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Article ; Online: African swine fever virus NAM P1/95 is a mixture of genotype I and genotype VIII viruses.

Goatley, Lynnette C / Freimanis, Graham L / Tennakoon, Chandana / Bastos, Armanda / Heath, Livio / Netherton, Christopher L

Microbiology resource announcements

2024 Volume 13, Issue 4, Page(s) e0006724

Abstract: African swine fever virus causes a lethal hemorrhagic disease of domestic pigs. The NAM P1/1995 isolate was originally described ... ...

Abstract	African swine fever virus causes a lethal hemorrhagic disease of domestic pigs. The NAM P1/1995 isolate was originally described as
Language	English
Publishing date	2024-03-25
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/mra.00067-24
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Article ; Online: A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus.

Chrzastek, Klaudia / Tennakoon, Chandana / Bialy, Dagmara / Freimanis, Graham / Flannery, John / Shelton, Holly

BMC genomics

2022 Volume 23, Issue 1, Page(s) 406

Abstract: Background: Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the ... ...

Abstract	Background: Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions. Methods: The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing. Results: The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 10 Conclusions: The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.
MeSH term(s)	COVID-19 ; Genome, Viral ; Humans ; Influenza A Virus, H1N1 Subtype ; RNA Viruses ; SARS-CoV-2/genetics ; Whole Genome Sequencing
Language	English
Publishing date	2022-05-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-022-08563-z
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Article ; Online: BATVI: Fast, sensitive and accurate detection of virus integrations.

Tennakoon, Chandana / Sung, Wing Kin

BMC bioinformatics

2017 Volume 18, Issue Suppl 3, Page(s) 71

Abstract: Background: The study of virus integrations in human genome is important since virus integrations were shown to be associated with diseases. In the literature, few methods have been proposed that predict virus integrations using next generation ... ...

Abstract	Background: The study of virus integrations in human genome is important since virus integrations were shown to be associated with diseases. In the literature, few methods have been proposed that predict virus integrations using next generation sequencing datasets. Although they work, they are slow and are not very sensitive. Results and discussion: This paper introduces a new method BatVI to predict viral integrations. Our method uses a fast screening method to filter out chimeric reads containing possible viral integrations. Next, sensitive alignments of these candidate chimeric reads are called by BLAST. Chimeric reads that are co-localized in the human genome are clustered. Finally, by assembling the chimeric reads in each cluster, high confident virus integration sites are extracted. Conclusion: We compared the performance of BatVI with existing methods VirusFinder and VirusSeq using both simulated and real-life datasets of liver cancer patients. BatVI ran an order of magnitude faster and was able to predict almost twice the number of true positives compared to other methods while maintaining a false positive rate less than 1%. For the liver cancer datasets, BatVI uncovered novel integrations to two important genes TERT and MLL4, which were missed by previous studies. Through gene expression data, we verified the correctness of these additional integrations. BatVI can be downloaded from http://biogpu.ddns.comp.nus.edu.sg/~ksung/batvi/index.html .
MeSH term(s)	Algorithms ; Cluster Analysis ; DNA, Viral/genetics ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Genome, Human ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions/genetics ; Humans ; Liver Neoplasms/diagnosis ; Liver Neoplasms/virology ; Models, Theoretical ; Sequence Analysis, DNA ; Software ; Telomerase/genetics ; Telomerase/metabolism ; Virus Integration
Chemical Substances	DNA, Viral ; DNA-Binding Proteins ; MLL4 protein, human (EC 2.1.1.43) ; TERT protein, human (EC 2.7.7.49) ; Telomerase (EC 2.7.7.49)
Language	English
Publishing date	2017-03-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-017-1470-x
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Article ; Online: BioCarian: search engine for exploratory searches in heterogeneous biological databases.

Zaki, Nazar / Tennakoon, Chandana

BMC bioinformatics

2017 Volume 18, Issue 1, Page(s) 435

Abstract: Background: There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web ... ...

Abstract	Background: There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. Results: We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . Conclusions: We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.
MeSH term(s)	Databases, Factual ; Internet ; Search Engine ; Software
Language	English
Publishing date	2017-10-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-017-1840-4
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Article ; Online: Full genome sequence analysis of African swine fever virus isolates from Cameroon.

