Pigs In India Research Articles

Pathomolecular epidemiology, antimicrobial resistance, and virulence genes of Streptococcus dysgalactiae subsp. equisimilis isolates from slaughtered pigs in India.

We aimed to investigate the prevalence, pathology, and characterization of Streptococcus dysgalactiae subsp. equisimilis (SDSE) in slaughtered pigs of India. We collected 1254 morbid tissues (lungs-627 and spleen-627) and 627 heart-blood from 627 slaughtered pigs. The bacterial isolation, antibiogram, virulence gene profiling, and mouse pathogenicity testing were performed for the detection and characterization of SDSE. A total of 177 isolates (heart-blood-160 and tissues-17) were recovered from 627 slaughtered pigs with higher isolation rate in heart-blood (25.51%). The prevalence of SDSE was 11% in morbid tissues by polymerase chain reaction. Majority of isolates showed higher detection of streptolysin O, followed by streptokinase and extracellular phospholipase A virulence genes with higher degree of resistance to azithromycin, clindamycin, erythromycin, and penicillin antibiotics. Mouse pathogenicity testing confirmed virulence based on histopathological lesions and re-isolation of SDSE. Our findings highlight the high prevalence of SDSE in slaughtered pigs. The presence of virulence genes and mouse pathogenicity testing confirm their pathogenic potential.

Rotavirus C infections in asymptomatic piglets in India, 2009-2013: genotyping and phylogenetic analysis of all genomic segments.

Asymptomatic infection with rotavirus C (RVC) was observed in pigs in India, with a detection rate of 20%. Sequencing of the VP6, VP7, and NSP4 genes of RVC strains identified the genotypes I7/I10, G1, and E5, respectively. Full genome sequencing of one of these strains revealed that the genotypes of the VP4, VP1, VP2, VP3, NSP1, NSP2, NSP3, and NSP5 genes were P1, R1, C1, M3, A1, N5, T5, and H1, respectively. The detection of porcine RVC strains at two different locations in India at different time points strongly suggests that they are circulating continuously in the pig population through asymptomatic infections.

First report on co-isolation and whole-genomic characterisation of mammalian orthorubulavirus 5 and mammalian orthoreovirus type 3 from domestic pigs in India.

During a surveillance study to monitor porcine epidemic diarrohoea virus and transmissible gastroenteritis virus in India, a total of 1043 swine samples including faeces (n = 264) and clotted blood (n = 779) were collected and tested. Five samples (four faecal and one serum) showed cytopathic effects in Vero cells. Transmission electron microscopy of infectious cell supernatant revealed the presence of two types of virions. Next-generation sequencing (de novo) allowed the complete genome sequence of mammalian orthorubulavirus 5 (MRuV5; 15246 bp) and that of all 10 gene segments of mammalian orthoreovirus to be determined. Genetic analysis of MRuV5 revealed grouping of the Indian MRuV5 with isolates from various mammalian species in South Korea and China, sharing more than 99% nucleotide sequence identity. The deduced amino acid sequences of the HN, NP, and F genes of MRuV5 isolates showed three (92L, 111R, 447H), two (86S, 121S), and two (139T, 246T) amino acid substitutions, respectively, compared to previously reported virus strains. Phylogenic analysis based on S1 gene sequences showed the Indian MRV isolates to be clustered in lineage IV of MRV type 3, with the highest nucleotide sequence identity (97.73%) to MRV3 strain ZJ2013, isolated from pigs in China. The protein encoded by the MRV3 S1 gene was found to contain the amino acid residues 198-204NLAIRLP, 249I, 340D, and 419E, which are known to be involved in sialic acid binding and neurotropism. This is the first report of co-isolation and whole-genomic characterisation of MRuV5 and MRV3 in domestic pigs in India. The present study lays a foundation for further surveillance studies and continuous monitoring of the emergence and spread of evolving viruses that might have pathogenic potential in animal and human hosts.

