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1.
Viruses ; 14(2)2022 01 18.
Article in English | MEDLINE | ID: covidwho-1715743

ABSTRACT

The African swine fever virus (ASFV) is a dsDNA virus that can cause serious, highly infectious, and fatal diseases in wild boars and domestic pigs. The ASFV has brought enormous economic loss to many countries, and no effective vaccine or treatment for the ASFV is currently available. Therefore, the on-site rapid and accurate detection of the ASFV is key to the timely implementation of control. The RNA-guided, RNA-targeting CRISPR effector CRISPR-associated 13 (Cas13a; previously known as C2c2) exhibits a "collateral effect" of promiscuous RNase activity upon the target recognition. The collateral cleavage activity of LwCas13a is activated to degrade the non-targeted RNA, when the crRNA of LwCas13a binds to the target RNA. In this study, we developed a rapid and sensitive ASFV detection method based on the collateral cleavage activity of LwCas13a, which combines recombinase-aided amplification (RAA) and a lateral flow strip (named CRISPR/Cas13a-LFD). The method was an isothermal detection at 37 °C, and the detection can be used for visual readout. The detection limit of the CRISPR/Cas13a-LFD was 101 copies/µL of p72 gene per reaction, and the detection process can be completed within an hour. The assay showed no cross-reactivity to eight other swine viruses, including classical swine fever virus (CSFV), and has a 100% coincidence rate with real-time PCR detection of the ASFV in 83 clinical samples. Overall, this method is sensitive, specific, and practicable onsite for the ASFV detection, showing a great application potential for monitoring the ASFV in the field.


Subject(s)
African Swine Fever Virus/isolation & purification , African Swine Fever/diagnosis , CRISPR-Cas Systems , African Swine Fever/virology , African Swine Fever Virus/genetics , Animals , Genotype , Reagent Strips , Recombinases/genetics , Recombinases/metabolism , Sensitivity and Specificity , Sus scrofa , Swine , Time Factors
2.
Sensors (Basel) ; 21(24)2021 Dec 08.
Article in English | MEDLINE | ID: covidwho-1592974

ABSTRACT

The encroachment of wild boars into urban areas is a growing problem. The occurrence of wild boars in cities leads to conflict situations. Socio-spatial conflicts can escalate to a varied degree. Assessments of these conflicts can be performed by analyzing spatial data concerning the affected locations and wild boar behaviors. The collection of spatial data is a laborious and costly process that requires access to urban surveillance systems, in addition to regular analyses of intervention reports. A supporting method for assessing the risk of wild boar encroachment and socio-spatial conflict in cities was proposed in the present study. The developed approach relies on big data, namely, multimedia and descriptive data that are on social media. The proposed method was tested in the city of Olsztyn in Poland. The main aim of this study was to evaluate the applicability of data crowdsourced from a popular social networking site for determining the location and severity of conflicts. A photointerpretation method and the kernel density estimation (KDE) tool implemented in ArcGIS Desktop 10.7.1 software were applied in the study. The proposed approach fills a gap in the application of crowdsourcing data to identify types of socio-spatial conflicts involving wild boars in urban areas. Validation of the results with reports of calls to intervention services showed the high coverage of this approach and thus the usefulness of crowdsourcing data.


Subject(s)
Social Media , Sus scrofa , Animals , Cities , Humans , Poland , Spatial Analysis , Swine
3.
Infect Genet Evol ; 96: 105140, 2021 12.
Article in English | MEDLINE | ID: covidwho-1565617

ABSTRACT

Classical swine fever virus (CSFV) is an RNA virus that incurs severe economic costs to swine industries worldwide. This study was conducted to investigate the genetic diversity among CSFV strains circulating in Vietnam, with a focus on their genetic variants relative to four vaccine strains. Samples from clinical cases were collected from different provinces of Central and Southern Vietnam from 2017 to 2019. 21 CSFV-positive samples were selected for amplification and sequencing of the full-length Erns and E2 genes. Phylogenetic analyses of these two genes showed that most CSFV strains circulating in Central and Southern Vietnam from 2017 to 2019 belong to subgroup 2.1c, whereas the remaining strains cluster into subgroup 2.2. All CSFV field strains in this study were genetically distant from group 1 strains. Analysis of the E2 and Erns genes indicated that all CSFV field strains have low sequence identity with the vaccine strains (80-83.5% and 82.3-86% sequence identity for E2 and Erns, respectively). Likewise, amino acid-level sequence analysis showed 87.3-91.1% and 87.6-91.6% sequence identity for E2 and Erns, respectively. Together, our findings indicate that CSFV strains circulating in Vietnam belong to subtypes 2.2 and 2.1c, and we also provide novel insights into the epidemiology, molecular characteristics, genetic diversity, and evolution of these circulating CSFV strains.


