Animals , COVID-19/epidemiology , COVID-19/veterinary , Humans , Pandemics , SARS-CoV-2 , Swine , Swine Diseases/epidemiology
10.
Vet Microbiol ; 270: 109447, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1805301

ABSTRACT

Enteric disease is the predominant cause of morbidity and mortality in young mammals including pigs. Viral species involved in porcine enteric disease complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses and pestiviruses among others. The virome of three groups of swine samples submitted to the Kansas State University Veterinary Diagnostic Laboratory for routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. All groups were designated by qRT-PCR test results for Porcine Rotavirus A, B, C and H such that samples positive for RVA only went in the RVA group, samples positive for > 1 rotavirus went in the RV group and samples negative for all were grouped in the RVNeg group. All of the animals had clinical enteric disease resulting in scours and swollen joints/lameness, enlarged heart and/or a cough. All samples were metagenomic sequenced and analyzed for viral species composition that identified 14 viral species and eight bacterial viruses/phages. Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and RV samples but were found at low or no prevalence in the RVNeg samples. Picobirnavirus was identified at a high proportion and prevalence in RVNeg and RV samples but at a low prevalence in the RVA group. Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg samples. A sequence analysis of the possible host of Picobirnaviruses revealed fungi as the most likely host. Various sequences were extracted from the sample reads and a phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA genotypes. These data are important for pathogen surveillance and control measures.


Subject(s)
Rotavirus Infections , Rotavirus , Swine Diseases , Animals , Diarrhea/epidemiology , Diarrhea/veterinary , Feces , Genotype , Humans , Mammals , Phylogeny , Rotavirus/genetics , Rotavirus Infections/epidemiology , Rotavirus Infections/veterinary , Swine , Swine Diseases/epidemiology , Virome
11.
Front Public Health ; 10: 836177, 2022.
Article in English | MEDLINE | ID: covidwho-1776039

ABSTRACT

Taenia solium cysticercosis is the most common cause of acquired epilepsy in pig-raising and pork-consuming parts of Africa, Latin America, and Asia. This review aimed to systematically compile and synthesize data on the epidemiology of porcine cysticercosis in the Eastern and Southern Africa (ESA) region. Comprehensive searching strategies were employed to retrieve the studies published or reported between January 1,1997 and March 1, 2021, from Pub Med, Hinari, and Google Scholar databases and search platforms. The identified studies that met the inclusion criteria were then appraised for methodological quality. Finally, 44 studies obtained from nine countries were selected and included in this review. Relevant data were extracted using standardized templates for qualitative synthesis and meta-analysis. The overall pooled prevalence estimate of porcine cysticercosis in the ESA region was 17% (95% CI: 14-20%). The prevalence level between and within countries showed high variability. The pooled estimate showed high heterogeneity among the reports (the inverse variance index value (I2) of 98.99%, p < 0.05). The meta-analysis sub-grouped by the type of diagnostic test showed the pooled prevalence estimate of 27% (95% CI: 9-50) by carcass dissection; 23% (95% CI: 14-33) by Antibody-based immunodiagnostic techniques; 23% (95% CI: 18-29) by antigen detecting (Ag)-ELISA, 12% (95% CI: 7-18) by meat inspection, and 9% (95% CI: 7-11) by lingual examination. The meta-analysis sub-grouped by region showed a relatively higher pooled prevalence estimate for the Southern region 22% (95% CI: 15-30) compared to 13% (95% CI: 11-15) in the Eastern region. The highest country-based pooled prevalence was obtained from South Africa (33%, 95% CI: 20-48) and Zambia (22%, 95% CI: 16-29), whereas the lowest pooled prevalence was identified in Madagascar (5%, 95% CI: 4-5) and Rwanda (7%, 95% CI: 6-8). The lack of latrine, traditional pig husbandry practices, unprotected water sources, and increase in age were identified as significant risk factors for the occurrence of porcine cysticercosis in the pooled studies. The findings of this review will provide context-specific input to prioritize the possible intervention programs for T. solium control in the ESA region. More sensitive and specific test-based prevalence estimates, detailed risk factor investigations, and financial losses analysis are needed to establish feasible control strategies. Systematic Review Registration: http://www.crd.york.ac.uk/PROSPERO/, identifier: CRD42021238931.