Complete genome analysis of African swine fever virus isolated from domestic pigs during the first ASF outbreaks in India

African swine fever (ASF), considered as the most dreadful swine disease due to its very high mortality, emerged in India in 2020. The complete genome analysis of ASF viruses isolated during the first outbreaks in India showed a few unique non-synonymous mutations in MGF 369-11L, MGF 505-4R, K205R and B263R genes. Frame shifts in the protein coding sequences were observed in DP60R, ASFV-G_ACD 00190, MGF 110-10-L-MGF110-14L fusion, MGF 360-14L and I267L genes of Indian ASF viruses as compared to ASFV/Georgia/2007. Complete genome based phylogenetic analysis of p72-genotype-II viruses showed the clustering of Indian isolates with ASFV/Wuhan/2019 in a separate clade. Phylogenetic analysis of concatenated sequences of 14 open reading frames (ORF) having single nucleotide polymorphisms (SNP) showed distinct grouping of Indian ASFVs with other Asian ASFVs. This is the first complete genome characterization of ASF viruses isolated from domestic pigs in India. The results indicate that number of Tandem Repeat Sequence (TRS) in the intergenic region between I73R and I329L genes, and the 14 ORFs with SNP reported in this study could be the genetic determinants to differentiate the closely related p72-genotype II viruses circulating in Asia.

Transmission of Novel Bacterial Pathogens through Pigs Transported from Myanmar to Mizoram

Background: Illegal migration of pigs/piglets from Myanmar to Mizoram is a common practice to meet the local demands. The migrated animals are suspected as potential carrier of various microbial pathogens. The present study was conducted on isolation, identification and molecular characterization of major bacterial pathogens (Actinobacillus pleuropneumoniae, Bordetella bronchiseptica, Haemophilus parasuis, Mycoplasma hyopneumoniae and Pasteurella multocida) in pigs illegally migrated from Myanmar to Mizoram. Methods: A total of 209 rectal swabs and 209 nasal swabs were collected from apparently healthy migrated pigs during October 2018 to April, 2019. All the samples were processed for PCR based detection of target bacterial species followed by isolation and identification by bacteriological techniques. The bacterial species were further confirmed by BD Phoenix automated bacterial identification system and selected virulence genes of the bacterial species were determined by specific PCR assay. Result: By species specific PCR, 110 samples were found to be positive for selected bacterial species, of which 20 (9.57%), 1 (0.478%), 86 (41.15%), 2 (0.956%) and 1 (0.478%) were A. pleuropneumoniae, B. bronchiseptica, H. parasuis, M. hyopneumoniae and P. multocida, respectively. A total of 52 bacterial strains were isolated and identified, of which 11, 1, 39 and 1 were A. pleuropneumoniae, B. bronchiseptica, H. parasuis, M. hyopneumoniae and P. multocida, respectively. Virulence genes were detected in A. pleuropneumoniae and H. parasuis isolates. Based upon the published literatures, this is the first ever report of isolation and identification of pathogenic A. pleuropneumoniae and H. parasuis in pigs in India.

Estimating Heterogeneity and Pooled Prevalence of Classical Swine Fever in Pigs in India: A Meta-analysis

Background: Classical swine fever (CSF) is caused by small enveloped RNA virus that belongs to the Flaviviridae family and causes high morbidity and mortality events for pig farming. In India, it is highly prevalent but with varied distribution in various geographical areas resulting in substantial economic losses to farmers. The discrepancy in prevalence estimates across studies needs to be evaluated in order to strengthen the prevention and control strategies of CSF in pigs. The aim of the present study was to provide the pooled estimate of the prevalence of classical swine fever (CSF) in India and to examine the consistency of those estimates between published studies.Methods: The data regarding prevalence of CSF in 7045 pigs were compiled from 22 published studies using comprehensive literature search for period from 1998 to 2018. The pooled prevalence of CSF was obtained under random effects model and heterogeneity between studies was determined using I² Index. Representation of meta-analysis was done using forest plot and followed by funnel plot, Baujat plot and radial plot.Result: The result of Meta-analysis revealed that pooled estimate of prevalence of CSF under random effects model was 45% (95% confidence interval: 35, 55%) in India. The heterogeneity statistic (Q) was found to be significant (p less than 0.001) with I² = 98% which indicated that prevalence of CSF was inconsistent between the studies. Likewise, results of funnel plot and Radial plot indicated heterogeneity between studies. Most influential studies for overall heterogeneity were identified using Baujat and radical plots.