Goatley, Lynnette C / Freimanis, Graham / Tennakoon, Chandana / Foster, Thomas J / Quershi, Mehnaz / Dixon, Linda K / Batten, Carrie / Forth, Jan Hendrik / Wade, Abel / Netherton, Christopher

PloS one

2024 Volume 19, Issue 3, Page(s) e0293049

Abstract: African swine fever (ASF) is a devastating disease of domestic pigs that has spread across the globe since its introduction into Georgia in 2007. The etiological agent is a large double-stranded DNA virus with a genome of 170 to 180 kb in length ... ...

Abstract	African swine fever (ASF) is a devastating disease of domestic pigs that has spread across the globe since its introduction into Georgia in 2007. The etiological agent is a large double-stranded DNA virus with a genome of 170 to 180 kb in length depending on the isolate. Much of the differences in genome length between isolates are due to variations in the copy number of five different multigene families that are encoded in repetitive regions that are towards the termini of the covalently closed ends of the genome. Molecular epidemiology of African swine fever virus (ASFV) is primarily based on Sanger sequencing of a few conserved and variable regions, but due to the stability of the dsDNA genome changes in the variable regions occur relatively slowly. Observations in Europe and Asia have shown that changes in other genetic loci can occur and that this could be useful in molecular tracking. ASFV has been circulating in Western Africa for at least forty years. It is therefore reasonable to assume that changes may have accumulated in regions of the genome other than the standard targets over the years. At present only one full genome sequence is available for an isolate from Western Africa, that of a highly virulent isolate collected from Benin during an outbreak in 1997. In Cameroon, ASFV was first reported in 1981 and outbreaks have been reported to the present day and is considered endemic. Here we report three full genome sequences from Cameroon isolates of 1982, 1994 and 2018 outbreaks and identify novel single nucleotide polymorphisms and insertion-deletions that may prove useful for molecular epidemiology studies in Western Africa and beyond.
MeSH term(s)	Swine ; Animals ; African Swine Fever Virus ; African Swine Fever/epidemiology ; Cameroon/epidemiology ; Sus scrofa/genetics ; Sequence Analysis ; Sequence Analysis, DNA
Language	English
Publishing date	2024-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0293049
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Article ; Online: An Improved αvβ6-Receptor-Expressing Suspension Cell Line for Foot-and-Mouth Disease Vaccine Production.

Harvey, Yongjie / Jackson, Ben / Carr, Brigid Veronica / Childs, Kay / Moffat, Katy / Freimanis, Graham / Tennakoon, Chandana / Juleff, Nicholas / Seago, Julian

Viruses

2022 Volume 14, Issue 3

Abstract: Foot-and-mouth disease (FMD) is endemic in large parts of sub-Saharan Africa, Asia and South America, where outbreaks in cloven-hooved livestock threaten food security and have severe economic impacts. Vaccination in endemic regions remains the most ... ...

Abstract	Foot-and-mouth disease (FMD) is endemic in large parts of sub-Saharan Africa, Asia and South America, where outbreaks in cloven-hooved livestock threaten food security and have severe economic impacts. Vaccination in endemic regions remains the most effective control strategy. Current FMD vaccines are produced from chemically inactivated foot-and-mouth disease virus (FMDV) grown in suspension cultures of baby hamster kidney 21 cells (BHK-21). Strain diversity means vaccines produced from one subtype may not fully protect against circulating disparate subtypes, necessitating the development of new vaccine strains that "antigenically match". However, some viruses have proven difficult to adapt to cell culture, slowing the manufacturing process, reducing vaccine yield and limiting the availability of effective vaccines, as well as potentiating the selection of undesired antigenic changes. To circumvent the need to cell culture adapt FMDV, we have used a systematic approach to develop recombinant suspension BHK-21 that stably express the key FMDV receptor integrin αvβ6. We show that αvβ6 expression is retained at consistently high levels as a mixed cell population and as a clonal cell line. Following exposure to field strains of FMDV, these recombinant BHK-21 facilitated higher virus yields compared to both parental and control BHK-21, whilst demonstrating comparable growth kinetics. The presented data supports the application of these recombinant αvβ6-expressing BHK-21 in future FMD vaccine production.
MeSH term(s)	Animals ; Cell Line ; Foot-and-Mouth Disease ; Foot-and-Mouth Disease Virus/genetics ; Vaccination ; Viral Vaccines/genetics
Chemical Substances	Viral Vaccines
Language	English
Publishing date	2022-03-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14030621
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Article ; Online: SiNPle: Fast and Sensitive Variant Calling for Deep Sequencing Data.