Subject(s)
Classical Swine Fever Virus/genetics , Genetic Variation , Membrane Glycoproteins/genetics , Viral Envelope Proteins/genetics , Animals , Classical Swine Fever/virology , Phylogeny , Sus scrofa , Swine , Vietnam
5.
Transbound Emerg Dis ; 68(6): 3194-3199, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1532923

ABSTRACT

African swine fever (ASF) is a contagious haemorrhagic disease in pigs and has become endemic in several Vietnam provinces since the first outbreak in 2019. The presence of carriers and the recurrence of disease in the surviving swine herd after an ASF outbreak has not previously been properly evaluated. In this study, pigs naturally infected with an acute form of ASF were allowed to recover from the disease. A serological follow-up was conducted for more than 14 months with 14 convalescent gilts and their offspring. All convalescent animals had long lasting high serum antibody levels without persistent viremia. They also did not excrete virus via nasal discharge post-recovery. These convalescent pigs could partially perform as replacement gilts despite the fact that ASF affected reproductive performance. Here, we confirmed that there were neither the carriers of nor recurrence of disease in the convalescent pigs and their offspring following the outbreak of acute ASF. These findings may facilitate efforts to design a new farming model in ASF endemic provinces in Vietnam where there is a lack of a repopulation strategy due to the limited funding received from the local regulatory authorities.


Subject(s)
African Swine Fever Virus , African Swine Fever , Swine Diseases , African Swine Fever/epidemiology , African Swine Fever Virus/genetics , Animals , Disease Outbreaks/veterinary , Female , Follow-Up Studies , Sus scrofa , Swine , Vietnam/epidemiology
6.
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
7.
Transbound Emerg Dis ; 68(5): 2787-2794, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1411002

ABSTRACT

African swine fever (ASF) is a severe haemorrhagic disease of domestic and wild pigs caused by the African swine fever virus (ASFV). In recent years, ASF has steadily spread towards new geographical areas, reaching Europe and Asia. On January 15th, 2019, Mongolia reported its first ASF outbreak to the World Organization for Animal Health (OIE), becoming, after China, the second country in the region affected by the disease. Following an event of unusual mortality in domestic pigs in Bulgan Province, a field team visited four farms and a meat market in the region to conduct an outbreak investigation and collect samples for laboratory analysis. Different organs were examined for ASF associated lesions, and total nucleic acid was extracted for real-time PCR, virus isolation and molecular characterization. The real-time PCR results confirmed ASFV DNA in 10 out of 10 samples and ASFV was isolated. Phylogenetic analysis established that ASFVs from Mongolia belong to genotype II and serogroup 8. The viruses were identical to each other, and to domestic pig isolates identified in China and Russia, based on the comparison of five genomic targets. Our results suggest a cross-border spread of ASFV, without indicating the source of infection.


Subject(s)
African Swine Fever Virus , African Swine Fever , Swine Diseases , African Swine Fever/epidemiology , African Swine Fever Virus/genetics , Animals , Genotype , Mongolia , Phylogeny , Sus scrofa , Swine
8.
Viruses ; 13(7)2021 06 30.
Article in English | MEDLINE | ID: covidwho-1335218

ABSTRACT

African swine fever (ASF) has been present in Lithuania since 2014. It is mainly the wild boar population that is affected. Currently, little is known about the epidemiological course of ASF in Lithuania. In the present study, ASF surveillance data from 2016-2021 were analyzed. The numbers of samples taken from hunted wild boar and wild boar found dead per year and month were recorded and the prevalence was estimated for each study month and administrative unit. A Bayesian space-time model was used to calculate the temporal trend of the prevalence estimates. In addition, population data were analyzed on a yearly basis. Most samples were investigated in 2016 and 2017 and originated from hunted animals. Prevalence estimates of ASF virus-positive wild boar decreased from May 2019 onwards. Seroprevalence estimates showed a slight decrease at the same time, but they increased again at the end of the study period. A significant decrease in the population density was observed over time. The results of the study show that ASF is still present in the Lithuanian wild boar population. A joint interdisciplinary effort is needed to identify weaknesses in the control of ASF in Lithuania and to combat the disease more successfully.


