ABSTRACT
Lumpy Skin Disease (LSD) is a viral disease predominantly affecting cattle and caused by a poxvirus belonging to the capripoxvirus genus. LSD is characterized by extensive cutaneous lesions, with severe consequent morbidity and sometimes mortality of the affected animal. Timely diagnosis and control of the spread of infections through measures including vaccination are therefore of great importance in preventing social and economic consequences of the disease. Genomic studies from outbreaks in the past have provided unique insights including the identification of recombinant variants in recent years. Genome sequencing and genomic surveillance of the disease therefore could provide useful insights into the evolution and epidemiology of the virus and could potentially also contribute to the development of diagnostic tools. Previous approaches for genome sequencing of the virus used a variety of approaches including amplicon-based sequencing as well as metagenomic approaches, which are tedious, time-consuming as well as costly. The wide availability of benchtop next-generation sequencing equipment and the application of sequencing-based approaches to enable genomic epidemiology of SARS-CoV-2 at scale, motivated us to create an amplicon-based approach based on the Illumina COVIDSeq assay1. for fast, scalable and cost-effective sequencing of the Lumpy Skin Disease Virus. This protocol is a modification of the previously published COVIDSeq assay 1 and can be adapted to any Illumina sequencing platform as an accelerated and scalable system for quick detection as well as genomic surveillance of LSD. For complete details on the use and execution of this protocol, please refer to Bhatt et al. (2023).2
Subject(s)
Piebaldism , Lumpy Skin DiseaseABSTRACT
Background: The SARS-CoV-2 Delta variant (B.1.617.2) was first detected in India in late 2020 and soon became the predominant lineage owing to its high transmissibility. Over time, the virus has acquired mutations and has evolved into many new sub-lineages. AY.4 is one such sub-lineage that grew in frequency globally. Therefore, we aimed to compare the severity of infection due to Delta sub-lineages to Delta infections in Pune, Maharashtra, India. Material and Methods: Whole-genome sequencing and analysis of 255 SARS-CoV-2 positive samples, collected between 1st August to 1st September 2021, by BJ Government Medical College, Pune, was carried out at the Indian Institute of Science Education and Research (IISER), Pune and the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi. Individual-level data on these patients were collected from ICMR COVID-19 Data Portal. Additional information regarding the presence of any symptoms, comorbidities, hospitalization, international travel history within 14 days and vaccination status was collected by telephonic interview with each patient by the BJGMC Sequencing Team.
ABSTRACT
In April 2021, after successfully enduring three waves of the SARS-CoV2 pandemic in 2020, and having reached population seropositivity of about 50%, Delhi, the national capital of India was overwhelmed by the fourth wave. Here, we trace viral, host, and social factors contributing to the scale and exponent of the fourth wave, when compared to preceding waves, in an epidemiological context. Genomic surveillance data from Delhi and surrounding states shows an early phase of the upsurge driven by the entry of the more transmissible B.1.1.7 variant of concern (VOC) into the region in January, with at least one B.1.1.7 super spreader event in February 2021, relatable to known mass gatherings over this period. This was followed by seeding of the B.1.617 VOC, which too is highly transmissible, with rapid expansion of B.1.617.2 sub-lineage outpacing all other lineages. This unprecedented growth of cases occurred in the background of high seropositivity, but with low median neutralizing antibody levels, in a serially sampled cohort. Vaccination breakthrough cases over this period were noted, disproportionately related to VOC in sequenced cases, but usually mild. We find that this surge of SARS-CoV2 infections in Delhi is best explained by the introduction of a new highly transmissible VOC, B.1.617.2, with likely immune-evasion properties; insufficient neutralizing immunity, despite high seropositivity; and social behavior that promoted transmission.