Ferretti, Luca / Tennakoon, Chandana / Silesian, Adrian / Ribeca, Graham Freimanis andPaolo

Genes

2019 Volume 10, Issue 8

Abstract: Current high-throughput sequencing technologies can generate sequence data and provide information on the genetic composition of samples at very high coverage. Deep sequencing approaches enable the detection of rare variants in heterogeneous samples, ... ...

Abstract	Current high-throughput sequencing technologies can generate sequence data and provide information on the genetic composition of samples at very high coverage. Deep sequencing approaches enable the detection of rare variants in heterogeneous samples, such as viral quasi-species, but also have the undesired effect of amplifying sequencing errors and artefacts. Distinguishing real variants from such noise is not straightforward. Variant callers that can handle pooled samples can be in trouble at extremely high read depths, while at lower depths sensitivity is often sacrificed to specificity. In this paper, we propose SiNPle (Simplified Inference of Novel Polymorphisms from Large coveragE), a fast and effective software for variant calling. SiNPle is based on a simplified Bayesian approach to compute the posterior probability that a variant is not generated by sequencing errors or PCR artefacts. The Bayesian model takes into consideration individual base qualities as well as their distribution, the baseline error rates during both the sequencing and the PCR stage, the prior distribution of variant frequencies and their strandedness. Our approach leads to an approximate but extremely fast computation of posterior probabilities even for very high coverage data, since the expression for the posterior distribution is a simple analytical formula in terms of summary statistics for the variants appearing at each site in the genome. These statistics can be used to filter out putative SNPs and indels according to the required level of sensitivity. We tested SiNPle on several simulated and real-life viral datasets to show that it is faster and more sensitive than existing methods. The source code for SiNPle is freely available to download and compile, or as a Conda/Bioconda package.
MeSH term(s)	DNA, Viral/genetics ; Genotyping Techniques/methods ; Genotyping Techniques/standards ; High-Throughput Nucleotide Sequencing/methods ; High-Throughput Nucleotide Sequencing/standards ; Polymorphism, Single Nucleotide ; Sensitivity and Specificity ; Sequence Analysis, DNA/methods ; Sequence Analysis, DNA/standards ; Software
Chemical Substances	DNA, Viral
Language	English
Publishing date	2019-07-25
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10080561
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Article: Comprehensive Intrinsic Disorder Analysis of 6108 Viral Proteomes: From the Extent of Intrinsic Disorder Penetrance to Functional Annotation of Disordered Viral Proteins

Kumar, Naveen / Kaushik, Rahul / Tennakoon, Chandana / Uversky, Vladimir N / Longhi, Sonia / Zhang, Kam Y. J / Bhatia, Sandeep

Journal of proteome research. 2021 Mar. 10, v. 20, no. 5

2021

Abstract: Much of our understanding of proteins and proteomes comes from the traditional protein structure–function paradigm. However, in the last 2 decades, both computational and experimental studies have provided evidence that a large fraction of functional ... ...

Abstract	Much of our understanding of proteins and proteomes comes from the traditional protein structure–function paradigm. However, in the last 2 decades, both computational and experimental studies have provided evidence that a large fraction of functional proteomes across different domains of life consists of intrinsically disordered proteins, thus triggering a quest to unravel and decipher protein intrinsic disorder. Unlike structured/ordered proteins, intrinsically disordered proteins/regions (IDPs/IDRs) do not possess a well-defined structure under physiological conditions and exist as highly dynamic conformational ensembles. In spite of this peculiarity, these proteins have crucial roles in cell signaling and regulation. To date, studies on the abundance and function of IDPs/IDRs in viruses are rather limited. To fill this gap, we carried out an extensive and thorough bioinformatics analysis of 283 000 proteins from 6108 reference viral proteomes. We analyzed protein intrinsic disorder from multiple perspectives, such as abundance of IDPs/IDRs across diverse virus types, their functional annotations, and subcellular localization in taxonomically divergent hosts. We show that the content of IDPs/IDRs in viral proteomes varies broadly as a function of virus genome types and taxonomically divergent hosts. We have combined the two most commonly used and accurate IDP predictors’ results with charge-hydropathy (CH) versus cumulative distribution function (CDF) plots to categorize the viral proteins according to their IDR content and physicochemical properties. Mapping of gene ontology on the disorder content of viral proteins reveals that IDPs are primarily involved in key virus–host interactions and host antiviral immune response downregulation, which are reinforced by the post-translational modifications tied to disorder-enriched viral proteins. The present study offers detailed insights into the prevalence of the intrinsic disorder in viral proteomes and provides appealing targets for the design of novel therapeutics.
Keywords	bioinformatics ; cumulative distribution ; gene ontology ; immune response ; penetrance ; proteome ; research ; therapeutics ; viral genome ; viruses
Language	English
Dates of publication	2021-0310
Size	p. 2704-2713.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.1c00011
Database	NAL-Catalogue (AGRICOLA)