Subject(s)
Cysticercosis , Swine Diseases , Africa, Southern , Animals , Cysticercosis/epidemiology , Cysticercosis/veterinary , Enzyme-Linked Immunosorbent Assay , Swine , Swine Diseases/epidemiology
12.
Transbound Emerg Dis ; 69(2): 396-412, 2022 Mar.
Article in English | MEDLINE | ID: covidwho-1774900

ABSTRACT

A limited understanding of the transmission dynamics of swine disease is a significant obstacle to prevent and control disease spread. Therefore, understanding between-farm transmission dynamics is crucial to developing disease forecasting systems to predict outbreaks that would allow the swine industry to tailor control strategies. Our objective was to forecast weekly porcine epidemic diarrhoea virus (PEDV) outbreaks by generating maps to identify current and future PEDV high-risk areas, and simulating the impact of control measures. Three epidemiological transmission models were developed and compared: a novel epidemiological modelling framework was developed specifically to model disease spread in swine populations, PigSpread, and two models built on previously developed ecosystems, SimInf (a stochastic disease spread simulations) and PoPS (Pest or Pathogen Spread). The models were calibrated on true weekly PEDV outbreaks from three spatially related swine production companies. Prediction accuracy across models was compared using the receiver operating characteristic area under the curve (AUC). Model outputs had a general agreement with observed outbreaks throughout the study period. PoPS had an AUC of 0.80, followed by PigSpread with 0.71, and SimInf had the lowest at 0.59. Our analysis estimates that the combined strategies of herd closure, controlled exposure of gilts to live viruses (feedback) and on-farm biosecurity reinforcement reduced the number of outbreaks. On average, 76% to 89% reduction was seen in sow farms, while in gilt development units (GDU) was between 33% to 61% when deployed to sow and GDU farms located in probabilistic high-risk areas. Our multi-model forecasting approach can be used to prioritize surveillance and intervention strategies for PEDV and other diseases potentially leading to more resilient and healthier pig production systems.


Subject(s)
Coronavirus Infections , Porcine epidemic diarrhea virus , Swine Diseases , Animals , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Coronavirus Infections/veterinary , Disease Outbreaks/prevention & control , Disease Outbreaks/veterinary , Ecosystem , Farms , Female , Swine , Swine Diseases/epidemiology , Swine Diseases/prevention & control
13.
Emerg Infect Dis ; 27(12): 3045-3051, 2021.
Article in English | MEDLINE | ID: covidwho-1613521

ABSTRACT

Influenza strains circulating among swine populations can cause outbreaks in humans. In October 2020, we detected a variant influenza A subtype H1N2 of swine origin in a person in Alberta, Canada. We initiated a public health, veterinary, and laboratory investigation to identify the source of the infection and determine whether it had spread. We identified the probable source as a local pig farm where a household contact of the index patient worked. Phylogenetic analysis revealed that the isolate closely resembled strains found at that farm in 2017. Retrospective and prospective surveillance using molecular testing did not identify any secondary cases among 1,532 persons tested in the surrounding area. Quick collaboration between human and veterinary public health practitioners in this case enabled a rapid response to a potential outbreak.


Subject(s)
Influenza A Virus, H1N1 Subtype , Influenza, Human , Orthomyxoviridae Infections , Swine Diseases , Alberta/epidemiology , Animals , Humans , Influenza A Virus, H1N2 Subtype , Influenza A Virus, H3N2 Subtype , Influenza, Human/epidemiology , Orthomyxoviridae Infections/epidemiology , Orthomyxoviridae Infections/veterinary , Phylogeny , Prospective Studies , Retrospective Studies , Swine , Swine Diseases/epidemiology
14.
Mol Biol Evol ; 39(2)2022 02 03.
Article in English | MEDLINE | ID: covidwho-1594013

ABSTRACT

The ongoing SARS (severe acute respiratory syndrome)-CoV (coronavirus)-2 pandemic has exposed major gaps in our knowledge on the origin, ecology, evolution, and spread of animal coronaviruses. Porcine epidemic diarrhea virus (PEDV) is a member of the genus Alphacoronavirus in the family Coronaviridae that may have originated from bats and leads to significant hazards and widespread epidemics in the swine population. The role of local and global trade of live swine and swine-related products in disseminating PEDV remains unclear, especially in developing countries with complex swine production systems. Here, we undertake an in-depth phylogeographic analysis of PEDV sequence data (including 247 newly sequenced samples) and employ an extension of this inference framework that enables formally testing the contribution of a range of predictor variables to the geographic spread of PEDV. Within China, the provinces of Guangdong and Henan were identified as primary hubs for the spread of PEDV, for which we estimate live swine trade to play a very important role. On a global scale, the United States and China maintain the highest number of PEDV lineages. We estimate that, after an initial introduction out of China, the United States acted as an important source of PEDV introductions into Japan, Korea, China, and Mexico. Live swine trade also explains the dispersal of PEDV on a global scale. Given the increasingly global trade of live swine, our findings have important implications for designing prevention and containment measures to combat a wide range of livestock coronaviruses.