Development of cost-effective quantitative PCR method for parallel detection of porcine circovirus2 and porcine parvovirus in perspective of North-eastern India.

Pig farming performs as an intricate part in the socio-economic situation in the north-eastern region of India. This region contributes 38% (3.95 million) of total pigs in India. In spite of this, the region unables to flourish as an enterprise as per the expectation due to a low productivity rate. Porcine infectious pathogens like porcine cirovirus2 (PCV2) and porcine parvovirus (PPV) have a direct economic impact on pig farming through slow growth rate, abortion, and mortality and ultimately maximize the production cost by increasing the usage of antibiotic or antiviral drugs. The veterinary diagnostic infrastructure is a fundamental aspect of the development of livestock status by rapid and effective detection of pathogens. Quantitative PCR (qPCR) is a precise and fast-track technique used for the routine diagnostic method. Hence, we developed a highly precise and comparatively cost-effective SYBR Green reporter dye-based qPCR assay for parallel identification of PCV2 and PPV. In the present assay, the correlation coefficient (R2) value was 0.99, and 10 copies of the gene/μl were the least limit of detection (LOD) concerning both viruses. Melt curve analysis of this study represented PCV2-specific melt curve (Tm) at 81.2 °C and PPV-specific melt curve (Tm) at 73.5 °C. Therefore, the assay easily differentiates the true positive amplicons of PCV2 and PPV through specific Tm values. Among the 50 field samples, 26 (52%) samples were PCV2 positive, 18 (36%) samples PPV positive, and 11 (22%) samples were co-infected of both the viruses. This method is cost-effective, precise, and sensitive to diagnose the concurrent or individual infection of the PCV2 and PPV in the pig. Hence, considering the impact of pig farming in the north-eastern part of the country, the present assay gives an unprecedented achievement in disease diagnosis.

Genetic characterization of African swine fever virus from domestic pigs in India.

African swine fever (ASF) is the most dreaded disease of pigs, which can cause mortality of up to 100%. Following disease outbreaks with high mortality in pigs in two states of north-east India, namely Arunachal Pradesh and Assam in early 2020, we confirmed the first occurrence of African swine fever (ASF) in domestic pigs in India by real-time PCR, virus isolation and nucleotide sequencing. Genetic analyses in three independent genomic regions (B646L gene encoding the p72 protein, E183L gene encoding the p54 protein and the central variable region (CVR) of B602L gene) showed that the Indian ASF viruses are similar to the post-2007-p72-genotype II viruses reported from Asia and Europe, suggesting the transboundary expansion of ongoing ASF outbreaks in the region.

Detection of coinfection of a divergent subgroup of genotype I Japanese encephalitis virus in multiple classical swine fever virus outbreaks in pigs of Assam, India.

A retrospective investigation of pig tissue samples from different classical swine fever virus (CSFV) outbreaks was undertaken employing RT-PCR for possible coinfection with other swine viruses. Four samples from three different outbreaks were found to be coinfected with Japanese encephalitis virus (JEV). Phylogenetic analysis was done based on complete E gene sequenced from all four coinfected samples. This revealed a new introduction of a divergent subgroup of JEV genotype I in India. This is the first report of detection of coinfection of JEV and CSFV in pigs and the first incidence of JEV genotype I in pigs in India.

