Viral Genomics and Bioinformatics (original) (raw)
Scrutinizing Virus Genome Termini by High-Throughput Sequencing
PLoS ONE, 2014
Analysis of genomic terminal sequences has been a major step in studies on viral DNA replication and packaging mechanisms. However, traditional methods to study genome termini are challenging due to the time-consuming protocols and their inefficiency where critical details are lost easily. Recent advances in next generation sequencing (NGS) have enabled it to be a powerful tool to study genome termini. In this study, using NGS we sequenced one iridovirus genome and twenty phage genomes and confirmed for the first time that the high frequency sequences (HFSs) found in the NGS reads are indeed the terminal sequences of viral genomes. Further, we established a criterion to distinguish the type of termini and the viral packaging mode. We also obtained additional terminal details such as terminal repeats, multi-termini, asymmetric termini. With this approach, we were able to simultaneously detect details of the genome termini as well as obtain the complete sequence of bacteriophage genomes. Theoretically, this application can be further extended to analyze larger and more complicated genomes of plant and animal viruses. This study proposed a novel and efficient method for research on viral replication, packaging, terminase activity, transcription regulation, and metabolism of the host cell.
InTech eBooks, 2012
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Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research
Journal of Virology, 2014
The beginning of the second century of research in the field of virology (the first virus 27 was discovered in 1898) was marked with its amalgamation with bioinformatics 28 resulting in the birth of a new domain -viroinformatics. The availability of more than 29 100 web servers and databases embracing all or specific viruses (for example dengue, 30 influenza, hepatitis, HIV, HFV, HPV, West Nile etc.) as well as distinct applications 31 (comparative/diversity analysis, viral recombination, siRNA/shRNA/miRNA studies, 32 RNA folding, protein-protein interaction, structural analysis, phylotyping/genotyping) 33 will definitely aid the development of effective drugs and vaccines. However, the 34 information about their access and utility is not available at any single 35 source/platform. Therefore, a compendium of various computational tools/resources 36 dedicated specifically to virology is presented in this article.
Application of next-generation sequencing technologies in virology
… of General Virology, 2012
The progress of science is punctuated by the advent of revolutionary technologies that provide new ways and scales to formulate scientific questions and advance knowledge. Following on from electron microscopy, cell culture and PCR, nextgeneration sequencing is one of these methodologies that is now changing the way that we understand viruses, particularly in the areas of genome sequencing, evolution, ecology, discovery and transcriptomics. Possibilities for these methodologies are only limited by our scientific imagination and, to some extent, by their cost, which has restricted their use to relatively small numbers of samples. Challenges remain, including the storage and analysis of the large amounts of data generated. As the chemistries employed mature, costs will decrease. In addition, improved methods for analysis will become available, opening yet further applications in virology including routine diagnostic work on individuals, and new understanding of the interaction between viral and host transcriptomes. An exciting era of viral exploration has begun, and will set us new challenges to understand the role of newly discovered viral diversity in both disease and health.
NucAmino: a nucleotide to amino acid alignment optimized for virus gene sequences
BMC Bioinformatics
Background: Current nucleotide-to-amino acid alignment software programs were developed primarily for detecting gene exons within eukaryotic genomes and were therefore optimized for speed across long genetic sequences. We developed a nucleotide-to-amino acid alignment program NucAmino optimized for virus sequencing. Results: NucAmino is an open source program written in the high-level language Go. NucAmino is more likely to align codons flush with a reference sequence's amino acids and can be modified to facilitate the placement of insertions and deletions at specific positions. We compared NucAmino to the nucleotide to amino acid alignment program Local Alignment Program (LAP) using 115,118 human immunodeficiency virus type 1 (HIV-1) protease, reverse transcriptase, and integrase sequences-three genes that are commonly sequenced in clinical laboratories. Discordances between NucAmino and LAP occurred in 512 (16.9%) of the 3,029 sequences containing gaps but in none of 112,910 sequences without gaps. For 242 of the sequences with discordances, NucAmino produced an alignment that was preferable to that found by LAP in that it was more likely to codon align insertions and deletions and to facilitate the placement of an important drug-resistance associated insertion at the position at which most laboratories expect it to occur. Conclusions: NucAmino is a nucleotide-to-amino acid alignment program with several advantages for clinical laboratories performing virus sequencing compared with older programs designed for gene finding.
Comparative Analysis of SARS-CoV2 with Special Emphasis on Genome Sequences
Journal of Pure and Applied Microbiology, 2020
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus – 2 (SARS-CoV-2), was declared a global pandemic on 11th March, 2020 by World Health Organization. As of now,27th May,2020, there are about 54,88,825 infected cases and 3,49,095 deaths globally. Coronavirus samples collected from all the countries have been sequenced for advanced studies in a bid to understand the structure and functioning of the virus. In our study we have tried working on every available sequence to setup both comparisons and co-relations. There is no such available study as of now for reference and hence it can become a pioneer stone in this direction. The mortality rate calculated turns out to be 9.19%,34.37% and 6.29% for SARS-2003, MERS-2012 and COVID-19 respectively. The basic reproduction rate R0 was 2-5 for SARS-2003, 0.3-0.8 for MERS-2012 and 1.4-5.7 for COVID-19. We found out the relation between number of mutations and mortality as well as phylogenetic relations. High number of mutations corresponded to higher mortality rate as in countries like Italy and Spain. Alpha and Beta-coronaviruses show a common ancestor from which they descended. Brazil and Iran have shown similar phylogenetic descent explaining their mortality rate. India however showed a distant relation from the common ancestor of other genome sequences. This study highlights the mutations of the SARS-CoV2 virus as well as sets up a comparison with the previous outbreaks. Similar type of studies should be conducted when more genome samples are present. These results can also contribute towards making an effective anti-viral therapy and vaccines.