Phylogenetic correlation of Greek and Italian orf virus isolates based on VIR gene

Contagious ecthyma in Egypt: Clinical, virological and molecular explorations

Contagious Ecthyma (CE) is a highly contagious viral disease of sheep and goats with worldwide distribution. The present study aimed to provide a clinical description of contagious ecthyma in four sheep flocks and screen the possible genetic variation in the B2L gene of the detected isolates. Oral lesions were collected and inoculated into chorioallantoic membrane (CAM) of 11 days embryonated chicken eggs. Polymerase chain reaction and direct sequencing of the B2L gene was conducted. Infected sheep exhibited anorexia with a development of nodular lesions evolving in proliferative thick scabs around oral commissures. The inoculated CAM showed small-sized white pock lesions accompanied with thickening of CAM. The partial length of B2L gene (592 bp) was successfully amplified in samples collected from four flocks. The isolated strains belong to genotype I/I and I/II. Sequence and evolutionary analysis illustrate that B2L gene (ORF011) are highly conserved among Orf viruses isolated from different countries.

Molecular Insights into the Genetic Variability of ORF Virus in a Mediterranean Region (Sardinia, Italy)

Orf virus (ORFV) represents the causative agent of contagious ecthyma, clinically characterized by mild papular and pustular to severe proliferative lesions, mainly occurring in sheep and goats. In order to provide hints on the evolutionary history of this virus, we carried out a study aimed to assess the genetic variation of ORFV in Sardinia that hosts a large affected small ruminant population. We also found a high worldwide mutational viral evolutionary rate, which resulted, in turn, higher than the rate we detected for the strains isolated in Sardinia. In addition, a well-supported genetic divergence was found between the viral strains isolated from sheep and those from goats, but no relevant connection was evidenced between the severity of lesions produced by ORFV and specific polymorphic patterns in the two species of hosts. Such a finding suggests that ORFV infection-related lesions are not necessarily linked to the expression of one of the three genes here analyzed and could rather be the effect of the expression of other genes or rather represents a multifactorial character.

Identification of strain diversity and phylogenetic analysis based on two major essential proteins of Orf viruses isolated from several clinical cases reported in Malaysia

There is a little information on the characterization of Orf virus strains that are endemic in Malaysia. The relationship between the severity of disease and the molecular genetic profile of Orf virus strains has not been fully elucidated. This study documented the first confirmed report of contagious ecthyma causing by Orf virus in goats from a selected state of eastern peninsular Malaysia. The disease causes significant debilitation due to the inability of affected animals to suckle which brings a great economic loss to the farmers. A total of 504 animals were examined individually to recognize the affected animals with Orf lesion. Skin scrapping was used to collect the scab material from the infected animals. The presence of Orf virus was confirmed by combination of methods including virus isolation on vero cells, identification by Transmission Electron Microscopy (TEM) and molecular technique using PCR and Sanger sequencing. The results showed the successful isolation of four Orf virus strains with a typical cytopathic effects on the cultured vero cells line. The morphology was confirmed to be Orf virus with a distinctive ovoid and criss cross structure. The phylogenetic analysis revealed that these isolated strains were closely related to each other and to other previously isolated Malaysian orf viruses. In addition these Orf virus strains were closely related to Orf viruses from China and India. This study provides more valuable insight in terms of genotype of Orf virus circulating in Malaysia.

An association of Orf virus infection among sheep and goats with herd health programme in Terengganu state, eastern region of the peninsular Malaysia

BACKGROUND

Orf virus causes a scabby skin lesions which decreases productivity in small ruminants. The unknown status of this disease in the eastern region of Peninsular Malaysia warrants a study to determine sero-prevalence of orf with regards to farmers' compliance level towards the Herd Health Program (HHP) programme.

