Recombination drives the emergence of orf virus diversity: evidence from the first complete genome sequence of an Indian orf virus isolate and comparative genomic analysis
Abstract:Contagious pustular dermatitis is a disease that primarily infects small ruminants and possesses zoonotic potential. It is caused by orf virus (ORFV), a member of the genus
Parapoxvirus
. In this study, we evaluated an ORFV outbreak in goats in Madhya Pradesh, a state in central India, during 2017. The transboundary potential of this virus was evaluated by constructing phylogenetic trees. The complete genome sequence of an ORFV isolate named Ind/MP/17 was found to be 139,807 bp in length… Show more
“…The strains from outbreak previously reported in Haryana by Kumar et al ( 2014 ) showed 99.98–99.99% nt identity with current strains from the region, implying that the same or closely related strains are involved or circulating in the region. The overall maximum nt identity (99.99%) of current study strains was observed with strain from Rajasthan by Maan et al ( 2014 ) and minimum identity (99.22%) with strains from Madhya Pradesh by Sahu et al ( 2022 ), signifying a close genetic relationship and high conservation of B2L gene (Fig. 4 ) as also previously reported (Maan et al 2014 ).…”
Section: Discussionsupporting
confidence: 86%
“…The B2L gene-based phylogenetic analysis of ORFV in China reported three different genotypes owing to clustering of the virus to different clusters, where Indian strains only clustered with Chinese strains in a single genotype (Zhang et al 2014 ). The previous Indian studies however also reported such clustering and close relation with Chinese strains of ORFV (Maan et al 2014 ; Kumar et al 2014 ; Sahu et al 2022 ) but the clustering of ORFV strains from Nigeria within the same clad with current study isolates provides useful and updated information for further understanding of the biology, epidemiology, and researches towards diagnosis and vaccine development. Fig.…”
Section: Discussionsupporting
confidence: 50%
“…Occasionally, the lesions can be found on the teats and rarely on other organs (Vikoren et al 2008 ). The orf outbreaks were reported across various Indian states, viz., Uttarakhand (Venkatesan et al 2011 ), Assam, Meghalaya (Bora et al 2012 ), Haryana (Kumar et al 2013 ), Uttar Pradesh (Kumar et al 2014 ), Rajasthan (Maan et al 2014 ), Tripura (Venkatesan et al 2018 ), Kashmir (Ahanger et al, 2018 ), Tamil Nadu (Nagarajan et al 2019 ), and Odisha (Sahu et al 2022 ). The ORFV circulating in India had been clustered with Indian and Chinese isolates using phylogenetic analysis previously (Maan et al 2014 ; Sahu et al 2022 ).…”
Section: Introductionmentioning
confidence: 99%
“…The orf outbreaks were reported across various Indian states, viz., Uttarakhand (Venkatesan et al 2011 ), Assam, Meghalaya (Bora et al 2012 ), Haryana (Kumar et al 2013 ), Uttar Pradesh (Kumar et al 2014 ), Rajasthan (Maan et al 2014 ), Tripura (Venkatesan et al 2018 ), Kashmir (Ahanger et al, 2018 ), Tamil Nadu (Nagarajan et al 2019 ), and Odisha (Sahu et al 2022 ). The ORFV circulating in India had been clustered with Indian and Chinese isolates using phylogenetic analysis previously (Maan et al 2014 ; Sahu et al 2022 ). Usually, CE is self-limiting in sheep and goats, but long-standing cases may provide opportunity for bacterial pathogens to invade the lesions leading to complications (Haig and Mercer, 1998 ).…”
Orf is an acute, highly contagious, and economically important viral disease of small ruminants. In this study, six orf suspected outbreaks among goats and sheep were investigated from Haryana state and adjoining areas of Rajasthan state during the year 2021. The disease was diagnosed on the basis of clinical signs and molecular identification. The causative agent of the disease, orf virus (ORFV), was confirmed using polymerase chain reaction (PCR) targeting immunodominant envelope antigen (B2L) gene and confirmed by sequencing. The morbidity in goats ranged from 8.75 to 100%, whereas in sheep, it ranged from 0 to 8%. The higher mortality was observed among flocks with mixed infections of orf and peste des petits (PPR) or orf and haemonchosis as compared to other outbreaks. The phylogenetic analysis of sequenced PCR products clustered the current study strains in the same clad with Indian as well as strains from other countries with nucleotide identity more than 99%, signifying a close genetic relationship. The study highlighted the circulation of strains of a single cluster among sheep and goats in Haryana and adjoining areas. Prompt diagnosis of the disease is highly important for facilitating the implementation of control measures to minimize the losses suffered by small and marginal farmers in this region. Further detailed studies are required to delineate the molecular details of ORFV for better understanding the dynamics and molecular epidemiology of strains circulating in the country and for designing the effective vaccines against the disease which are currently lacking in the country.
