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Potato virus M (PVM) is one of the most prevalent viruses infecting potatoes worldwide, showing a wide range of diversity in their populations; however, the diversity and genome information of PVM occurring in India is hardly known. The present study serologically detected the PVM in 22.8% of leaf samples collected from the potato fields, generated 13 coat protein (CP) genes and one complete genome sequence for the isolates from India, and identified four dierential hosts confirming PVM-Del-144 as a distinct strain of PVM occurring in India. The phylogenetic analyses conducted based on the CP gene sequences (14 from India and 176 from other countries) suggested the existence of three evolutionary divergent lineages (PVM-o, PVM-d, and a new divergent group) in the PVM population, where isolates from India belong to only two clusters (PVM-o and PVM-d) within four sub-clusters. High levels of nucleotide diversity (0.124) and genetic distance (0.142) recorded among the isolates from India may be due to the deviation from the neutral evolution and experiencing population expansion in the past. The complete genome of the isolate Del-144 (KJ194171; 8,526 nucleotides) shared 92.2–93.9% nt sequence identity with the population of PVM-o, whereas it shared only 70.2–72.1% identity with PVM-d. In the phylogenetic analyses, Del144 clustered with the isolates of PVM-o; however, it formed a separate branch away from all other isolates, indicating the diversity of the strain. Overall, this study revealed the diversity of the isolates of PVM from India and reported the first complete genome sequence of a distinct strain of PVM occurring in India [ABSTRACT FROM AUTHOR]

Plant viruses are a major threat to legume production worldwide. In recent years, new virus strains have emerged with increasing frequencies in various legume cropping systems, which demands the development of cutting-edge virus surveillance techniques. In this study, we surveyed the common bean fields of Kashmir valley for virus infection using a total of 140 symptomatic and non-symptomatic leaf samples collected from different locations. The genetic diversity of viruses was examined by high-throughput sequencing (HTS) with three viruses being identified, namely, Bean Common Mosaic Virus (BCMV), Bean Common Mosaic Necrosis Virus (BCMNV), and Clover Yellow Vein Virus (ClYVV). BCMNV and ClYVV are new reports from India. De novo assembly of transcriptome constructed near-complete genomes of these viruses. RT-PCR results confirmed the presence of these viruses with an emerge incidence of 56. 4% for BCMV, 27.1% for BCMNV and 16.4 for ClYVV in the valley. Several samples were found to contain multiple virus infections with BCMV being the most predominant. Recombination events were detected in the genomes of BCMV and ClYVV, but not BCMNV. Phylogenetic and pairwise identity matrix evidence suggests viral import from multiple countries. Our results demonstrate thatHTS followed bymultiplex PCR assay is a simple, rapid, and reliable approach for simultaneous diagnosis of plant viruses. [ABSTRACT FROM AUTHOR]

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 with 63.7% GC content and 132 open reading frames (ORFs) flanked by 3,910-bp inverted terminal repeats (ITRs). An investigation into evolutionary parameters such as selection pressure (θ = dN/dS) and nucleotide diversity (π) demonstrated that ORFV has undergone purifying selection. A total of 40 recombination events were identified, 21 of which were evident in the Ind/MP/17 genome, indicating its ability to generate new variants. [ABSTRACT FROM AUTHOR]

• Dengue virus serotypes were tested in 4963 samples collected across India in 2018. • DENV-2 was the most prevalent serotype in many states of India. • Two genotypes of DENV-1 (I and V) were circulating. • Two lineages of DENV-2 genotype IV were circulating. • DENV-3 genotype III and DENV-4 genotype-I were circulating. A retrospective study was undertaken to investigate the circulating dengue virus (DENV) serotypes and genotypes in India in 2018. In total, 4963 samples referred to virus research diagnostic laboratories (n=21), the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV) and ICMR-NIV field units (n =2) for diagnosis of dengue in 2018 were tested using a real-time reverse transcription polymerase chain reaction assay for the presence of DENV serotypes. Representative samples were sequenced for the envelope (E) gene. Regional diversity was observed with regard to the dominant circulating serotypes. DENV-2 was found to be the most common serotype in many states. Thrombocytopenia, petechiae and malaise were associated with DENV-2 infection. Phylogenetic analyses of DENV E gene sequences revealed the circulation of genotypes I and V of DENV-1, two lineages of DENV-2 genotype IV, DENV-3 genotype III and DENV-4 genotype I. This study found regional differences in the prevalence of circulating DENV serotypes in India, and provides baseline data for continuous molecular surveillance. Molecular surveillance may have implications for predicting large-scale outbreaks of dengue if regional shifts in the predominantly circulating serotypes and genotypes are detected during the early phase of the dengue season. [ABSTRACT FROM AUTHOR]

