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No full textNot AvailableBackground: India recorded the first outbreak of African swine fever (ASF) in North-eastern
region (NER) in the year 2020.
Aim: The current study was undertaken to investigate the transmission of African swine
fever virus (ASFV) in the wild boars of Northeast India, particularly of Assam.
Material and Methods: ASF suspected mortal tissue remains and blood samples of wild
boars collected from different locations of Assam were screened for molecular detection of
swine viruses which includes Classical swine fever virus, Porcine Circovirus 2, Porcine reproductive and respiratory syndrome virus and ASFV.
Results: One sample each from Manas and Nameri National Parks was detected positive for
ASFV. Besides this, one of the samples was positive for CSFV and one of the ASFV positive samples was also positive for PCV2. Several striking gross and microscopic alterations were noticed
in different organs of ASFV infected animals. Sequencing and phylogenetic analysis of B646L
gene confirmed the presence of ASFV genotype-II in wild boars. Circulation of similar genotype
in domestic pigs of NER in the contemporary period as well as locations near to the aforementioned national parks indicates the transmission of ASFV from domestic to wild boars.
Clinical Relevance: The detection of ASFV in the wild boars of Assam is alarming as it is an
impending threat to pig population and other endangered species (particularly Pygmy hog),
making it increasingly daunting to control the disease.
Conclusion: Chances are high for ASFV to become endemic in Assam region if stringent
measures are not taken at proper time.Not Availabl
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No full textNot AvailableCrimean Congo Hemorrhagic Fever (CCHF), is an emerging zoonosis globally and in India. The present study focused on identifying the risk factors for occurrence of CCHF in the Indian state of Gujarat and development of risk map for India. The past CCHF outbreaks in India were collated for the analyses. Influence of land use change and climatic factors in determining the occurrence of CCHF in Gujarat was assessed using Bayesian spatial models. Change in maximum temperature in affected districts was analysed to identify the significant change points over 110 years. Risk map was developed for Gujarat using Bayesian Additive Regression Trees (BART) model with remotely sensed environmental variables and host (livestock and human) factors. We found the change in land use patterns and maximum temperature in affected districts to be contributing to the occurrence of CCHF in Gujarat. Spatial risk map developed using CCHF occurrence data for Gujarat identified density of buffalo, minimum land surface temperature and elevation as risk determinants. Further, spatial risk map for the
occurrence of CCHF in India was developed using selected variables. Overall, we found that combination of factors such as change in land-use patterns, maximum temperature, buffalo density, day time minimum land surface temperature and elevation led to the emergence and further spread of the disease in India. Mitigation measures for CCHF in India could be designed considering disease epidemiology and initiation of surveillance strategies based on the risk map developed in this study.Not Availabl
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No full textNot AvailableBackground: Tobacco mosaic virus (TMV) stands as a highly studied virus and consequently, its features and composition are extensively understood. It has been found to induce diverse infections in numerous plant species, with tobacco leaves being notably affected, showing mottled browning. Presently, the sole available method to control its spread is by removing infected plants. Understanding codon use bias is crucial as it could play a pivotal role in molecular interventions aimed at halting the virus’s replication and multiplication, thereby helping to contain its propagation.
Methods: Currently, the research focuses on assessing codon bias within six genes related to the replicase/coat protein of TMV, namely TMVgp1, TMVgp2, TMVgp3, TMVgp4, TMVgp5 and TMVgp6. To conduct this analysis, various methods such as relative dinucleotide abundance, relative synonymous codon usage (RSCU), neutrality plot and parity rule 2 (PR2) plot were employed.
Result: All of the identified genes had a modest codon bias, according to the study on codon usage, as well as the function of mutation pressure in gene TMVgp3 and natural selection in genes TMVgp1, TMVgp2, TMVgp4, TMVgp5 and TMVgp6. The Research into codon use bias showed that the TMV virus’s chosen genes are subjected to naturally occurring selection as well as mutational pressure.Not Availabl
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No full textNot AvailableIn this study, we assessed the PPR disease status, its economic cost, the financial viability of
vaccination, and the perspectives of field veterinarians on the PPR vaccination programme implemented in Karnataka state, India. In addition to secondary data, cross-sectional surveys undertaken
during 2016–17 (survey I) and 2018–19 (survey II) from 673 sheep and goat flocks and data collected
from 62 veterinarians were analysed. The economic costs and perceptions of veterinarians were
analysed using deterministic models and the Likert scale, respectively, and the financial viability
of vaccination programmes under the best (15%), base (20%), and worst-case (25%) PPR incidence
scenarios, considering two different vaccination plans (plan I and plan II), was assessed. The disease
incidence in sheep and goats was found to be 9.8% and 4.8% in survey I and survey II, respectively.