Subject(s)
African Swine Fever Virus/immunology , African Swine Fever/epidemiology , African Swine Fever/immunology , Epidemiological Monitoring/veterinary , Sus scrofa/virology , African Swine Fever Virus/pathogenicity , Animals , Bayes Theorem , Lithuania/epidemiology , Population Density , Prevalence , Seroepidemiologic Studies , Swine
9.
Viruses ; 13(6)2021 06 17.
Article in English | MEDLINE | ID: covidwho-1286941

ABSTRACT

In European countries, autochthonous acute hepatitis E cases are caused by Hepatitis E Virus (HEV) genotype 3 and are usually observed as sporadic cases. In mid/late September 2019, a hepatitis E outbreak caused by HEV genotype 3 was recognized by detection of identical/highly similar HEV sequences in some hepatitis E cases from two Italian regions, Abruzzo and Lazio, with most cases from this latter region showing a link with Abruzzo. Overall, 47 cases of HEV infection were finally observed with onsets from 8 June 2019 to 6 December 2019; they represent a marked increase as compared with just a few cases in the same period of time in the past years and in the same areas. HEV sequencing was successful in 35 cases. The phylogenetic analysis of the viral sequences showed 30 of them grouped in three distinct molecular clusters, termed A, B, and C: strains in cluster A and B were of subtype 3e and strains in cluster C were of subtype 3f. No strains detected in Abruzzo in the past years clustered with the strains involved in the present outbreak. The outbreak curve showed partially overlapped temporal distribution of the three clusters. Analysis of collected epidemiological data identified pork products as the most likely source of the outbreak. Overall, the findings suggest that the outbreak might have been caused by newly and almost simultaneously introduced strains not previously circulating in this area, which are possibly harbored by pork products or live animals imported from outside Abruzzo. This possibility deserves further studies in this area in order to monitor the circulation of HEV in human cases as well as in pigs and wild boars.


Subject(s)
Disease Outbreaks , Genotype , Hepatitis E virus/classification , Hepatitis E virus/genetics , Hepatitis E/epidemiology , Hepatitis E/transmission , Adult , Aged , Aged, 80 and over , Animals , Female , Hepatitis E/virology , Hepatitis E virus/pathogenicity , Humans , Italy/epidemiology , Male , Middle Aged , Phylogeny , Pork Meat/virology , RNA, Viral , Risk Factors , Sus scrofa/virology , Swine , Swine Diseases/transmission , Swine Diseases/virology
10.
Chaos ; 31(6): 061102, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1272874

ABSTRACT

African swine fever (ASF) is a highly contagious hemorrhagic viral disease of domestic and wild pigs. ASF has led to major economic losses and adverse impacts on livelihoods of stakeholders involved in the pork food system in many European and Asian countries. While the epidemiology of ASF virus (ASFV) is fairly well understood, there is neither any effective treatment nor vaccine. In this paper, we propose a novel method to model the spread of ASFV in China by integrating the data of pork import/export, transportation networks, and pork distribution centers. We first empirically analyze the overall spatiotemporal patterns of ASFV spread and conduct extensive experiments to evaluate the efficacy of a number of geographic distance measures. These empirical analyses of ASFV spread within China indicate that the first occurrence of ASFV has not been purely dependent on the geographical distance from existing infected regions. Instead, the pork supply-demand patterns have played an important role. Predictions based on a new distance measure achieve better performance in predicting ASFV spread among Chinese provinces and thus have the potential to enable the design of more effective control interventions.


Subject(s)
African Swine Fever Virus , African Swine Fever , African Swine Fever/epidemiology , Animals , Asia , China/epidemiology , Sus scrofa , Swine
11.
Artif Organs ; 45(10): 1173-1182, 2021 Oct.
Article in English | MEDLINE | ID: covidwho-1243590