Four gastroenteritis viruses were responsible for 54% of the acute gastroenteritis (AGE) cases in children hospitalized between May 2017 and December 2019 in Pune city of Maharashtra state, Western India. The majority (79%) of the children were <2 years of age. The prevalence of Rotavirus A (RVA) was 30.5% followed by 14.3% for norovirus, 8.4% for adenovirus, and 5.5% for astrovirus. The severity of the disease was highest in patients with coinfections compared with the patients with a single infection or negative for all (p = 0.024). Genotyping analysis showed that the majority of the RVA‐positive samples (66%) could be typed as G3P[8], 63.6% of the norovirus as GII.4 Sydney [P16], 44% of the adenovirus as type 41%, and 56.2% of the astrovirus as astrovirus type 1. The almost equivalent prevalence of rotavirus and nonrotaviruses and acute gastroenteritis (AGE) cases without known etiology in around 46% of the cases was noted in the present study. Our data highlight that after the recent inclusion of rotavirus vaccines as a part of the National Immunization schedule in India, conducting extensive AGE surveillance in children should include nonrotaviruses such as norovirus. Highlights: Four gastroenteritis viruses were responsible for 54% of the acute gastroenteritis (AGE) cases in children, Western India.Significant decline in Rotavirus A (RVA) AGE cases in children age <5 years.Dominance of RVA G3P[8] and decline of G1P[8] & G2P[4] genotype strains.Highly transmissible GII.P16‐GII.4 genotype strains in 63.6% of norovirus infections.Clinical severity of the disease showed, no correlation with regard to different RVA genotypes or norovirus strains. [ABSTRACT FROM AUTHOR]

Whole genome analysis of SARS-CoV-2 is important to identify its genetic diversity. Moreover, accurate detection of SARS-CoV-2 is required for its correct diagnosis. To address these, first we have analysed publicly available 10 664 complete or near-complete SARS-CoV-2 genomes of 73 countries globally to find mutation points in the coding regions as substitution, deletion, insertion and single nucleotide polymorphism (SNP) globally and country wise. In this regard, multiple sequence alignment is performed in the presence of reference sequence from NCBI. Once the alignment is done, a consensus sequence is build to analyse each genomic sequence to identify the unique mutation points as substitutions, deletions, insertions and SNPs globally, thereby resulting in 7209, 11700, 119 and 53 such mutation points respectively. Second, in such categories, unique mutations for individual countries are determined with respect to other 72 countries. In case of India, unique 385, 867, 1 and 11 substitutions, deletions, insertions and SNPs are present in 566 SARS-CoV-2 genomes while 458, 1343, 8 and 52 mutation points in such categories are common with other countries. In majority (above 10%) of virus population, the most frequent and common mutation points between global excluding India and India are L37F, P323L, F506L, S507G, D614G and Q57H in NSP6, RdRp, Exon, Spike and ORF3a respectively. While for India, the other most frequent mutation points are T1198K, A97V, T315N and P13L in NSP3, RdRp, Spike and ORF8 respectively. These mutations are further visualised in protein structures and phylogenetic analysis has been done to show the diversity in virus genomes. Third, a web application is provided for searching mutation points globally and country wise. Finally, we have identified the potential conserved region as target that belongs to the coding region of ORF1ab, specifically to the NSP6 gene. Subsequently, we have provided the primers and probes using that conserved region so that it can be used for detecting SARS-CoV-2. Contact: indrajit@nitttrkol.ac.in Supplementary information: Supplementary data are available at http://www.nitttrkol.ac.in/indrajit/projects/COVID-Mutation-10K [ABSTRACT FROM AUTHOR]