RESULTS

Out of 504 animals, 115 were positive for Orf-virus antibodies. An overall prevalence rate of 22.8% indicated a high prevalence of orf disease in this region. It was observed that 25.1% (92/367) of goats were positive and 16.8% (23/137) of sheep sero-converted for Orf virus antibody. Several factors were measured for their possible association with prevalence of Orf virus infection. The prevalence was higher in LY farm, JC breed, kid and female animals, and in the presence of disease lesion. Chi-square analysis showed a significant association of three risk factors which are species, age and sex of the animals (P < 0.05). Notwithstanding, all other variables showed no significant difference (P > 0.05). Farms surveyed usually practised intensive management system, keeping animals in the shade at all time, due to limited availability of suitable land as a free-range grazing area. An interview with small holder farmers revealed a lack of awareness of the main goals of herd health programme. An overall compliance level of 42.7% was observed for all HHP parameters. Among the 14 main components of HHP modules, animal identification had recorded highest compliance level (84.62%) while milking management recorded the least compliance (- 82.69%). That explained why there was a high sporadic prevalence of Orf infection in this region.

CONCLUSION

Good herd health supervision is a rehearsal target to prevent an outbreak and the spread of diseases thus reduces economic losses among farmers. Therefore, a good herd health programme should be in place, in order to prevent and control disease transmission as well as to improve herd immunity.

Poxviral E3L ortholog (Viral Interferon resistance gene) of orf viruses of sheep and goats indicates species-specific clustering with heterogeneity among parapoxviruses

Orf is a contagious disease posing a serious threat to animal and human health. E3L is one of the evolutionarily acquired immunomodulatory proteins present in orf virus (ORFV) and is responsible for conferring resistance to interferons among poxviruses. Genetic analysis of ORFV isolates of different geographical regions including Indian subcontinent targeting viral interferon resistance (VIR) gene (a homolog of vaccinia virus E3L gene) revealed a high percentage of identity among themselves and other ORFV isolates at both nt and aa levels as compared to low identity among parapoxviruses (PPVs). Phylogenetic analysis showed species-specific clustering among PPVs along with sub-clusters based on host species of origin among ORFVs infecting sheep and goats. Conserved amino acids in N-terminal Z-DNA binding domain and C-terminal ds RNA binding domain of VIR proteins of PPVs corresponding to ORFV VIR positions namely N37, Y41, P57, and W59 (necessary for Z-DNA binding) and E116, F127, F141, and K160 (necessary for dsRNA binding) were found. Further, the predicted protein characteristics and homology model of VIR protein of ORFV showed high structural conservation among poxviruses. This study on E3L genetic analysis of ORFV isolates may provide a better understanding of the molecular epidemiology of circulating strains in India and neighboring countries. Also, E3L deleted or mutated ORFV may be an as vaccine candidate and/or compounds blocking E3L may prove as an effective method for treating broad spectrum poxviral infections, suggesting a wider application in control of poxvirus infections.

TaqMan-based real-time quantitative fluorescence PCR for detection of Orf virus

Contagious ecthyma, also known as scabby mouth or Orf, is a zoonosis, which is caused by the Orf virus (ORFV). Human contact with infected animals can cause cutaneous lesions. To prevent and control ORFV effectively, rapid detection method is very important and highly needed. Real-time quantitative fluorescence PCR (qPCR) assay is considered as a rapid techonology to detect ORFV, and has been used for clinical diagnosis and epidemiological investigation. In present study, we developed a TaqMan-based qPCR assay for detection of ORFV. Beacon Designer 7.9 was used to design specific primers and probes were based on the ORFV020 gene sequence of the virus (GenBank Accession No. KF666563.1). The method had no cross-reactions with other common bacteria and viruses, was highly specific; the sensitivity test result showed that it could detect 10 copies of ORFV genomic DNA, and was more sensitive than conventional PCR. Both intra- and inter-variabilities were less than 2%, indicating the high stability and repeatability of the method. Additionally, 99 clinical samples from sheep and goats with suspected contagious ecthyma were tested using the developed assay and conventional PCR. The results showed that the developed assay was more sensitive and faster than conventional PCR. It can be concluded that the assay was suitable for routine detection of the ORFV and the epidemiological investigation.

