Molecular characterization and phylogenetic analysis of foot and mouth disease virus isolates in Sulaimani province, Iraq.
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ABSTRACT:
SUBMITTER: Baba Sheikh M
PROVIDER: S-EPMC8328259 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Aim:This study was directed during an outbreak of suspected foot-and-mouth disease (FMD) in cattle in Al-Qadisiyah province, Iraq 2016. The disease has made a huge economic loss in livestock. It was suspected that the vaccination has failed to protect the animals from the infection because of the difference in the strains. Consequently, we designed the study to make the diagnosis and detect the strain of the causative virus. Materials and Methods:The extraction of the DNA was done on 73 samples and Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) was used in the detection of FMD virus (FMDV) for primary diagnosis, and serotype-specific diagnosis was done with universal primer sets 1F/1R, A-1C612, and O-ARS4 with the expected band of 329, 865, and 1301 bp, respectively. Results:Universal primer pair 1F/1R detected FMD in 55 of 73 (75.3%); of these, 37 (67.3%) were females and 18 (32.7%) were males, with high significance (p<0.01) between males and females in the PCR positivity ratio. The tested samples with positive universal primer were amplified with specific primers A-IC612 with no reaction for serotype O-ARS4. Conclusion:The products of RT-PCR were sent for RNA sequencing, and the results were 100% positive to serotype A which means that it is the predominant type in Iraq. It may help in the importing or production of the vaccine to make a preventive plan for the disease. The virus of FMD is contagious and dangerous due to its role in the huge economic loses. The detection of this virus is widely explained in lots of articles, but it is more specific and sensitive in RT-PCR and sequencing. Consequently, the authorities responsible for importing and/or production vaccines have to avoid the importing of other serotypes because it will be losing money and more outbreaks will explode.
| S-EPMC6200567 | biostudies-literature
Project description:Foot-and-mouth disease virus (FMDV) serotypes O, A and Asia1 are responsible for a significant number of disease outbreaks in Iraq. The current study can be considered as the first molecular characterization of serotype Asia1 in Iraq. The present investigation reports the detection of serotype FMDV Asia1 from local farms in Sulaimani districts in 2012 and 2014 outbreaks. Phylogenetic analysis of the complete VP1 gene has shown that FMDV Asia1 field isolates were under genetic novel variant Sindh-08 (group VII) including PAK/iso/11 and TUR/13 strains. The VP1 protein sequence of circulatory FMDV Asia1 genotype showed heterogeneity of nine amino acid substitutions within the G-H loop with the vaccine strain As1/Shamir/89 (JF739177) that is currently used in vaccination program in Iraq. Our result indicated that differences in VP1 protein at G-H loop of the locally circulated FMDV serotype Asia1 strain may be a reason for current vaccination failure.
| S-EPMC5674446 | biostudies-literature
Project description:Background and aimInfectious laryngotracheitis (ILT) of chickens is a substantial issue to be studied in Iraq because this disease is one of the most highly contagious respiratory diseases in the world caused by a herpesvirus. However, in Iraq, the ILT virus (ILTV) infection and disease have yet not been confirmed in layers, so farm owners do not vaccinate these layers. The current study aimed to document the detection and characterization of ILTV in layer hens from Al-Diwaniyah city, for the first time in Iraq, using molecular techniques like polymerase chain reaction (PCR) and sequencing.Materials and methodsFour layer farms (15,000 unvaccinated layers/farm) in Al-Diwaniyah province, Iraq, suffered a severe ILT outbreak, was diagnosed and reported by clinical and PCR tests. This disease has been reported in Iraq, and more recently, it began to show outbreaks in Al-Diwaniyah city. The current work opted to investigate the ILTV using PCR and DNA sequencing techniques. The study targeted the p32 gene of ILTV using pooled tracheal swabs and organs including the trachea, lung, and kidneys which were collected from dead and clinically infected chickens.ResultsThe analyses revealed that four of six suspected field samples showed positive results by PCR. The DNA sequencing results showed the homology of the amplified fragments with the studied gene.ConclusionThis study confirmed the presence of ILTV in hens with respiratory signs during the outbreak.