Detection and genetic characterization of porcine circovirus 3 (PCV3) in pigs in India.

Porcine circovirus type 3 (PCV3), a novel circovirus, has been reported recently from major swine growing countries globally, and the virus is associated with diseases like porcine dermatitis, nephropathy syndrome and reproductive failure. This report describes the identification of PCV3 associated with reproductive failure in sows and piglet mortality and circulation of the virus in healthy pigs in India. The pathological changes in various tissues from stillborn piglet and characterization of the virus genomes were reported. The genome sequences of Indian PCV3 strains showed 91.4%-99.8% nucleotide identity with other sequences of PCV3 strains circulating worldwide. The phylogenetic analysis showed clustering of Indian strains into a separate group with the isolate from USA (MN/2016) under PCV3a genotype. The results confirmed the circulation of PCV3 in Indian pigs and its association with clinical cases. This study speculates emergence of PCV3 as an important pig pathogen in the country, which warrants the thorough investigation on PCV3 epidemiology, pathogenesis and to implement the control measures.

Identification and genotypic characterization of porcine teschovirus from selected pig populations in India

Porcine teschovirus (PTV) previously classified as porcine enteroviruses in the family Picornaviridae are associated with a wide range of illnesses in swine ranging from asymptomatic infection to acute fatal encephalomyelitis, diarrhea, and pneumonia. This study was planned to investigate whether porcine teschovirus is prevalent among pigs in India and to characterize the PTV identified in the study population. The study conducted in certain farms of North India revealed that 13 of 190 (6.84%) fecal samples were PTV positive by RT-PCR. Three viruses were successfully isolated from fecal samples using IB-RS-2 cell lines which were confirmed by RT-PCR and sequencing. Molecular characterization based on the VP1 region of the viral genome identified the isolated viruses as serotype 5 and serotype 8 of PTV. A new variant of teschovirus was also identified which showed significant nucleotide diversity from the known serotypes of the teschoviruses. This is the first report of isolation, identification, and characterization of porcine teschoviruses in India.

Prevalence, molecular detection and risk factors investigation for the occurrence of Toxoplasma gondii in slaughter pigs in North India

BackgroundToxoplasma gondii, an important food borne zoonotic parasite, infects almost all warm-blooded animals including pigs. People primarily become infected with T. gondii via consuming meat of infected animals. Status of T. gondii is largely unknown in pigs in India including northern regions. We, therefore, determined the prevalence of T. gondii infection in pigs from North India.ResultsDNA of T. gondii was detected in 6.7% (54/810) of the tested slaughter pigs. Highest prevalence was observed in pigs from Punjab (8.2%) followed by Chandigarh (5.3%) and Uttarakhand (4.8%). Phylogenetic analysis revealed that the isolates from pigs had 96–100% nucleotide identity with Type I RH strain (AF179871), 96–99.7% with VEG type III strain (LN714499) and 67–72% with type II ME 49 strain (XM002370240). However, low level of polymorphism in the targeted B1 gene did not allow the determination of the clonal lineages of the isolates. Antibodies against T. gondii was reported in 48.3% (73/151) of the sera obtained from pigs slaughtered at Chandigarh abattoir, and scavenging by pigs was a significant risk factor.ConclusionPrevalence of T. gondii DNA was low in pigs in North India, however, presence of the parasite warrants food safety concerns. Further studies are required to identify the clonal lineage of T. gondii circulating in pigs reared in North India. Pig farmers should be educated about the hygienic management practices.

Estimation of economic losses due to classical swine fever in pigs in Mizoram

Classical swine fever (CSF) also known as 'hog choleraâ' is an important viral disease of pigs in India with serious economic concern due to morbidity and mortality, and affects a vast section of the pig population in India. In present study, a structured sampling design was adopted, which covered the major regions of the Mizoram, to ascertain the economic losses due to CSF in pigs. Available estimates of the economic losses of Mizoram due to CSF are based on single values of various epidemiological and economic parameters. Overall annual morbidity, mortality and case fatality rates of CSF in Mizoram were 8.35, 5.07 and 60.70% respectively. The expected annual economic loss due to CSF in pigs in Mizoram was ` 16,69,34,465. Losses due to mortalities contributed the most to the total economic loss caused by CSF in pigs, followed by loss in body weight. This study revealed significant losses due to the incidence of CSF in pigs of Mizoram.

