The genome sequence of lumpy skin disease virus from an outbreak in India suggests a distinct lineage of the virus.

Although previously confined to regions within Africa, lumpy skin disease virus (LSDV) infections have caused significantly large outbreaks in several regions of the world in recent years. In 2019, an outbreak of the disease was reported in India with low rates of morbidity and no reported mortality. However, in 2022, an ongoing outbreak of LSDV spanning over seven states in India resulted in the loss of over 80,000 cattle over a period of three months. Here, we report complete genome sequences of six isolates of LSDV collected from affected cattle during an ongoing outbreak of the disease in Rajasthan, India. Analysis of these sequences showed that the genome isolates from the 2022 outbreak have a large number of genetic variations compared to the reference strain and that they form a distinct genetic lineage. This report thus highlights the importance of genome sequencing and surveillance of transboundary infectious agents to track the prevalence and emergence of variants.

Protocol for next-generation sequencing of the LSD virus genome using an amplicon-based approach.

Lumpy skin disease (LSD) is a viral disease predominantly affecting cattle caused by a poxvirus belonging to the capripoxvirus genus. Here, we present a protocol for next-generation sequencing of the LSD virus genome using an amplicon-based approach. We describe steps for DNA extraction, viral DNA enrichment, amplicon pooling and purification, and library preparation and pooling. We then detail procedures for sequencing and computational analysis. This protocol can be adapted to any Illumina sequencing platform as an accelerated and scalable system. For complete details on the use and execution of this protocol, please refer to Bhatt et al.1,2.

Detection of African genotype in Hyalomma tick pools during Crimean Congo hemorrhagic fever outbreak, Rajasthan, India, 2019.

Crimean Congo hemorrhagic fever (CCHF) is a zoonotic viral disease presenting with fever and hemorrhagic manifestations in humans. After several outbreaks of CCHF being reported from Gujarat since 2011 till 2019 and from Rajasthan in 2014 and 2015, the present study reports the CCHF outbreak which was recorded from five human cases in three districts Jodhpur, Jaisalmer, and Sirohi of Rajasthan state since August 2019 till November 2019. A high percent of positivity was recorded in livestock animal samples for the CCHFV IgG antibody. CCHF virus (CCHFV) positive human blood samples and Hyalomma tick pool samples were sequenced using next-generation sequencing method. Two different M segment genotypes, encoding glycoprotein precursor, were identified from tick pools in the study: first from Asian and second from African lineage. The L gene (polymerase) and the S gene (nucleocapsid) clustered in the Asian lineage. The present study illustrates the existence of two different CCHFV lineages being circulating within the Hyalomma tick pools in the Rajasthan state, India. We also observed 3.56% amino acid changes between the death and the survived case of CCHFV in the M gene. This report also sets an alarm to enhance human, tick and livestock surveillance in other districts of Rajasthan and nearby states of India. Biosafety measures, barrier nursing along with the availability of personal protective equipment and ribavirin drug will always be a mainstay in preventing nosocomial infection for proper case management.

Serological surveillance and clinical investigation of glanders among indigenous equines in India from 2015 to 2018.

Equine glanders is an infectious and notifiable bacterial disease caused by Burkholderia mallei. The disease has been reported in South American, African and Asian countries including India. Here, we present the outcome of glanders serosurveillance carried out between January 2015 and December 2018 to know the status of equine glanders among different states in India. A total of 102,071 equid sera from 299 districts of twenty-one states and one union territory were tested for glanders. Samples were screened with Hcp1 indirect ELISA followed by confirmatory diagnosis by CFT. During this four-year surveillance, a total of 932 glanders-positive cases were detected from 120 districts of 12 states. The study also revealed increasing trend of glanders from 2016 onwards with maximum occurrence in northern India. Overall seroprevalence ranged between 0.62% (95% CI, 0.52-0.72) and 1.145% (95% CI, 1.03-1.25). Seasonal shifting from winter to summer (March to June) coincided with highest number glanders incidence with corresponding seroprevalences of 1.2% (95% CI, 1.09-1.30). The present surveillance unveils territorial ingression of glanders to six states like Jammu & Kashmir, Gujarat, Rajasthan, Madhya Pradesh, Delhi and Tamil Nadu. In addition, re-emerging cases have been reported in Maharashtra, Haryana and Punjab after a gap of 10 years. Lack of awareness, little veterinary care and unrestricted movement of equids across state borders might have led to the introduction and establishment of the infection to these states. We believe that information from this study will provide a baseline data on glanders for devising surveillance and control strategies in India. Being a zoonotic disease, the persistence of glanders poses a potential threat to occupationally exposed humans especially equine handlers and veterinarians. Therefore, targeted surveillance of human population from each glanders outbreak is also recommended.