In consonance with the increased vaccination coverage, the number of reported PPR outbreaks in
the state declined significantly. The estimated farm-level loss of PPR varied between the surveyed
years. Even under the best-incidence scenario, under vaccination plan-I and plan-II, the estimated
benefit–cost ratio (18.4:1; 19.7:1), the net present value (USD 932 million; USD 936 million) and the
internal rate of return (412%) implied that the vaccination programmes were financially viable and
the benefits outweighed the cost. Though the majority of veterinarians perceived that the control
programme was well planned and rolled out in the state, a few of them disagreed or were neutral
towards the plan per se, towards the coordination between functionaries, the availability of funding,
and the programme acceptance by farmers. Despite many years of vaccination, PPR still persists in
the Karnataka state for various reasons and in order to eradicate the disease, a review of the existing
control programme with strong facilitation from the federal government is needed.Not Availabl
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No full textNot AvailableBackground
The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature.
Methods
We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes.
Results
We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases.
Conclusions
Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes.Not Availabl
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No full textNot AvailableWe evaluated the genetic diversity of a newly available collection of 94 almond [Prunus dulcis (Mill.) D.A.
Webb] accessions from the former Improving Perennial Plants for Food and Bioenergy (IPPFBE) Foundation. Most
of the collection (87 accessions) were collected as seeds from trees growing in the central Asian nations of Kyrgyzstan,
Tajikistan, and Uzbekistan, and included several examples of Prunus bucharica (Korsh.) Hand.-Mazz, and related
wild species. Of the remaining accessions, six were sourced from a nursery in northern Utah in the United States,
and one was a seedling of ‘Nonpareil’, a major commercial cultivar. DNA fingerprints were generated from 10 simple
sequence repeat markers. To evaluate the comparative diversity of these new accessions, 66 accessions from the US
Department of Agriculture, National Plant Germplasm System (NPGS) almond germplasm collection near Davis,
CA, USA, were also included. These NPGS accessions were chosen to represent those collected in similar regions of
Central Asia and the Caucasus. The fingerprints were analyzed via hierarchical clustering, principal components
analysis (PCA), and discriminant analysis of principal components (DAPC). Hierarchical clustering suggested that
half of the Utah-sourced accessions are closely related to each other and to the ‘Nonpareil’ seedling. Additional close
relationships were detected (including at least one duplication or mislabeling), and two P. bucharica accessions from
the IPPFBE collection were separated from the rest of the collection. A plot of the first two principal components
clearly separated wild almond relatives (P. bucharica and Prunus fenzliana Fritsch) from the remaining accessions.
PCA after removal of the wild species separated the ‘Nonpareil’ seedling, the Utah-sourced accessions, and many of the
IPPFBE accessions (mostly from Uzbekistan) from nearly all other individuals. The third principal component identi-
fied an additional population structure that separated groups of predominantly IPPFBE or NPGS accessions. DAPC
showed a considerable admixture of accessions from Azerbaijan, and a little to no admixture of accessions from Georgia
and Tajikistan. These results suggest that central Asian/Caucasian almond germplasm is generally distinct from ‘Non-
pareil’ and its relatives, and that although there is overlap between the NPGS and IPPFBE collections from this region,
the IPPFBE collection does enhance the diversity of available almond germplasm.Not Availabl
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No full textChapter 3 of Training manual “Nanotechnological Applications in Fisheries”Not AvailableNot Availabl
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No full textChapter 13 of Training manual “Seafood Quality Assurance”Not AvailableNot Availabl
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No full textChapter 14 of Training manual “Seafood Quality Assurance”Not AvailableNot Availabl