| S-EPMC6515827 | biostudies-literature
Project description:This study aimed at determining the seroprevalence of foot-and-mouth disease (FMD) in domestic ruminants and at characterizing the virus strains circulating in four areas of Chad (East Batha, West Batha, Wadi Fira and West Ennedi). The study was carried out between October and November 2016. A total of 1,520 sera samples (928 cattle, 216 goats, 254 sheep and 122 dromedaries) were collected randomly for FMD serological analyses. Nine epithelial tissue samples were also collected from cattle showing clinical signs, for FMDV isolation and characterization. Serological results showed an overall NSP seroprevalence of 40% (375/928) in cattle in our sample (95% CrI [19-63]). However, seroprevalences of 84% (27/32), 78% (35/45) and 84% (21/25) were estimated in cattle over 5 years of age in East Batha, West Batha and Wadi Fira, respectively. In cattle under 1 year of age, 67% (18/27) seroprevalence was estimated in Wadi Fira, 64% (14/22) in East Batha and 59% (13/22) in West Batha. It was found that the high seroprevalences have been obtained in areas where pastures are shared by several different herds but also in farms where two to three species (bovine, caprine and ovine) are raised together. ELISA PrioCHECK® FMDV types O and A and in-house solid phase competition ELISA serotyping results showed that the four O, A, SAT1 and SAT2 serotypes have circulated in Chad in 2016. However, the type SAT2 dominated with an overall seroprevalence of 43% (29/67) and was present in the four areas investigated. The phylogenetic analyses of the VP1 coding sequence allowed determining the serotype SAT2 topotype VII, close to viral strains found in Cameroon in 2015 with a similarity of 98.60%.
| S-EPMC7036305 | biostudies-literature
Project description:Comparison of nucleotide sequences of the partial 1D region of foot-and-mouth disease type C viruses of Indian origin with those of European, South American, and Southeast Asian viruses revealed that the Indian viruses form a distinct genotype. The vaccine strain C IND/51/79 belongs to this genotype and may be a prototype strain of this genotype.
| S-EPMC548106 | biostudies-literature
Project description:Abortion in small ruminants is a significant problem in Iraq and causes severe economic losses in sheep farms. Chlamydia abortus causes enzootic abortion in ewes and is associated with reproductive problems in sheep in Sulaimani province - Northern Iraq. During a lambing season in 2017, abortion was widespread among several sheep flocks in different regions of Sulaimani (Kalar, Said Sadiq, and Chamchamal), and C. abortus was one of the causes. Accordingly, we carried out this study to isolate and identify C. abortus in aborted ewes in these regions. We collected 30 samples of aborted fetuses from five herds in which abortions had been observed. The pathogen isolation was done by inoculation into embryonated chicken eggs and conventional PCR was used to identify C. abortus in clinical specimens. C. abortus was identified in one of the 30 aborted fetuses (3.33%) from the Kalar district, and all the remaining 29 samples (96.66%) were found positive to Brucella abortus. The gene ompA encoding the outer membrane protein of C. abortus was sequenced and got the accession number MK643153 in NCBI GenBank. The sequence was named C. abortus strain Sul/2017. Our isolate showed 99.79% homology with Sul/014 (accession No. KY399850) and differed from the latter by two amino acid substitutions at E115K and K259N. The topology of the phylogenetic tree based on the ompA gene showed that the isolate belongs to C. abortus and has a common ancestor with isolates of sheep in Iraq and Tunisia with accession numbers KY399850 and HQ62243, respectively.Abortion in small ruminants is a significant problem in Iraq and causes severe economic losses in sheep farms. Chlamydia abortus causes enzootic abortion in ewes and is associated with reproductive problems in sheep in Sulaimani province – Northern Iraq. During a lambing season in 2017, abortion was widespread among several sheep flocks in different regions of Sulaimani (Kalar, Said Sadiq, and Chamchamal), and C. abortus was one of the causes. Accordingly, we carried out this study to isolate and identify C. abortus in aborted ewes in these regions. We collected 30 samples of aborted fetuses from five herds in which abortions had been observed. The pathogen isolation was done by inoculation into embryonated chicken eggs and conventional PCR was used to identify C. abortus in clinical specimens. C. abortus was identified in one of the 30 aborted fetuses (3.33%) from the Kalar district, and all the remaining 29 samples (96.66%) were found positive to Brucella abortus. The gene ompA encoding the outer membrane protein of C. abortus was sequenced and got the accession number MK643153 in NCBI GenBank. The sequence was named C. abortus strain Sul/2017. Our isolate showed 99.79% homology with Sul/014 (accession No. KY399850) and differed from the latter by two amino acid substitutions at E115K and K259N. The topology of the phylogenetic tree based on the ompA gene showed that the isolate belongs to C. abortus and has a common ancestor with isolates of sheep in Iraq and Tunisia with accession numbers KY399850 and HQ62243, respectively.
| S-EPMC7256821 | biostudies-literature
Project description:Echovirus 9 (E9) belongs to the species Enterovirus B. So far, 12 whole genome sequences of E9 are available in GenBank. In this study, we determined the whole genomic sequences of five E9 strains isolated from the stools of patients with hand-foot-and-mouth disease in Kunming, Yunnan Province, China, in 2019. Their nucleotide and amino acid sequences shared 80.8-80.9% and 96.4-96.8% identity with the prototype Hill strain, respectively, and shared 99.3-99.9% and 99.1-99.8% mutual identity, respectively. Recombination analyses revealed that intertype recombination had occurred in the 2C and 3D regions of the five Yunnan E9 strains with coxsackieviruses B5 and B4, respectively. This study augmented the whole genome sequences of E9 in the GenBank database and extended the molecular characterization of this virus in China.