Detection and phylogenetic analysis of Orf virus in Kashmir Himalayas

Orf virus (ORFV) is a zoonotic pathogen that primarily infects sheep and goats, and is responsible for significant economic losses. ORFV is endemic in all the major sheep and goat rearing areas of the world including Indian subcontinent. However, the nature of ORFV circulating among sheep and goat in Kashmir Himalayas has not yet been characterized. In the present study, we describe natural outbreaks of ORFV in sheep and goats of Kashmir Himalayas. We detected the presence of ORFV in the scab lesion by PCR amplification of the major envelope protein (B2L) gene. We sequenced the virus interferon resistance (VIR) gene and determined their phylogenetic relationship with that of the published reference sequences. Phylogenetic analysis based on VIR gene revealed that the ORFV isolates from Kashmir Himalayas separated into main two clusters. The sheep isolates showed genetic homology with the sheep strains reported from Greece and Italy, whereas the goat-specific strain show homology with the goat strains reported from China. This study demonstrates the presence of ORFV infection in sheep and goats, and report first phylogenetic analysis of the ORFV strains prevalent in the Kashmir Himalayas.

The whole genomic analysis of orf virus strain HN3/12 isolated from Henan province, central China

Background

The Orf virus (ORFV) is the causative agent of orf, a globally-occurring, acute, pustular, contagious disease affecting sheep, goats and humans with a worldwide distribution. Currently, the genomic analysis of four ORFV strains from the Fujian province in southern China and a NA1/11 strain isolated from the Jilin province in northeast China have been reported. However, little is known about the genomic information of ORFV strains from central China.

Results

From a recent outbreak in a sheep herd in the Henan province of central China, a novel ORFV strain (HN3/12) was isolated and cultured in ovine fetal turbinate (OFTu) cells. The strain was identified as HN3/12 and verified by PCR based on the DNA sequences of 011 and 059 genes. The whole genomic sequence of this isolate was determined by Next Generation Sequencing technology. To determine the genetic characteristics of the HN3/12 strain, phylogenetic analysis of the 011 and 059 genes and amino acid sequence alignment of the HN3/12 strain were performed and compared with reference parapoxvirus strains.

Conclusions

The HN3/12 genome is 136,643 bp in length, contains 63.67% G + C and encodes 132 putative genes. Phylogenetic analysis of the 011 and 059 nucleotide sequences showed that this viral strain was similar to the NA1/11 isolate. The homology analysis indicates that HN3/12 has 93% to 98% identity with published ORFV strains at amino acid level. When open reading frames (ORFs) were aligned among the HN3/12 and four Fujian ORFV strains, most of them have identities greater than 90% and only a few less than 60%. The availability of the whole genomic sequence of HN3/12 aids in our understanding of, and provides new insights into, the genetic diversity of ORFV.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-017-1178-1) contains supplementary material, which is available to authorized users.

Isolation and phylogenetic analysis of caprine Orf virus in Malaysia

Orf virus is a DNA virus that causes contiguous ecthyma in goat and sheep. Infection of animals with this virus cause high mortality in young animals resulting in huge economic losses. In this study, we investigated an outbreak of Orf in a goat farm in Malaysia. Samples were collected from infected animals and viral isolation was done using both LT and MDCK cell lines. Molecular detection was done by conventional PCR for specific primers; B2L and F1L genes and phylogenetic analysis was done on the sequence data obtained. Cytopathic effects (CPE) were observed in both cell lines after 3 days of inoculation and were 50 % by the sixth day. PCR showed positive bands for both B2L and F1L genes and phylogenetic analysis showed that the Malaysian strain had close homology to the Chinese and Indian Orf virus isolates. This study gives more insight into the existing Orf viral strains in Malaysia and their relationship with other strains globally.