ABSTRACT

Extracorporeal membrane oxygenation (ECMO) plays an important role in the coronavirus disease 2019 (COVID-19) pandemic. Management of thrombi in ECMO is generally an important issue; especially in ECMO for COVID-19 patients who are prone to thrombus formation, the thrombus formation in oxygenators is an unresolved issue, and it is very difficult to deal with. To prevent thromboembolic complications, it is necessary to develop a method for early thrombus detection. We developed a novel method for detailed real-time observation of thrombi formed in oxygenators using indocyanine green (ICG) fluorescence imaging. The purpose of this study was to verify the efficacy of this novel method through animal experiments. The experiments were performed three times using three pigs equipped with veno-arterial ECMO comprising a centrifugal pump (CAPIOX SL) and an oxygenator (QUADROX). To create thrombogenic conditions, the pump flow rate was set at 1 L/min without anticoagulation. The diluted ICG (0.025 mg/mL) was intravenously administered at a dose of 10 mL once an hour. A single dose of ICG was 0.25mg. The oxygenator was observed with both an optical detector (PDE-neo) and the naked eye every hour after measurement initiation for a total of 8 hours. With this dose of ICG, we could observe it by fluorescence imaging for about 15 minutes. Under ICG imaging, the inside of the oxygenator was observed as a white area. A black dot suspected to be the thrombus appeared 6-8 hours after measurement initiation. The thrombus and the black dot on ICG imaging were finely matched in terms of morphology. Thus, we succeeded in real-time thrombus detection in an oxygenator using ICG imaging. The combined use of ICG imaging and conventional routine screening tests could compensate for each other's weaknesses and significantly improve the safety of ECMO.


Subject(s)
Extracorporeal Membrane Oxygenation/adverse effects , Fluorescent Dyes , Indocyanine Green , Optical Imaging , Thrombosis/diagnostic imaging , Animals , Disease Models, Animal , Humans , Predictive Value of Tests , Sus scrofa , Thrombosis/etiology , Time Factors
12.
Biochem Biophys Res Commun ; 553: 25-29, 2021 05 14.
Article in English | MEDLINE | ID: covidwho-1147359

ABSTRACT

The current COVID-19 pandemic is caused by infections with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A sex-bias has been observed, with increased susceptibility and mortality in male compared to female patients. The gene for the SARS-CoV-2 receptor ACE2 is located on the X chromosome. We previously generated TP53 mutant pigs that exhibit a sex-specific patho-phenotype due to altered regulation of numerous X chromosome genes. In this study, we explored the effect of p53 deficiency on ACE2 expression in pigs. First, we identified the p53 binding site in the ACE2 promoter and could show its regulatory effect on ACE2 expression by luciferase assay in porcine primary kidney fibroblast cells. Later, quantitative PCR and western blot showed tissue- and gender-specific expression changes of ACE2 and its truncated isoform in p53-deficient pigs. We believe these findings will broaden the knowledge on ACE2 regulation and COVID-19 susceptibility.


Subject(s)
Angiotensin-Converting Enzyme 2/metabolism , Gene Expression Regulation , Organ Specificity , Sex Characteristics , Sus scrofa/metabolism , Tumor Suppressor Protein p53/metabolism , Angiotensin-Converting Enzyme 2/chemistry , Angiotensin-Converting Enzyme 2/genetics , Animals , Base Sequence , Binding Sites , COVID-19/metabolism , COVID-19/virology , Disease Models, Animal , Female , Fibroblasts , Gene Deletion , Male , Promoter Regions, Genetic/genetics , Tumor Suppressor Protein p53/deficiency , Tumor Suppressor Protein p53/genetics , X Chromosome/genetics
13.
Sci Rep ; 11(1): 3359, 2021 02 09.
Article in English | MEDLINE | ID: covidwho-1074114

ABSTRACT

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.


Subject(s)
Coronavirus Infections/genetics , Genetic Variation , Sus scrofa/genetics , Angiotensin-Converting Enzyme 2/genetics , Animals , Breeding , CD13 Antigens/genetics , Dipeptidyl Peptidase 4/genetics , Gene Frequency , Genetics, Population , High-Throughput Nucleotide Sequencing , Humans , INDEL Mutation , One Health , Polymorphism, Single Nucleotide , Receptors, Virus/genetics , Serine Endopeptidases/genetics , Swine , Whole Genome Sequencing
14.
Prev Vet Med ; 188: 105281, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1051106

