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
We report a case of SARS-CoV-2 Omicron variant co-infection with influenza A H3N2 detected from Kerala, India. The patient, a 10-year-old girl, had symptoms of low-grade fever, cough, and cold. As part of the ongoing surveillance, a throat swab was taken and sent for testing, and the influenza A virus isolated from the patient was identified as subtype H3N2. Whole-genome sequencing and analysis of the viral isolates suggested that the SARS-CoV-2 isolate belonged to BA.4.1 sublineage of Omicron while the influenza A isolate belonged to the 2a.3 clade of H3N2 and clustered with other H3N2 genomes from Maldives, India, Bangladesh, and the United Arab Emirates. The report highlights the importance of genomic surveillance of SARS-CoV-2 co-infections with other respiratory illnesses for understanding the prevalence of co-infections and their rapid detection and prevention.
Subject(s)
Coinfection , Fever , CoughABSTRACT
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.
Subject(s)
Severe Acute Respiratory SyndromeABSTRACT
Ever since the breakout of COVID-19 disease, ceaseless genomic research to inspect the epidemiology and evolution of the pathogen has been undertaken globally. Large scale viral genome sequencing and analysis have uncovered the functional impact of numerous genetic variants in disease pathogenesis and transmission. Emerging evidence of mutations in spike protein domains escaping antibody neutralization is reported. We have a precise collation of manually curated variants in SARS-CoV-2 from literature with potential escape mechanisms from a range of neutralizing antibodies. This comprehensive repository encompasses a total of 532 variants accounting for 146 unique variants tested against 75 antibodies and patient convalescent plasma. This resource enables the user to gain access to an extensive annotation of SARS-CoV-2 escape mutations which we hope would contribute to exploring and understanding the underlying mechanisms of immune response against the pathogen. The resource is available at http://clingen.igib.res.in/esc/.
Subject(s)
COVID-19ABSTRACT
Coronavirus disease (COVID-19) emerged from a city in China and has now spread as a global pandemic affecting millions of individuals. The causative agent, SARS-CoV-2 is being extensively studied in terms of its genetic epidemiology using genomic approaches. Andhra Pradesh is one of the major states of India with the third-largest number of COVID-19 cases with limited understanding of its genetic epidemiology. In this study, we have sequenced 293 SARS-CoV-2 genome isolates from Andhra Pradesh with a mean coverage of 13,324X. We identified 564 high-quality SARS-CoV-2 variants, out of which 15 are novel. A total of 18 variants mapped to RT-PCR primer/probe sites, and 4 variants are known to be associated with an increase in infectivity. Phylogenetic analysis of the genomes revealed the circulating SARS-CoV-2 in Andhra Pradesh majorly clustered under the clade A2a (94%), while 6% fall under the I/A3i clade, a clade previously defined to be present in large numbers in India. To the best of our knowledge, this is the most comprehensive genetic epidemiological analysis performed for the state of Andhra Pradesh.
Subject(s)
Coronavirus Infections , COVID-19ABSTRACT
Many antibody and immune escape variants in SARS-CoV-2 are now documented in literature. The availability of SARS-CoV-2 genome sequences enabled us to investigate the occurrence and genetic epidemiology of the variants globally. Our analysis suggests that a number of genetic variants associated with immune escape have emerged in global populations.
ABSTRACT
COVID-19 represents a real threat to the global population, and understanding the biological features of the causative virus (SARS-CoV-2) is imperative to aid in mitigating this threat. Analyses of proteins such as primary receptors and co-receptors (co-factors) that are involved in SARS-CoV-2 entry into host cells will provide important clues to help control the virus. Here, we identified host cell membrane protein candidates that were present in proximity to the attachment sites of SARS-CoV-2 spike proteins through the use of proximity labeling and proteomics analysis. The identified proteins represent candidate key factors that may be required for viral entry. Our results indicated that a number of membrane proteins, including DPP4, Cadherin-17, and CD133, were identified to co-localize with cell membrane-bound SARS-CoV-2 spike proteins in Caco-2 cells that were used to expand the SARS-CoV-2 virion. We anticipate that the information regarding these protein candidates will be utilized for the future development of vaccines and antiviral agents against SARS-CoV-2.
Subject(s)
COVID-19ABSTRACT
Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.
Subject(s)
COVID-19ABSTRACT
The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.
Subject(s)
COVID-19ABSTRACT
From an isolated epidemic, COVID-19 has now emerged as a global pandemic. The availability of genomes in the public domain following the epidemic provides a unique opportunity to understand the evolution and spread of the SARS-CoV-2 virus across the globe. The availability of whole genomes from multiple states in India prompted us to analyse the phylogenetic clusters of genomes in India. We performed whole-genome sequencing for 64 genomes making a total of 361 genomes from India, followed by phylogenetic clustering, substitution analysis, and dating of the different phylogenetic clusters of viral genomes. We describe a distinct phylogenetic cluster (Clade I / A3i) of SARS-CoV-2 genomes from India, which encompasses 41% of all genomes sequenced and deposited in the public domain from multiple states in India. Globally 3.5% of genomes, which till date could not be mapped to any distinct known cluster fall in this newly defined clade. The cluster is characterized by a core set of shared genetic variants - C6312A (T2016K), C13730T (A88V/A97V), C23929T, and C28311T (P13L). Further, the cluster is also characterized by a nucleotide substitution rate of 1.4 x 10-3 variants per site per year, lower than the prevalent A2a cluster, and predominantly driven by variants in the E and N genes and relative sparing of the S gene. Epidemiological assessments suggest that the common ancestor emerged in the month of February 2020 and possibly resulted in an outbreak followed by countrywide spread, as evidenced by the low divergence of the genomes from across the country. To the best of our knowledge, this is the first comprehensive study characterizing the distinct and predominant cluster of SARS-CoV-2 in India.