Phylogenetic analysis of three orf virus strains isolated from different districts in Shandong Province, East China

Orf virus (ORFV) is the causative agent of contagious ecthyma, which is a zoonotic disease that affects sheep, goats, wild small ruminants and humans. Shandong Province in East China is one of the main producing areas in China for sheep and goats. Here, we conducted epidemiological surveys in different areas in this Province, isolated three orf virus strains, SDLC, SDTA and SDJN, from goat flocks and then analyzed the genetic evolution of these strains. The ORFV011, ORFV059, ORFV109, ORFV110 and ORFV127 genes of these three strains were amplified, sequenced and analyzed. Phylogenetic analysis showed that ORFV011 of the SDLC and SDTA strains cluster together with the Gansu, Liaoning, Shanxi, Nantou, Hoping and FJ-YX strains, while SDJN clusters with the FJ-GS and FJ-GO strains. ORFV059 of the SDLC and SDTA strains cluster together with the FJ-YX strain, while SDJN clusters with the FJ-GS and FJ-GO strains. ORFV059 and ORFV127 of these three strains were similar to those of the OV-SA00 strain. The results suggested that SDLC, SDTA and SDJN originated from Fujian Province and formed a complex group of viruses in Shandong Province. As the role of ORFV127 gene responsible for the immune evasion of ORFV, the pathogenesis of these three virus strains may similar to that of OV-SA00. These three strains first isolated in Shandong Province are novel ORFV strains, and the data reported here will be helpful for further research about ORFV and its comprehensive prevention and control.

Orf virus infection in sheep or goats

Orf virus, a member of the genus Parapoxvirus, is the causative agent of contagious ecthyma ('Orf'). It is a pathogen with worldwide distribution, causing significant financial losses in livestock production. The disease mainly affects sheep and goats, but various other ruminants and mammals have been reported to be infected as well. It is also a zoonotic disease, affecting mainly people who come in direct or indirect contact with infected animals (e.g. farmers, veterinarians). The disease is usually benign and self-limiting, although in many cases, especially in young animals, it can be persistent and even fatal. Production losses caused by Orf virus are believed to be underestimated, as it is not a notifiable disease. This review of literature presents all latest information regarding the virus; considerations regarding treatment and prevention will be also discussed.

Phylogenetic analysis of B2L gene of Egyptian orf virus from naturally infected sheep

Orf is a viral disease caused by a parapoxvirus, affecting primarily sheep and goats and causes severe economic losses. In this study, a total of 500 sheep from a farm in El-Beheira Governorate, Egypt were examined during spring, 2014. Out of them, 30 sheep showed clinical signs of orf virus infection. The diseased sheep exhibited proliferative lesions on the lips and around the mouth. Polymerase chain reaction (PCR) was used for diagnosis of the disease. For genetic characterization of the Egyptian orf virus, the sequence of a major and highly immunogenic envelope protein gene (B2L gene) was identified and compared with the sequences available from different parts of the world. The virus was detected in 24 out of 30 collected samples (80 %) by PCR. Phylogenetic analyses of the Egyptian orf virus B2L gene showed close genetic relationship with Israel orf viruses those were identified in 2012. In conclusion, this study reports identification and genetic characterization of Egyptian orf virus in sheep in Egypt.

Comparative genomic sequence analysis of Chinese orf virus strain NA1/11 with other parapoxviruses

Orf virus (ORFV) is a typical member of the genus Parapoxvirus. The parapoxvirus genome consists of highly variable terminal regions and relatively conserved central regions with a high G + C content. In our previous study, a novel ORFV strain, NA1/11, was isolated from northeastern China. To fully characterize this strain, we sequenced the entire genome of NA1/11 and conducted a comparative analysis using multiple parapoxviruses. The genomic sequence of NA1/11 was found to consist of 137,080 nucleotides with a G + C content of 63.6 %, but it did not contain the terminal hairpin sequence. Alignment of ORFs from NA1/11 with NZ2, IA82 and SA00 revealed several highly variable ORFs, while the most evident ones are ORFs 001, 103, 109-110, 116 and 132. An odd phenomenon in the region of ORFs 118-120 is that the non-coding fragments are almost as long as the coding fragments. By comparative analysis of inverted terminal repeats, we identified one repeat motif and a long conserved fragment. By comparing the ITRs of SA00 with those of three other ORFVs, more clues were obtained about the correlation between ITR sequence and host adaption. Comparison of the NA1/11 genome with the sequences of other strains of ORFV revealed highly variable regions, thus providing new insights into the genetic diversity of ORFV.