| S-EPMC8831506 | biostudies-literature
Project description:Foot-and-mouth disease (FMD) is a highly contagious and economically devastating disease of cloven-hoofed animals with an almost-worldwide distribution. Conventional FMD vaccines consisting of chemically inactivated viruses have aided in the eradication of FMD from Europe and remain the main tool for control in endemic countries. Although significant steps have been made to improve the quality of vaccines, such as improved methods of antigen concentration and purification, manufacturing processes are technically demanding and expensive. Consequently, there is large variation in the quality of vaccines distributed in FMD-endemic countries compared with those manufactured for emergency use in FMD-free countries. Here, we have used reverse genetics to introduce haemagglutinin (HA) and FLAG tags into the foot-and-mouth disease virus (FMDV) capsid. HA- and FLAG-tagged FMDVs were infectious, with a plaque morphology similar to the non-tagged parental infectious copy virus and the field virus. The tagged viruses utilized integrin-mediated cell entry and retained the tag epitopes over serial passages. In addition, infectious HA- and FLAG-tagged FMDVs were readily purified from small-scale cultures using commercial antibodies. Tagged FMDV offers a feasible alternative to the current methods of vaccine concentration and purification, a potential to develop FMD vaccine conjugates and a unique tool for FMDV research.
| S-EPMC3542126 | biostudies-literature
Project description:A total of 1134 freshwater fishes belonging to Cyprinidae (Acanthobrama marmid (n=20), Alburnus caeruleus (n=7), Alburnus mossulensis (n=62), Arabibarbus grypus (n=123), Barbus lacerta (n=7), Capoeta trutta (n=222), C. umbla (n=161), Carasobarbus kosswigi (n=5), C. luteus (n=89), Carassius auratus (n=54), Chondrostoma regium (n=52), Cyprinion kais (n=10) and C. macrostomum (n=322)) were collected in different water bodies in Sulaimani Province, Kurdistan Region-Iraq for the presence of larval nematode of the genus Conteacaecum. This investigation revealed that 17 fishes belonged to five species (A. marmid, A. grypus, C. trutta, C. luteus and C. regium) were infected with Contracaecum larvae with prevalence of 35 %, 0.81 %, 0.90 %, 4.49 % and 5.76 %, respectively. The third- larval stage was morphologically studied by optical microscopy, and the ultrastructure was investigated using scanning electron microscopy (SEM). In addition, molecular analysis was carried out by amplifying, sequencing and comparing different gene loci, including internal transcribed spacers (ITS-1 and ITS-2) and cytochrome oxidase c subunit-II (COX-2), of the different isolated Contracaecum larvae. These sequences were also compared with closely related nematode sequences from the GenBank. Fifteen sequences were obtained for this study from the collected Contracaecum larvae. ITS-1, ITS-2 and COX-2 were amplified by polymerase chain reaction (PCR) and sequenced. The sequences of ITS-1, ITS-2 and COX-2 revealed that the collected Contracaecum larval specimens from all infected fish species represented one species (Contracaecum rudolphii B) based on the identity percentage in the GenBank database. The genetic characterisation of the parasite in the present study is available in the GenBank database, and the obtained ITS-1, ITS-2 and COX-2 sequences were deposited in GenBank. The present study provides information on the accurate identification and molecular analysis of Contracaecum larvae in the infected fish species in Sulaimani Province, Kurdistan Region-Iraq.
| S-EPMC7912228 | biostudies-literature
Project description:Foot-and-mouth disease virus (FMDV) causes a highly contagious viral disease of even-toed ungulates and is one of the most important economic diseases of livestock. Most studies of FMDV are done in countries where control measures are being implemented. In contrast, in areas such as sub-Saharan Africa, where FMDV is endemic and new strains are likely to emerge, there are only sporadic submissions to the World Reference Laboratory, Pirbright, United Kingdom. This paper describes the molecular epidemiology of FMDV in the Adamawa province of Cameroon based on a population sample of cattle herds. Serotypes SAT2 and A were isolated in the cross-sectional study. SAT2 isolates were all similar, with phylogenetic distances of <6%, and were most closely related to published sequences of isolates from Eritrea and Saudi Arabia. Serotype A isolates were more variable, with phylogenetic distances of 0 to 11%, and were most closely related to historic isolates from Cameroon. Use of a population-based sample gives a representative sample of virus diversity and will improve our understanding of the evolution of FMDV and its epidemiology. A supplementary study of pigs passing through the railhead collection yard at Ngaoundere detected a serotype O virus. A third pilot longitudinal study monitored viral persistence in three cattle herds over 12 months, and serotype O and A viruses were recovered from a herd 12 months after it was first recorded as being infected with SAT2 virus. The pig type O isolate was not closely related to that recovered from the cattle, suggesting that the pigs had not introduced the O virus into the cattle herds.
| S-EPMC404612 | biostudies-literature