Subject(s)
Coronavirus , Porcine epidemic diarrhea virus , Swine Diseases , Animals , China , Pandemics , Phylogeny , Phylogeography , Porcine epidemic diarrhea virus/genetics , Swine , Swine Diseases/epidemiology , United States
15.
Emerg Microbes Infect ; 11(1): 91-94, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1541488

ABSTRACT

In order to assess the risk of SARS-CoV-2 infection, transmission and reservoir development in swine, we combined results of an experimental and two observational studies. First, intranasal and intratracheal challenge of eight pigs did not result in infection, based on clinical signs and PCR on swab and lung tissue samples. Two serum samples returned a low positive result in virus neutralization, in line with findings in other infection experiments in pigs. Next, a retrospective observational study was performed in the Netherlands in the spring of 2020. Serum samples (N =417) obtained at slaughter from 17 farms located in a region with a high human case incidence in the first wave of the pandemic. Samples were tested with protein micro array, plaque reduction neutralization test and receptor-binding-domain ELISA. None of the serum samples was positive in all three assays, although six samples from one farm returned a low positive result in PRNT (titers 40-80). Therefore we conclude that serological evidence for large scale transmission was not observed. Finally, an outbreak of respiratory disease in pigs on one farm, coinciding with recent exposure to SARS-CoV-2 infected animal caretakers, was investigated. Tonsil swabs and paired serum samples were tested. No evidence for infection with SARS-CoV-2 was found. In conclusion, Although in both the experimental and the observational study few samples returned low antibody titer results in PRNT infection with SARS-CoV-2 was not confirmed. It was concluded that sporadic infections in the field cannot be excluded, but large-scale SARS-CoV-2 transmission among pigs is unlikely.


Subject(s)
COVID-19/veterinary , SARS-CoV-2/physiology , Swine Diseases/epidemiology , Swine Diseases/transmission , Swine Diseases/virology , Animals , Environmental Exposure , Netherlands/epidemiology , Public Health Surveillance , Retrospective Studies , Swine
16.
Parasit Vectors ; 14(1): 282, 2021 May 26.
Article in English | MEDLINE | ID: covidwho-1523322

ABSTRACT

Trichinellosis is a foodborne disease caused by several Trichinella species around the world. In Chile, the domestic cycle was fairly well-studied in previous decades, but has been neglected in recent years. The aims of this study were to analyze, geographically, the incidence of trichinellosis in Chile to assess the relative risk and to analyze the incidence rate fluctuation in the last decades. Using temporal data spanning 1964-2019, as well as geographical data from 2010 to 2019, the time series of cases was analyzed with ARIMA models to explore trends and periodicity. The Dickey-Fuller test was used to study trends, and the Portmanteau test was used to study white noise in the model residuals. The Besag-York-Mollie (BYM) model was used to create Bayesian maps of the level of risk relative to that expected by the overall population. The association of the relative risk with the number of farmed swine was assessed with Spearman's correlation. The number of annual cases varied between 5 and 220 (mean: 65.13); the annual rate of reported cases varied between 0.03 and 1.9 cases per 105 inhabitants (mean: 0.53). The cases of trichinellosis in Chile showed a downward trend that has become more evident since the 1980s. No periodicities were detected via the autocorrelation function. Communes (the smallest geographical administrative subdivision) with high incidence rates and high relative risk were mostly observed in the Araucanía region. The relative risk of the commune was significantly associated with the number of farmed pigs and boar (Sus scrofa Linnaeus, 1758). The results allowed us to state that trichinellosis is not a (re)emerging disease in Chile, but the severe economic poverty rate of the Mapuche Indigenous peoples and the high number of backyard and free-ranging pigs seem to be associated with the high risk of trichinellosis in the Araucanía region.