Pathogenesis in lambs and sequence analysis of putative virulence genes of Brazilian orf virus isolates

The parapoxvirus orf virus (ORFV) is the agent of contagious ecthyma, an ubiquitous mucocutaneous disease of sheep and goats that may present variable clinical presentations. We herein studied the pathogenesis of ORFV infection in lambs and analyzed three putative virulence genes of four Brazilian ORFV isolates. Lambs inoculated in the labial commissures with each ORFV isolate (n=4, viral titer 10(5.6) TCID50/ml) developed classical orf lesions, characterized by a progressive course of erythema/macules, vesicles, pustules and proliferative scabs. Lesions lasted an average of 22.9 days (18-26) and virus shedding was detected for approximately 24.6 days (18-30). Two isolates (SV269/11 and SV820/10) produced more severe, long-lasting lesions resulting in highest clinical scores. Lambs inoculated with isolate SV581/11 developed lesions markedly milder (lower clinical scores [p<0.05]) and more limited than the other groups. Virus shedding by SV581/11 group, however, lasted similarly or even longer than the other groups. Sequence analysis of three virulence genes (VEGF, VIR and IL-10v) revealed amino acid deletions and mutations in VEGF and IL-10v genes of SV581/11 and SV252/11, the isolate(s) producing milder lesions. Additionally, the VEGF gene of isolate SV581/11 presented the lowest amino acid identity with the other isolates and with ORFV standard strain OV-IA82. Thus, these results demonstrate that ORFV isolates may display differential virulence in lambs and these differences might be associated with genetic changes in putative virulence genes.

Isolation and characterization of orf viruses from Korean black goats

Five cases of orf virus infection in Korean black goats were diagnosed in our laboratory between 2010 and 2011. One orf virus (ORF/2011) was isolated from an ovine testis cell line (OA3.Ts) for use as a vaccine candidate. Sequences of the major envelope protein and orf virus interferon resistance genes were determined and compared with published reference sequences. Phylogenetic analyses revealed that orf viruses from Korean black goats were most closely related to an isolate (ORF/09/Korea) from dairy goats in Korea. This result indicates that the orf viruses might have been introduced from dairy goats into the Korean black goat population.

Phylogenetic analysis of strains of Orf virus isolated from two outbreaks of the disease in sheep in Greece

Background

Although orf is endemic around the world, there are few descriptions of Orf virus strains and comparisons of these strains. We report the sequence and phylogenetic analysis of the partial B2L gene of Orf virus from two outbreaks of the disease in Greece. The first was an outbreak of genital form of the disease in a flock imported from France, whilst the second was an outbreak of the disease in the udder skin of ewes and around the mouth of lambs in an indigenous flock.

Results

Phylogenetic analysis was performed on a part (498 bp) of the B2L gene of 35 Parapoxvirus isolates, including the two Orf virus isolates recovered from each of the two outbreaks in the present study. This analysis revealed that the maximum nucleotide and amino-acid variation amongst Orf virus strains worldwide (n = 33) was 8.1% and 9.6%, respectively. The homology of the nucleotide and amino-acid sequences between the two Greek isolates was 99.0% and 98.8%, respectively. The two Greek isolates clustered only with Orf virus strains.

Conclusions

We suggest that there can be differences between strains based on their geographical origin. However, differences in the origin of strains or in the clinical presentation of the disease may not be associated with their pathogenicity. More work is required to determine if differing clinical presentations are linked to viral strain differences or if other factors, e.g., flock immunity, method of exposure or genetic susceptibility, are more important to determine the clinical presentation of the infection.