ABSTRACT

Pigs (Sus scrofa) may be important surveillance targets for risk assessment and risk-based control planning against emerging zoonoses. Pigs have high contact rates with humans and other animals, transmit similar pathogens as humans including CoVs, and serve as reservoirs and intermediate hosts for notable human pandemics. Wild and domestic pigs both interface with humans and each other but have unique ecologies that demand different surveillance strategies. Three fundamental questions shape any surveillance program: where, when, and how can surveillance be conducted to optimize the surveillance objective? Using theory of mechanisms of zoonotic spillover and data on risk factors, we propose a framework for determining where surveillance might begin initially to maximize a detection in each host species at their interface. We illustrate the utility of the framework using data from the United States. We then discuss variables to consider in refining when and how to conduct surveillance. Recent advances in accounting for opportunistic sampling designs and in translating serology samples into infection times provide promising directions for extracting spatio-temporal estimates of disease risk from typical surveillance data. Such robust estimates of population-level disease risk allow surveillance plans to be updated in space and time based on new information (adaptive surveillance) thus optimizing allocation of surveillance resources to maximize the quality of risk assessment insight.


Subject(s)
Communicable Diseases, Emerging/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Public Health Surveillance/methods , Swine Diseases/epidemiology , Swine Diseases/virology , Zoonoses/epidemiology , Animals , Animals, Wild/virology , Coronavirus/isolation & purification , Disease Reservoirs/virology , Humans , Sus scrofa/virology , Swine/virology , Zoonoses/transmission
15.
Parasitology ; 148(3): 311-326, 2021 03.
Article in English | MEDLINE | ID: covidwho-912827

ABSTRACT

Cysticercosis caused by the metacestode larval stage of Taenia hydatigena formerly referred to as Cysticercus tenuicollis is a disease of veterinary importance that constitutes a significant threat to livestock production worldwide, especially in endemic regions due to condemnation of visceral organs and mortality rate of infected young animals. While the genetic diversity among parasites is found to be potentially useful in many areas of research including molecular diagnostics, epidemiology and control, that of T. hydatigena across the globe remains poorly understood. In this study, analysis of the mitochondrial DNA (mtDNA) of adult worms and larval stages of T. hydatigena isolated from dogs, sheep and a wild boar in China showed that the population structure consists of two major haplogroups with very high nucleotide substitutions involving synonymous and non-synonymous changes. Compared with other cestodes such as Echinococcus spp., the genetic variation observed between the haplogroups is sufficient for the assignment of major haplotype or genotype division as both groups showed a total of 166 point-mutation differences between the 12 mitochondrial protein-coding gene sequences. Preliminary analysis of a nuclear protein-coding gene (pepck) did not reveal any peculiar changes between both groups which suggests that these variants may only differ in their mitochondrial makeup.


Subject(s)
DNA, Helminth/genetics , DNA, Mitochondrial/genetics , Taenia/genetics , Taeniasis/veterinary , Amino Acid Sequence , Animals , China , DNA, Helminth/chemistry , DNA, Helminth/metabolism , DNA, Mitochondrial/chemistry , DNA, Mitochondrial/metabolism , Dog Diseases/parasitology , Dogs , Haplotypes , Larva/genetics , Larva/growth & development , Phylogeny , Sequence Alignment , Sheep , Sheep Diseases/parasitology , Sheep, Domestic , Sus scrofa , Swine , Swine Diseases/parasitology , Taenia/growth & development , Taenia/metabolism , Taeniasis/parasitology
16.
Vet Med Sci ; 6(3): 527-534, 2020 08.
Article in English | MEDLINE | ID: covidwho-888146

ABSTRACT

BACKGROUND: While porcine biological hazards have had the potential to be transmitted through feed and feed mills for decades, the emerging threat of foreign animal disease has elevated the concern that these may enter or be transmitted throughout the domestic swine herd via a feed vehicle. OBJECTIVE: The goal of this review was to describe the current classification for emerging porcine biological pathogen transmission through the feed supply chain so resources can be best directed towards those of highest risk. METHODS: By assessing the pathogen severity to pigs and the probability of pathogen transmission through feed, an overall risk can be established using a hazard analysis matrix. RESULTS: There is negligible risk for feed-based transmission of a transmissible spongiform encephalopathy, Trichinella spiralis, Toxoplasma gondii, Salmonella Choleraesuis, Salmonella spp. except Choleraesuis and I 4,[5],12:i:-, porcine deltacoronavirus, Senecavirus A, mammalian orthoreovirus 3, foot and mouth disease virus, classical swine fever virus or Chinese pseudorabies virus. However, the combined severity and probability of Salmonella enterica serotype I 4,[5],12:i:-, porcine epidemic diarrhoea virus and African swine fever virus warrant a moderate risk characterization for transmission through the US feed supply chain. CONCLUSIONS: This risk can be maintained below critical status by minimizing the likelihood that a pathogen can enter the feed supply chain, such as by excluding high-risk ingredients from facilities, extending biosecurity to mills, and considering proactive mitigation strategies. In reality, all these actions may be necessary to prevent the detrimental transmission of porcine biological hazards into the US swine herd through the feed supply chain.