In 2017, Tamil Nadu, a southern state, had the second highest number of dengue cases from India. In the present study, the serotype‐specific differences in the clinical manifestations and laboratory parameters among hospitalized children with dengue were investigated and molecular characterization of the circulating dengue virus (DENV) serotypes during 2017 in Tamil Nadu was performed. Eighty children with dengue‐like symptoms consecutively admitted to a tertiary care hospital and positive for DENV NS1 antigen were investigated for DENV serotype utilizing a real‐time reverse transcriptase based polymerase chain reaction assay. Complete envelope (E) gene sequencing of the DENV strains was performed. Seventy samples were positive for serotyping (25 DENV‐1, 17 DENV‐2, six DENV‐3, and 22 DENV‐4). DENV‐4 infections were associated with elevated levels of liver enzymes; Alanine aminotransferase (P =.021) and aspartate aminotransferase (P =.001). However, none of the serotype was associated with any specific clinical features and severe dengue. Asian and American/African genotypes of DENV‐1 were cocirculating. The circulating genotype was cosmopolitan for DENV‐2 with multiple lineages, genotype III for DENV‐3 and genotype I for DENV‐4. Unique mutations were present in the 2017 DENV‐4 isolates. The present study suggests the association of DENV‐4 with elevated liver enzymes in children hospitalized for dengue. Further, the study reports the genetic diversity of DENV circulating in Tamil Nadu during 2017. The study calls for continuous monitoring of the circulating serotypes and genotypes at regional level in India which might result in a region wise database useful in predicting future outbreaks. Research Highlights: In Tamil Nadu, India, Asian and American/African genotypes of DENV‐1, cosmopolitan genotype of DENV‐2, genotype III of DENV‐3 and genotype I of DENV‐4 strains were circulating during 2017.DENV‐4 was associated with elevated levels of liver enzymes in children hospitalized for dengue.DENV serotypes were not associated with disease severity in children hospitalized for dengue.The study calls for continuous monitoring of the circulating serotypes and genotypes at regional level in India. [ABSTRACT FROM AUTHOR]

Documentation of the emergence of Porcine circovirus 2 (PCV2) infection and economic losses incurred due to high mortality has been reported worldwide. The prevalence and genetic diversity of the virus has been reported in Northeast India including the possible chances of Classical swine fever virus (CSFV) vaccine failure in pig population in this region resulting in major disease outbreak. Irrespective of the genetic variability, the emergence of a novel cluster (based on the ORF2 phylogeny) was reported last year. The present study describes a state-wide (Meghalaya, India) molecular epidemiological investigation of PCV2 strains in pig population by amplification, sequencing and undertaking phylogenetic analyses. The results indicate the identification of a novel cluster of PCV2 originating from the inter-genotypic recombination between PCV2c and PCV2d. Multiple sequence alignment of amino acids indicates possible substitution in the A, B and C domains of the capsid protein. Molecular structural modelling of the capsid protein of PCV2 indicated possible motif variations in the secondary structure including presence of a tunnel, encountered at the interface region on each chain facilitating in transportation of molecules and acting as an active site for attachment and penetration. The baseline data strengthens the existing control programme of PCV2 and is possibly helpful in the planning of active surveillance strategy in this region. • This article will provide a state-wide (Meghalaya) molecular epidemiological investigation of PCV2 strains in pig population by amplification, sequencing and phylogenetic analysis. • The results indicated the identification of a novel cluster of PCV2 originating from the inter-genotypic recombination between PCV2c and PCV2d. • Through molecular structural modelling of the capsid protein of PCV2 indicated possible motif variation in the secondary structure including presence of a tunnel. [ABSTRACT FROM AUTHOR]

We report the complete genome sequence of five bean yellow mosaic virus (BYMV) isolates (CK-GL1, CK-GL3, CK-GL4, CK-GL5 and Vfaba2) that share 74.6-98.9% (nucleotide) and 81.5-99.1% (amino acid) identity with globally available BYMV sequences. Phylogenetic analysis clustered them specifically in BYMV phylogenetic group-IV within the existing nine groups. The CK-GL1, CK-GL2, CK-GL4 and CK-GL5 isolates formed a discrete cluster within group-IV. The present study suggests subdivision of group-IV into subgroup-IVa and IVb. Moreover, infectivity assays using in vitro RNA transcripts from subgroup-IVa (CK-GL3 isolate) and IVb (CK-GL1 isolate) showed distinct biological differences between the isolates supporting subdivision. [ABSTRACT FROM AUTHOR]