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Article: An Improved αvβ6-Receptor-Expressing Suspension Cell Line for Foot-and-Mouth Disease Vaccine Production

Harvey, Yongjie / Jackson, Ben / Carr, Brigid Veronica / Childs, Kay / Moffat, Katy / Freimanis, Graham / Tennakoon, Chandana / Juleff, Nicholas / Seago, Julian

Viruses. 2022 Mar. 16, v. 14, no. 3

2022

Abstract	Foot-and-mouth disease (FMD) is endemic in large parts of sub-Saharan Africa, Asia and South America, where outbreaks in cloven-hooved livestock threaten food security and have severe economic impacts. Vaccination in endemic regions remains the most effective control strategy. Current FMD vaccines are produced from chemically inactivated foot-and-mouth disease virus (FMDV) grown in suspension cultures of baby hamster kidney 21 cells (BHK-21). Strain diversity means vaccines produced from one subtype may not fully protect against circulating disparate subtypes, necessitating the development of new vaccine strains that “antigenically match”. However, some viruses have proven difficult to adapt to cell culture, slowing the manufacturing process, reducing vaccine yield and limiting the availability of effective vaccines, as well as potentiating the selection of undesired antigenic changes. To circumvent the need to cell culture adapt FMDV, we have used a systematic approach to develop recombinant suspension BHK-21 that stably express the key FMDV receptor integrin αvβ6. We show that αvβ6 expression is retained at consistently high levels as a mixed cell population and as a clonal cell line. Following exposure to field strains of FMDV, these recombinant BHK-21 facilitated higher virus yields compared to both parental and control BHK-21, whilst demonstrating comparable growth kinetics. The presented data supports the application of these recombinant αvβ6-expressing BHK-21 in future FMD vaccine production.
Keywords	Foot-and-mouth disease virus ; cell culture ; cell lines ; food security ; foot-and-mouth disease ; growth models ; hamsters ; integrins ; kidneys ; livestock ; strain differences ; vaccination ; vaccine development ; vaccines ; viruses ; Asia ; South America ; Sub-Saharan Africa
Language	English
Dates of publication	2022-0316
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14030621
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Deletion of the s2m RNA Structure in the Avian Coronavirus Infectious Bronchitis Virus and Human Astrovirus Results in Sequence Insertions.

Keep, Sarah / Dowgier, Giulia / Lulla, Valeria / Britton, Paul / Oade, Michael / Freimanis, Graham / Tennakoon, Chandana / Jonassen, Christine Monceyron / Tengs, Torstein / Bickerton, Erica

Journal of virology

2023 Volume 97, Issue 3, Page(s) e0003823

Abstract: Coronaviruses infect a wide variety of host species, resulting in a range of diseases in both humans and animals. The coronavirus genome consists of a large positive-sense single-stranded molecule of RNA containing many RNA structures. One structure, ... ...

Abstract	Coronaviruses infect a wide variety of host species, resulting in a range of diseases in both humans and animals. The coronavirus genome consists of a large positive-sense single-stranded molecule of RNA containing many RNA structures. One structure, denoted s2m and consisting of 41 nucleotides, is located within the 3' untranslated region (3' UTR) and is shared between some coronavirus species, including infectious bronchitis virus (IBV), severe acute respiratory syndrome coronavirus (SARS-CoV), and SARS-CoV-2, as well as other pathogens, including human astrovirus. Using a reverse genetic system to generate recombinant viruses, we investigated the requirement of the s2m structure in the replication of IBV, a globally distributed economically important
MeSH term(s)	Animals ; Humans ; 3' Untranslated Regions/genetics ; Chickens/virology ; Infectious bronchitis virus/genetics ; Mamastrovirus/genetics ; Mutagenesis, Insertional/genetics ; Poultry Diseases/virology ; RNA, Viral/genetics ; Virus Replication/genetics ; RNA Stability/genetics ; Sequence Deletion/genetics
Chemical Substances	3' Untranslated Regions ; RNA, Viral
Language	English
Publishing date	2023-02-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.00038-23
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