Subject(s)
Swine Diseases/transmission , Animal Feed/analysis , Animals , Sus scrofa , Swine
17.
Vet Med Sci ; 6(4): 854-859, 2020 11.
Article in English | MEDLINE | ID: covidwho-826351

ABSTRACT

Porcine deltacoronavirus (PDCoV) has been detected sporadically in China since its first description in 2012. In our study, 62 faecal and intestinal samples from pigs with diarrhoea were collected in Guangxi Province, China, during 2017 and 2018. Twelve samples (19.4%, 12/62) were positive for PDCoV. Five complete genomes of PDCoV were then determined, and sequence alignment revealed that the five strains had discontinuous deletions at 400-401 aa in non-structural protein 2 (NSP2) and 758-760 aa in non-structural protein 3 (NSP3) compared with the respective proteins in the HKU15-44 strain. Notably, the CHN-GX81-2018 strain contained two insertions in the S gene and 3'-UTR. Multiple sequence alignment and phylogenetic analysis showed that four strains shared 98.2%-98.4% nucleotide identity with CHN-AH-2004 and were classified into a new cluster of China lineage strains, whereas the CHN-GX81-2018 strain shared 98.7% nucleotide identity with Vietnam/Binh21/2015 and belonged to the Vietnam/Laos/Thailand lineage. Recombination analyses revealed that four strains were the result of recombination between CHN-HB-2014 and Vietnam/Binh21/2015 strains. This study demonstrated the co-existence of multiple lineages of PDCoV in China, and our findings will aid the reorganization and evolution of the virus.


Subject(s)
Coronavirus Infections/veterinary , Deltacoronavirus/isolation & purification , Swine Diseases/epidemiology , Animals , China/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Phylogeny , Prevalence , Sequence Alignment , Sequence Analysis, DNA/veterinary , Sus scrofa , Swine , Swine Diseases/virology
18.
J Vet Diagn Invest ; 32(4): 572-576, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-823306

ABSTRACT

Porcine epidemic diarrhea, a disease caused by porcine epidemic diarrhea virus (PEDV), results in large economic losses to the global swine industry. To manage this disease effectively, it is essential to detect PEDV early and accurately. We developed a sensitive and accurate droplet digital PCR (ddPCR) assay to detect PEDV. The optimal primer-to-probe concentration and melting temperature were identified as 300:200 nM and 59.2°C, respectively. The specificity of the ddPCR assay was confirmed by negative test results for common swine pathogens. The detection limit for the ddPCR was 0.26 copies/µL, which is a 5.7-fold increase in sensitivity compared to that of real-time PCR (rtPCR). Both ddPCR and rtPCR assays exhibited good linearity, although ddPCR provided higher sensitivity for clinical detection compared to that of rtPCR. Our ddPCR methodology provides a promising tool for evaluating the PEDV viral load when used for clinical testing, particularly for detecting samples with low-copy viral loads.


Subject(s)
Coronavirus Infections/veterinary , Polymerase Chain Reaction/veterinary , Porcine epidemic diarrhea virus/isolation & purification , Swine Diseases/diagnosis , Viral Load/veterinary , Animals , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Polymerase Chain Reaction/methods , Sensitivity and Specificity , Sus scrofa , Swine , Swine Diseases/virology
19.
Prev Vet Med ; 175: 104848, 2020 Feb.
Article in English | MEDLINE | ID: covidwho-831031