First report and genetic characterization of porcine astroviruses of lineage 4 and 2 in diarrhoeic pigs in India.

Porcine astroviruses (PAstVs) have extended their distribution globally and have a high prevalence; however, their clinical significance is still under investigation. Thus far, information about their prevalence and diversity in the Indian pig population is unknown. This study is the first report on the prevalence and genetic characterization of PAstVs in diarrhoeic piglets in India. From January 2013 to December 2017, 757 samples were screened using an RT-PCR assay and PAstV infection was detected in 17.6% (133/757) pigs. Of the 133 positive samples, 79 (59.4%) were positive for PAstV alone, whereas 54 (40.6%) were found to be co-infected with porcine rotavirus A (PoRVA). Phylogenetic analysis of RdRp/capsid gene region revealed high genetic heterogeneity among PAstV sequences, with a predominance of PAstV lineage 4 and detection of lineage 2. The lineage 4 PAstVs exhibited 61.2%-94.5% sequence similarity at the nucleotide level to other reported sequences, whereas lineage 2 strain shared 66.0%-71.6% sequence identity with cognate sequences of the same lineage. This is the first report on PAstV and circulation of lineages 4 and 2 in India. Further, phylogenetic analysis indicates a multiphyletic origin of PAstV strains and suggests cross-border circulation of PAstVs with a similar genetic configuration in Asian countries.

Meta-analysis of classical swine fever prevalence in pigs in India: A 5-year study.

Aim:The aim of the study was to determine the overall prevalence of classical swine fever (CSF) in pigs in India, through a systematic review and meta-analysis of published data.Materials and Methods:Consortium for e-Resources in Agriculture, India, Google Scholar, PubMed, annual reports of All India Coordinated Research Project on Animal Disease Monitoring and Surveillance, and All India Animal Disease database of NIVEDI (NADRES) were used for searching and retrieval of CSF prevalence data (seroprevalence, virus antigen, and virus nucleic acid detection) in India using a search strategy combining keywords and related database-specific subject terms from January 2011 to December 2015 in English only.Results:A total of 22 data reports containing 6,158 samples size from 18 states of India were used for the quantitative synthesis, and overall 37% (95% confidence interval [CI]=0.24, 0.51) CSF prevalence in India was estimated. The data were classified into 4 different geographical zones of the country: 20% (95% CI=0.05, 0.55), 31% (95% CI=0.18, 0.47), 55% (95% CI=0.32, 0.76), and 34% (95% CI=0.14, 0.62). CSF prevalence was estimated in northern, eastern, western, and southern regions, respectively.Conclusion:This study indicates that overall prevalence of CSF in India is much lower than individual published reports.

Bacterial diseases of pigs in India: A review

Bacterial diseases of pigs are important as they cause considerable economic loss due to high morbidity and mortality of the animals. A number of bacterial diseases have been reported by various workers from different parts of the country. Besides the common bacterial diseases, there are incidence of brucellosis, swine erysipelas, greasy pig disease, Streptococcus suis infection and methicillin resistant Staphylococcus aureus infection in pigs. Identification of different serotypes and virulence genes of some of the bacterial pathogens has also been made. An overall picture of bacterial diseases of pigs in India is given in this short review.

Dynamics of cytokine gene expression in peripheral blood mononuclear cells of indigenous and exotic breeds of pigs in India.