“…The strains from outbreak previously reported in Haryana by Kumar et al ( 2014 ) showed 99.98–99.99% nt identity with current strains from the region, implying that the same or closely related strains are involved or circulating in the region. The overall maximum nt identity (99.99%) of current study strains was observed with strain from Rajasthan by Maan et al ( 2014 ) and minimum identity (99.22%) with strains from Madhya Pradesh by Sahu et al ( 2022 ), signifying a close genetic relationship and high conservation of B2L gene (Fig. 4 ) as also previously reported (Maan et al 2014 ).…”
Section: Discussionsupporting
confidence: 86%
“…The B2L gene-based phylogenetic analysis of ORFV in China reported three different genotypes owing to clustering of the virus to different clusters, where Indian strains only clustered with Chinese strains in a single genotype (Zhang et al 2014 ). The previous Indian studies however also reported such clustering and close relation with Chinese strains of ORFV (Maan et al 2014 ; Kumar et al 2014 ; Sahu et al 2022 ) but the clustering of ORFV strains from Nigeria within the same clad with current study isolates provides useful and updated information for further understanding of the biology, epidemiology, and researches towards diagnosis and vaccine development. Fig.…”
Section: Discussionsupporting
confidence: 50%
“…Occasionally, the lesions can be found on the teats and rarely on other organs (Vikoren et al 2008 ). The orf outbreaks were reported across various Indian states, viz., Uttarakhand (Venkatesan et al 2011 ), Assam, Meghalaya (Bora et al 2012 ), Haryana (Kumar et al 2013 ), Uttar Pradesh (Kumar et al 2014 ), Rajasthan (Maan et al 2014 ), Tripura (Venkatesan et al 2018 ), Kashmir (Ahanger et al, 2018 ), Tamil Nadu (Nagarajan et al 2019 ), and Odisha (Sahu et al 2022 ). The ORFV circulating in India had been clustered with Indian and Chinese isolates using phylogenetic analysis previously (Maan et al 2014 ; Sahu et al 2022 ).…”
Section: Introductionmentioning
confidence: 99%
“…The orf outbreaks were reported across various Indian states, viz., Uttarakhand (Venkatesan et al 2011 ), Assam, Meghalaya (Bora et al 2012 ), Haryana (Kumar et al 2013 ), Uttar Pradesh (Kumar et al 2014 ), Rajasthan (Maan et al 2014 ), Tripura (Venkatesan et al 2018 ), Kashmir (Ahanger et al, 2018 ), Tamil Nadu (Nagarajan et al 2019 ), and Odisha (Sahu et al 2022 ). The ORFV circulating in India had been clustered with Indian and Chinese isolates using phylogenetic analysis previously (Maan et al 2014 ; Sahu et al 2022 ). Usually, CE is self-limiting in sheep and goats, but long-standing cases may provide opportunity for bacterial pathogens to invade the lesions leading to complications (Haig and Mercer, 1998 ).…”
Orf is an acute, highly contagious, and economically important viral disease of small ruminants. In this study, six orf suspected outbreaks among goats and sheep were investigated from Haryana state and adjoining areas of Rajasthan state during the year 2021. The disease was diagnosed on the basis of clinical signs and molecular identification. The causative agent of the disease, orf virus (ORFV), was confirmed using polymerase chain reaction (PCR) targeting immunodominant envelope antigen (B2L) gene and confirmed by sequencing. The morbidity in goats ranged from 8.75 to 100%, whereas in sheep, it ranged from 0 to 8%. The higher mortality was observed among flocks with mixed infections of orf and peste des petits (PPR) or orf and haemonchosis as compared to other outbreaks. The phylogenetic analysis of sequenced PCR products clustered the current study strains in the same clad with Indian as well as strains from other countries with nucleotide identity more than 99%, signifying a close genetic relationship. The study highlighted the circulation of strains of a single cluster among sheep and goats in Haryana and adjoining areas. Prompt diagnosis of the disease is highly important for facilitating the implementation of control measures to minimize the losses suffered by small and marginal farmers in this region. Further detailed studies are required to delineate the molecular details of ORFV for better understanding the dynamics and molecular epidemiology of strains circulating in the country and for designing the effective vaccines against the disease which are currently lacking in the country.
“…Polymerase chain reaction (PCR) technology targeting specific DNA fragments of ORFV has been widely used for ORFV diagnosis. F1L (ORFV059) gene and B2L (ORFV011) gene are the most commonly used targets for ORFV diagnosis while other conserved genes of ORFV can also be selected as candidates (Sahu et al 2022;Wang et al 2019a, b, c). First, the virus genome is extracted from clinical samples using a viral genome extraction kit.…”
Orf virus (ORFV), the prototype species of the Parapoxvirus genus, is an important zoonotic virus, causing great economic losses in livestock production. At present, there are no effective drugs for orf treatment. Therefore, it is crucial to develop accurate and rapid diagnostic approaches for ORFV. Over decades, various diagnostic methods have been established, including conventional methods such as virus isolation and electron microscopy; serological methods such as virus neutralization test (VNT), immunohistochemistry (IHC) assay, immunofluorescence assay (IFA), and enzyme-linked immunosorbent assay (ELISA); and molecular methods such as polymerase chain reaction (PCR), real-time PCR, loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and recombinase-aided amplification (RAA) assay. This review provides an overview of currently available diagnostic approaches for ORFV and discusses their advantages and limitations and future perspectives, which would be significantly helpful for ORFV early diagnosis and surveillance to prevent outbreak of orf.
Key points• Orf virus emerged and reemerged in past years • Rapid and efficient diagnostic approaches are needed and critical for ORFV detection • Novel and sensitive diagnostic methods are required for ORFV detection Keywords Orf virus • Diagnostic approach • Conventional methods • Serological methods • Molecular methods
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