Comparative sequence analysis of poxvirus A32 gene encoded ATPase protein and carboxyl terminal heterogeneity of Indian orf viruses

Thirteen orf virus (ORFV) isolates from natural outbreaks in sheep and goats belonging to different geographical regions of India were analysed on the basis of ORF108 (a homologue of poxviral A32 gene), which is known to encode for ATPase and involved in virion DNA packaging. Comparative sequence analysis of ATPase proteins revealed highly conserved N-terminal region with five different motifs [Walker A, Walker B, A32L specific motifs (III and IV) and a novel AYDG (motif-V)] among all poxviruses and divergent carboxyl terminus with either single or double RGD sequences among all Indian ORFV isolates. A homology model and secondary structure predictions of N-terminal region of ORFV A32 revealed that most of the poxviruses including ORFV ATPase protein belong to a distinct clade of the HerA/FtsK super family of DNA packaging proteins. Despite differences in host cell specificity and poxvirus infections among animals, DNA packaging motor domain of poxviruses presumed to share remarkable similarities as indicated by the presence of conserved ATPase motifs in the present investigation. The study also indicated the circulation of heterogeneous strains of ORFV in India and possibilities of differentiation of ORFV strains based on C-terminal heterogeneity.

Phylogenetic analysis and characterization of Korean orf virus from dairy goats: case report

An outbreak of orf virus infection in dairy goats in Korea was investigated. Suspected samples of the skin and lip of affected goats were sent to the laboratory for more exact diagnosis. Orf virus was detected by electron microscopy and viral DNA was identified by PCR. To reveal the genetic characteristics of the Korean strain (ORF/09/Korea), the sequences of the major envelope protein (B2L) and orf virus interferon resistance (VIR) genes were determined and then compared with published reference sequences. Phylogenetic analysis revealed that the ORF/09/Korea strain was closest to the isolates (Taiping) from Taiwan. This is believed to be the first report on the molecular characterization of orf virus in Korea.

Identification and phylogenetic analysis of orf virus from goats in Taiwan

An outbreak of contagious ecthyma in goats in central Taiwan was investigated. The disease was diagnosed by physical and histopathologic examinations, and the etiology of the disease was identified as orf virus by electron microscopy and polymerase chain reaction (PCR) and sequence of major envelope protein (B2L) gene. The entire protein-coding region of B2L gene were cloned and sequenced. Phylogenetic analysis of B2L amino acid sequences showed that the orf virus identified in this outbreak was closer to the Indian ORFV-Mukteswar 59/05 isolate. This is the first report on the molecular characterization of orf virus in Taiwan.

Variation analysis of two cucumber mosaic viruses and their associated satellite RNAs from sugar beet in China

Two cucumber mosaic virus (CMV) isolates XJ1 and XJ2 were obtained from sugar beet showing yellow mosaic symptom in Shihezi, Xinjiang Uigur municipality of China. The coat protein gene of the two CMV isolates and their associated satellite RNAs were amplified by reverse transcriptase polymerase chain reaction (RT-PCR) and were cloned and sequenced. Comparison of CP gene sequences showed that XJ1 and XJ2 have the highest sequence identity with that of CMV-Danshen (97.8%) and CMV-SD (98.7%), respectively. Two types of satellite RNAs (XJs1 and XJs2) were found to be associated with the two CMV isolates consisting of 384 nucleotides and 336 nucleotides, respectively. Sequence comparisons revealed that XJs1 and XJs2 were most closely related to CS2-sat and CS1-sat, respectively, with 98.9% and 98.5% nucleotide sequence identity. Phylogenetic analysis of nucleotide sequence and deduced amino acid sequence of coat protein gene revealed that XJ1 and XJ2 belong to subgroup IB but there exist some variation between them. Parallel analyses of nucleotide sequence of XJsl and XJs2 suggested that these two satellite RNAs probably originated from China.