Subject(s)
Swine Diseases/epidemiology , Trichinellosis/epidemiology , Animals , Bayes Theorem , Chile/epidemiology , Disease Outbreaks , Geographic Mapping , History, 20th Century , History, 21st Century , Incidence , Risk Assessment , Swine , Trichinella , Trichinellosis/history
17.
Transbound Emerg Dis ; 68(6): 3349-3359, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1526423

ABSTRACT

The influenza D virus (IDV) was first identified and characterized in 2011. Considering the virus' zoonotic potential, its genome nature (segmented RNA virus), its worldwide circulation in livestock and its role in bovine respiratory disease, an increased interest is given to IDV. However, few data are available on drivers of emergence of IDV. We first listed fifty possible drivers of emergence of IDV in ruminants and swine. As recently carried out for COVID-19 in pets (Transboundary and Emerging Diseases, 2020), a scoring system was developed per driver and scientific experts (N = 28) were elicited to (a) allocate a score to each driver, (b) weight the drivers' scores within each domain and (c) weight the different domains among themselves. An overall weighted score was calculated per driver, and drivers were ranked in decreasing order. Drivers with comparable likelihoods to play a role in the emergence of IDV in ruminants and swine in Europe were grouped using a regression tree analysis. Finally, the robustness of the expert elicitation was verified. Eight drivers were ranked with the highest probability to play a key role in the emergence of IDV: current species specificity of the causing agent of the disease; influence of (il)legal movements of live animals (ruminants, swine) from neighbouring/European Union member states and from third countries for the disease to (re-)emerge in a given country; detection of emergence; current knowledge of the pathogen; vaccine availability; animal density; and transport vehicles of live animals. As there is still limited scientific knowledge on the topic, expert elicitation of knowledge and multi-criteria decision analysis, in addition to clustering and sensitivity analyses, are very important to prioritize future studies, starting from the top eight drivers. The present methodology could be applied to other emerging animal diseases.


Subject(s)
COVID-19 , Influenza, Human , Orthomyxoviridae Infections , Swine Diseases , Animals , COVID-19/veterinary , Cattle , Europe/epidemiology , Humans , Orthomyxoviridae Infections/epidemiology , Orthomyxoviridae Infections/prevention & control , Orthomyxoviridae Infections/veterinary , SARS-CoV-2 , Swine , Swine Diseases/epidemiology , Swine Diseases/prevention & control
18.
Parasit Vectors ; 14(1): 248, 2021 May 10.
Article in English | MEDLINE | ID: covidwho-1506030

ABSTRACT

BACKGROUND: Swine coccidiosis, a protozoan disease caused by coccidia, can result in diarrhoea and weight loss in piglets and even economic losses in the pig industry. Here, we report the first systematic review and meta-analysis of the prevalence of coccidia (including Eimeria spp. and Cystoisospora suis) in pigs in China. METHODS: Five databases (PubMed, ScienceDirect, Chinese Web of Knowledge, Wanfang, and Chongqing VIP) were searched and 50 studies (46,926 domestic pigs, 22 provinces) ultimately identified pertaining to the prevalence of coccidia infection from 1980 to 2019. We incorporated the effect size using the random-effects model in the "meta" package in R software and conducted univariate and multivariate meta-regression analyses using a mixed-effects model. RESULTS: The pooled prevalence rate of coccidia in pigs was 21.9%, including the C. suis infection rate of 9.1%. The highest prevalence of coccidia (39.6%) was found in northwest China, and this region also presented the lowest prevalence of C. suis (4.7%). In the subgroup analysis based on sampling year, the highest prevalence of coccidia was detected in 2001 or earlier (32.6%), whereas the lowest rate was found in 2012 or later (14.3%). An opposite trend was observed for C. suis (5.5% in 2000 or earlier vs 14.4% in 2000 or later). The prevalence of coccidia in extensive farming systems (29.5%) was higher than that in intensive farming systems (17.3%). In contrast, the point estimate of C. suis prevalence was lower in the extensive farming systems (5.1%) than in the intensive farming systems (10.0%), but the difference was not significant (P > 0.05). Among the four age categories, the highest total coccidia prevalence (26.2%) was found in finishing pigs, followed by suckling piglets (19.9%), whereas the highest prevalence of C. suis (14.9%) was observed in suckling piglets. CONCLUSIONS: Our findings suggest that coccidia infection in Chinese pigs is common, although the prevalence of C. suis in pigs does not receive sufficient attention. We recommend the rational use of anticoccidial drugs to avoid drug resistance and the development of preventive and control measures for C. suis to reduce the incidence of swine coccidiosis.