Highlights: [•] Foorkey disease of large cardamom is known to exist in India since last 77 years. [•] Nine novel DNA components of the virus (CBDV) in foorkey were characterized. [•] Overall genome sequence identity of CBDV was ≤62.0% with ABTV and BBTV. [•] CBDV is the first babuvirus (Nanoviridae) that infects plant outside Musaceae. [•] Our study provides evidence of further diversity in the genus Babuvirus. [Copyright &y& Elsevier]

The movement protein ( NSm) gene of Groundnut bud necrosis virus (GBNV) isolates from pea, mungbean, cowpea, French bean, tomato and potato collected from different locations of India were compared to study their diversity. The NSm gene sequences of all the GBNV isolates were highly conserved and had only 0-3% diversity in amino acids and 0-10% in nucleotides. Comparison of amino acid sequence of NSm gene of 25 GBNV isolates revealed the presence of many conserved regions. Both 'D-motif' and 'G-residue', the conserved regions of '30K superfamily' of virus movement protein, were present in all the isolates. Clustering of the GBNV isolates does not appear to be based on their place of origin and host plant species. [ABSTRACT FROM AUTHOR]

• Even in developing countries like India, KFD remain challenges that mandate attention from health authorities. • The infection has a socioeconomic effect on the livelihood communities of individuals who are relying on the forest area. • The genetic data for Haemaphysalis bispinosa was comparatively available in sufficient extent than the other species. • The molecular analysis revealed that the Karnataka and Maharashtra states were more vulnerable to KFD infection. The deadly effects of KFD have been pointed in southern India; however, the infecting regions have been getting larger in recent epochs. People who live or work in regions where KFDV infected tick vectors are present are severely prone to procuring the infection. Being aware of tick vectors and infectious agents' geospatial location is vital to direct sustenance approaches to prevent and manage such infectious diseases as KFD. The present investigation has focussed on the spatial distribution, Extensive genetic Diversity, and phylogeography to forecast the probable KFD disease risk provinces in the Western Ghats. The statistical analysis for diversity indices and community comparison has been performed by using SPSS version 24.0.0 and R software version 3.4.2. The nucleotide sequences of the respective ticks and KFDV were retrieved from NCBI. The first strand of this investigation revealed that, around the world, the Indian province was found to exhibit a maximum range of diversity for tick vectors. The next strands prophesied the KFD transmission risk areas in the Western Ghats region, India, with computational spatial analysis and phylogeography. The final strand exposed the genetic diversity of the KFD virus and the tick vectors in terms of their spatial distribution worldwide. [ABSTRACT FROM AUTHOR]

Papaya ringspot virus (PRSV) is the major constraint to papaya ( Carica papaya ) production in Bangladesh. Disease symptoms occurred in 90 to 100% of the plants surveyed. Full-length genomes of PRSV strains from severely infected papaya plants were determined using the Illumina NextSeq 500 platform, followed by Sanger DNA sequencing of viral genomes obtained by reverse-transcription PCR(RT-PCR). The genome sequences of two distinct PRSV strains, PRSV BD-1 (10,300 bp) and PRSV BD-2 (10,325 bp) were 74 and 83% identical to each other, respectively, at the nucleotide and amino acid levels. PRSV BD-1 and PRSV BD-2 were 74 to 75% and 79 to 88% identical, respectively, to other full-length PRSV sequences at the nucleotide level. Based on phylogenetic analysis, PRSV BD-2 was most closely related to PRSV-Meghalaya (MF356497) from papaya in India. PRSV BD-1 formed a branch distinct from the other PRSV sequences based on nucleotide and amino acid sequence comparisons. Comparisons of the genome sequences of these two strains with other sequenced PRSV genomes indicated two putative recombination events in PRSV BD-2. One recombinant event contained a 2,766-nucleotide fragment highly identical to PRSV-Meghalaya (MF356497). The other recombinant event contained a 5,105-nucleotide fragment highly identical to PRSV-China (KY933061). The occurrence rates of PRSV BD-1 and PRSV BD-2 in the sampled areas of Bangladesh were approximately 19 and 69%, respectively. Plants infected with both strains (11%) exhibited more severe symptoms than plants infected with either strain alone. The full-length genome sequences of these new PRSV strains and their distribution provide important information regarding the dynamics of papaya ringspot virus infections in papaya in Bangladesh.