To incorporate immune competence traits in swine breeding programs, association between immune responsiveness and susceptibility to specific infectious diseases must be established. In order to understand the differences in immune competence between indigenous (Zovawk) and exotic (Large White Yorkshire: LWY) pigs reared in India, we carried out a time course expression analysis of immune-regulating key cytokine genes (interleukin (IL)-2, interferon (IFN)-γ, IL-4 and IL-10) in the phytohemagglutinin-P stimulated peripheral blood mononuclear cells (PBMCs). The IL-2 transcript levels in PBMCs increased several thousand-fold when compared to unstimulated cells in both the breeds, albeit the response in that of Zovawk was remarkably higher. Higher and earlier IFN-γ and IL-4 expression levels in Zovawk pigs suggest that both TH 1 and TH 2 immune responsiveness of this indigenous breed affords better preparedness for danger signals. Moreover, the low expression levels of IL-10 depict a regulated adaptive immune responsiveness. Remarkable difference between the two breeds of the pigs is evident showing a clear advantage of the Zovawk over LWY in terms of a shorter lag period of adaptive immune response. These findings provide a lead for understanding the genetic differences with respect to immune competence levels of indigenous pigs compared to exotic counterparts.

Porcine sapelovirus among diarrhoeic piglets in India.

Porcine sapelovirus (PSV) A belongs to the genus Sapelovirus, family Picornaviridae. PSV infections in pigs have been reported from European countries, United States, Japan, China, Korea and Brazil. The virus has been isolated/detected from faeces of healthy pigs as well as those affected with diarrhoea, respiratory signs, encephalitis, skin lesions and fertility disorders. This study was planned to investigate whether PSV is prevalent among pigs in India and to characterize PSV encountered in the study population. The study revealed that five of 70 (7.14%) faecal samples were found positive for PSV using RT-PCR. Three viruses were successfully isolated from faecal samples using IB-RS-2 cell line. Complete genome sequencing and analysis of one Indian PSV isolate revealed highest homology (88%) with V13 strain from England. Phylogenetic analysis of the complete polyprotein nucleotide sequences of 14 strains of PSV classified the viruses into four distinct clades. This first report from India adds to our knowledge on genetic diversity of PSV detected so far among pigs in different countries. A large-scale surveillance of the virus is required to understand its genomic diversity and economic impact.

Prevalence of gastro intestinal parasites in pigs in Punjab, India.

Gastrointestinal parasites are a common problem in pigs in India. The important risk factors include coprophagic behaviour of pigs and their free access to garbage. To investigate the gastrohelmenthic spectrum in pigs of Punjab, we examined 265 faecal samples from farm (n=47) and scavenging pigs (n=218) using faecal floatation method. Ascaris suum, unsporulated oocysts, Trichuris spp. and Strongyloides were recorded in 27.5, 15.4, 1.8 and 4.5% of the pig faecal samples, respectively. Overall prevalence was significantly higher in pigs >1year (56.5%) than pigs ≤1year (39.6; p=0.01) Parasite positivity was neither significantly related with location (p=0.309) nor with management practices (p=0.69). High prevalence of gastro intestinal parasites in pigs in Punjab warrants intervention policies to control this problem.

Isolation and genetic characterization of swinepox virus from pigs in India.

Swinepox virus (SWPV), a member of the genus Suipoxvirus causes generalized pock-like lesions on the body of domestic and wild pigs. Although outbreak has been reported in India since 1987, virus isolation and genetic characterization remained elusive. In September 2013, an outbreak of acute skin infection occurred in piglets in a commercial piggery unit at Rohtak district in Haryana, India. The presence of SWPV in scab samples collected from piglets succumbed to infection was confirmed by virus isolation, PCR amplification of SWPV-specific gene segments and nucleotide sequencing. Phylogenetic analysis of host-range genes of the SWPV revealed that the Indian isolate is genetically closely related to reference isolate SWPV/pig/U.S.A/1999/Nebraska. To the best of our knowledge this is the first report on isolation and genetic characterization of SWPV from pigs in India.