Subject(s)
Coccidiosis/epidemiology , Swine Diseases/epidemiology , Animals , China/epidemiology , Coccidia/classification , Coccidia/genetics , Coccidia/isolation & purification , Coccidia/physiology , Coccidiosis/parasitology , Feces/parasitology , Prevalence , Swine , Swine Diseases/parasitology
19.
Transbound Emerg Dis ; 69(4): e505-e516, 2022 Jul.
Article in English | MEDLINE | ID: covidwho-1434843

ABSTRACT

African swine fever (ASF) is a contagious disease with high mortality in domestic and feral swine populations. Although it is not a zoonosis, its spread may have severe socio-economic and public health consequences. The activities of veterinary services are essential for controlling ASF outbreaks within a country, but also for diminishing its threat of spread to neighbouring countries, and for recognizing its entry into countries that are currently free. ASF requires quick responses and permanent monitoring to identify outbreaks and prevent spread, and both aspects can be heavily undercut during the COVID-19 pandemic. This paper analyses changing patterns of the main drivers and pathways for the potential introduction of ASFV into the United States during the COVID-19 pandemic, including international movements of people, swine products and by-products. Data on commercial flights and merchant ships was used as a proxy to indirectly assess the flow of illegal products coming from ASF affected countries. Results from this study highlight a decreasing trend in the legal imports of swine products and by-products from ASF affected countries (Sen's slope = -99, 95% CI: -215.34 to -21.26, p-value < 0.05), while no trend was detected for confiscations of illegal products at ports of entry. Additionally, increasing trends were detected for the monthly number of merchant ships coming from ASF affected countries (Sen's slope = 0.46, 95%CI 0.25-0.59), the monthly value of imported goods ($) through merchant ships (Sen's slope = 1513196160, 95%CI 1072731702-1908231855), and the monthly percentage of commercial flights (Sen's slope = 0.005, 95%CI 0.003-0.007), with the majority of them originating from China. Overall, the findings show an increased connection of the United States with ASF affected countries, highlighting the risk posed by ASF during a global public health crisis.


Subject(s)
African Swine Fever Virus , African Swine Fever , COVID-19 , Swine Diseases , African Swine Fever/epidemiology , African Swine Fever/prevention & control , Animals , COVID-19/epidemiology , COVID-19/veterinary , Disease Outbreaks/prevention & control , Disease Outbreaks/veterinary , Humans , Pandemics , Risk Factors , Sus scrofa , Swine , Swine Diseases/epidemiology , United States/epidemiology
20.
Transbound Emerg Dis ; 68(5): 2722-2732, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1411004

ABSTRACT

African Swine Fever Virus (ASFV) is a highly contagious pathogen that causes disease in pigs, commonly characterized by acute haemorrhagic fever. Prior to August 2018, African Swine Fever (ASF) had not been reported in Asia, but has since spread throughout China, Mongolia, Korea, Vietnam, Laos, Cambodia, Myanmar, the Philippines, Hong Kong, Indonesia, Timor-Leste and Papua New Guinea. Using data collated from reports of confirmed cases, we applied spatio-temporal analysis to describe ASFV spread throughout Asia during its early phase-from 1 August 2018 (reported start date) to 31 December 2019-to provide an overview and comparative analysis. Analysis revealed a propagating epidemic of ASFV throughout Asia, with peaks corresponding to increased reports from China, Vietnam and Laos. Two clusters of reported outbreaks were found. During the epidemic, ASFV primarily spread from the North-East to the South-East: A larger, secondary cluster in the North-East represented earlier reports, while the smaller, primary cluster in the South-East was characterized by later reports. Significant differences in country-specific epidemics, morbidity, mortality and unit types were discovered. The initial number of outbreaks and enterprise size are likely predictors of the speed of spread and the effectiveness of ASFV stamping out procedures. Biosecurity methods, wild boar populations and the transportation of pigs and movement of infected fomites are discussed as likely risk factors for facilitating ASFV spread across Asia.


Subject(s)
African Swine Fever Virus , African Swine Fever , Swine Diseases , African Swine Fever/epidemiology , Animals , Disease Outbreaks/veterinary , Hong Kong , Sus scrofa , Swine , Swine Diseases/epidemiology
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