ABSTRACT

It is well known that infectious diseases such as porcine reproductive and respiratory syndrome (PRRS) and porcine epidemic diarrhea (PED) decrease herd productivity and lead to economic loss. It is believed that biosecurity practices are effective for the prevention and control of such infectious diseases. Therefore, the objective of the present study was to investigate whether or not an association between biosecurity level and herd productivity, as well as disease status exists on Japanese commercial swine farms. The present study was conducted on 141 farms. Biosecurity in each farm was assessed by a biosecurity assessment tool named BioAsseT. BioAsseT has a full score of 100 and consists of three sections (external biosecurity, internal biosecurity and diagnostic monitoring). Production data for number of pigs weaned per sow per year (PWSY) and post-weaning mortality per year (PWM) were collected for data analysis. Regarding PRRS status, the farms were categorized into two groups: unknown or unstable and stable or negative. In addition, these farms were categorized based on their PED status, either positive or negative. The total BioAsseT score was associated with herd productivity: as total score increased by 1, PWSY increased by 0.104 pigs and PWM decreased by 0.051 % (P < 0.05). Herd productivity was associated with the score of external and internal biosecurity (P < 0.05), but did not correlate with the score of diagnostic monitoring. Regarding PRRS status, farms with an unknown or unstable status had lower total score than those with stable or negative status (P < 0.05). Similarly, PED positive farms had a lower total score compared to PED negative farms (P < 0.05). In conclusion, the present study provides evidence for the association between high biosecurity levels and increased herd productivity as well as a decreased risk for novel introductions of infectious diseases such as PED.


Subject(s)
Animal Husbandry/methods , Porcine epidemic diarrhea virus/physiology , Porcine respiratory and reproductive syndrome virus/physiology , Swine Diseases/mortality , Animals , Coronavirus Infections/mortality , Coronavirus Infections/veterinary , Female , Japan/epidemiology , Porcine Reproductive and Respiratory Syndrome/mortality , Reproduction , Sus scrofa/physiology , Swine
20.
Acta Vet Scand ; 62(1): 35, 2020 Jun 24.
Article in English | MEDLINE | ID: covidwho-799111

ABSTRACT

BACKGROUND: Respiratory diseases are major health concerns in the pig production sector worldwide, contributing adversely to morbidity and mortality. Over the past years there was a rise in reported incidents of respiratory disease in pigs in Norway, despite population wide freedom from Aujeszky´s disease, porcine reproductive and respiratory syndrome, porcine respiratory corona virus and enzootic pneumonia. The main objective of this study was to investigate acute outbreaks of respiratory disease in conventional Norwegian fattening pig herds. The study included 14 herds. In seven herds with reported outbreaks of acute respiratory disease, data on clinical signs was recorded and samples for laboratory examination were collected. Diagnostic protocols were compared by parallel analysis of clinically healthy pigs from seven non-outbreak herds. RESULTS: The most commonly reported clinical signs were sudden deaths and dyspnea. An average compartment morbidity of 60%, mortality of 4% and case fatality of 9% was recorded in the outbreak herds. Post-mortem examinations revealed acute lesions resembling porcine pleuropneumonia in all 28 pigs investigated from the outbreak herds and in 2 of the 24 (8%) pigs from the non-outbreak herds. Chronic lesions were recorded in another 2 pigs (8%) from the non-outbreak herds. Actinobacillus pleuropneumoniae serovar 8 was isolated from lungs and/or pleura from all tested pigs (n = 28) in the outbreak herds, and from 2 out of 24 pigs (8%) in the non-outbreak herds, one pig with an acute and another pig with a chronic infection. No other significant bacterial findings were made. Seroconversion to A. pleuropneumoniae antibodies was detectable in all outbreak herds analyzed and in six out of seven non-outbreak herds, but the risk ratio for seroconversion of individual pigs was higher (risk ratio 2.3 [1.50- 3.43 95% CI; P < 0.001]) in the outbreak herds. All herds tested positive for porcine circovirus type 2 and negative for influenza A viruses on oral fluid RT-qPCR. CONCLUSION: The main etiological pathogen found during acute outbreaks of respiratory disease was A. pleuropneumoniae serovar 8. All pigs from outbreak herds had typical lesions of acute porcine pleuropneumonia, and only A. pleuropneumoniae serovar 8 was identified. Co-infections were not found to impact disease development.


Subject(s)
Acute Disease/epidemiology , Disease Outbreaks/veterinary , Respiratory Tract Diseases/veterinary , Swine Diseases/epidemiology , Animals , Norway/epidemiology , Respiratory Tract Diseases/epidemiology , Respiratory Tract Diseases/microbiology , Respiratory Tract Diseases/virology , Sus scrofa , Swine , Swine Diseases/microbiology , Swine Diseases/virology
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