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  1. Article: Erratum: Avian and serpentine endogenous foamy viruses, and new insights into the macroevolutionary history of foamy viruses.

    Aiewsakun, Pakorn

    Virus evolution

    2020  Volume 6, Issue 1, Page(s) veaa015

    Abstract: This corrects the article DOI: 10.1093/ve/vez057.][This corrects the article DOI: 10.1093/ve/vez057.]. ...

    Abstract [This corrects the article DOI: 10.1093/ve/vez057.][This corrects the article DOI: 10.1093/ve/vez057.].
    Language English
    Publishing date 2020-02-20
    Publishing country England
    Document type Published Erratum
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veaa015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Avian and serpentine endogenous foamy viruses, and new insights into the macroevolutionary history of foamy viruses.

    Aiewsakun, Pakorn

    Virus evolution

    2020  Volume 6, Issue 1, Page(s) vez057

    Abstract: This study reports and characterises two novel distinct lineages of foamy viruses (FVs) in the forms of endogenous retroviruses (ERVs). Several closely related elements were found in the genome of oriental stork ( ...

    Abstract This study reports and characterises two novel distinct lineages of foamy viruses (FVs) in the forms of endogenous retroviruses (ERVs). Several closely related elements were found in the genome of oriental stork (
    Language English
    Publishing date 2020-01-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/vez057
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Genomic Interactions Between

    Palittapongarnpim, Prasit / Tantivitayakul, Pornpen / Aiewsakun, Pakorn / Mahasirimongkol, Surakameth / Jaemsai, Bharkbhoom

    Annual review of genomics and human genetics

    2024  

    Abstract: Mycobacterium ... ...

    Abstract Mycobacterium tuberculosis
    Language English
    Publishing date 2024-04-19
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2037670-4
    ISSN 1545-293X ; 1527-8204
    ISSN (online) 1545-293X
    ISSN 1527-8204
    DOI 10.1146/annurev-genom-021623-101844
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  4. Article ; Online: Analysis of whiB7 in Mycobacterium tuberculosis reveals novel AT-hook deletion mutations.

    Davies-Bolorunduro, Olabisi Flora / Jaemsai, Bharkbhoom / Ruangchai, Wuthiwat / Phumiphanjarphak, Worakorn / Aiewsakun, Pakorn / Palittapongarnpim, Prasit

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 13324

    Abstract: Mutations in whiB7 have been associated with both hypersusceptibility and resistance to various antibiotics in Mycobacterium tuberculosis (Mtb). Unlocking the secrets of antibiotic resistance in the bacterium, we examined mutations in the coding ... ...

    Abstract Mutations in whiB7 have been associated with both hypersusceptibility and resistance to various antibiotics in Mycobacterium tuberculosis (Mtb). Unlocking the secrets of antibiotic resistance in the bacterium, we examined mutations in the coding sequences of whiB7 of over 40,000 diverse Mtb isolates. Our results unveil the dominant c.191delG (Gly64delG) mutation, present in all members of the lineage L1.2.2 and its impact on WhiB7's conserved GVWGG-motif, causing conformational changes and deletion of the C-terminal AT-hook. Excitingly, we discovered six unique mutations associated with partial or total deletion of the AT-hook, specific to certain sublineages. Our findings suggest the selective pressures driving these mutations, underlining the potential of genomics to advance our understanding of Mtb's antibiotic resistance. As tuberculosis remains a global health threat, our study offers valuable insights into the diverse nature and functional consequences of whiB7 mutations, paving the way for the development of novel therapeutic interventions.
    MeSH term(s) Mycobacterium tuberculosis/genetics ; AT-Hook Motifs ; Anti-Bacterial Agents ; Exons ; Sequence Deletion
    Chemical Substances Anti-Bacterial Agents
    Language English
    Publishing date 2023-08-16
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-023-40152-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Spatiotemporal evolution of SARS-CoV-2 in the Bangkok metropolitan region, Thailand, 2020-2022: implications for future outbreak preparedness.

    Aiewsakun, Pakorn / Jamsai, Bharkbhoom / Phumiphanjarphak, Worakorn / Sawaengdee, Waritta / Palittapongarnpim, Prasit / Mahasirimongkol, Surakameth

    Microbial genomics

    2023  Volume 9, Issue 12

    Abstract: Thailand experienced five waves of coronavirus disease 2019 (COVID-19) between 2020 and 2022, with the Bangkok Metropolitan Region (BMR) being at the centre of all outbreaks. The molecular evolution of the causative agent of the disease, severe acute ... ...

    Abstract Thailand experienced five waves of coronavirus disease 2019 (COVID-19) between 2020 and 2022, with the Bangkok Metropolitan Region (BMR) being at the centre of all outbreaks. The molecular evolution of the causative agent of the disease, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has previously been characterized in Thailand, but a detailed spatiotemporal analysis is still lacking. In this study, we comprehensively reviewed the development and timelines of the five COVID-19 outbreaks in Thailand and the public health responses, and also conducted a phylogenetic analysis of 27 913 SARS-CoV-2 genomes from Thailand, together with 7330 global references, to investigate the virus's spatiotemporal evolution during 2020 and 2022, with a particular focus on the BMR. Limited cross-border transmission was observed during the first four waves in 2020 and 2021, but was common in 2022, aligning well with the timeline of change in the international travel restrictions. Within the country, viruses were mostly restricted to the BMR during the first two waves in 2020, but subsequent waves in 2021 and 2022 saw extensive nationwide transmission of the virus, consistent with the timeline of relaxation of disease control measures employed within the country. Our results also suggest frequent epidemiological connections between Thailand and neighbouring countries during 2020 and 2021 despite relatively stringent international travel controls. The overall sequencing rate of the viruses circulating in the BMR was ~0.525 %, meeting the recommended benchmark, and our analysis supports that this is sufficient for tracking of the trend of the virus burden and genetic diversity. Our findings reveal insights into the local transmission dynamics of SARS-CoV-2 in Thailand, and provide a valuable reference for planning responses to future outbreaks.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/epidemiology ; Phylogeny ; Thailand/epidemiology ; Disease Outbreaks
    Language English
    Publishing date 2023-12-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.001170
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Reply to 'Evolutionary stasis of viruses?'

    Simmonds, Peter / Aiewsakun, Pakorn / Katzourakis, Aris

    Nature reviews. Microbiology

    2019  Volume 17, Issue 5, Page(s) 329–330

    MeSH term(s) Adaptation, Physiological ; Biological Evolution ; Viruses
    Language English
    Publishing date 2019-03-20
    Publishing country England
    Document type Letter ; Comment
    ZDB-ID 2139054-X
    ISSN 1740-1534 ; 1740-1526
    ISSN (online) 1740-1534
    ISSN 1740-1526
    DOI 10.1038/s41579-019-0169-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  7. Article ; Online: Early origin and global colonisation of foot-and-mouth disease virus.

    Aiewsakun, Pakorn / Pamornchainavakul, Nakarin / Inchaisri, Chaidate

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 15268

    Abstract: In this study, we compiled 84-year worth (1934-2017) of genomic and epidemiological data of foot-and-mouth disease virus (FMDV), and performed comprehensive analyses to determine its early origin and transmission route. We found that recombination is a ... ...

    Abstract In this study, we compiled 84-year worth (1934-2017) of genomic and epidemiological data of foot-and-mouth disease virus (FMDV), and performed comprehensive analyses to determine its early origin and transmission route. We found that recombination is a key feature of FMDV, and that the genomic regions coding for structural and non-structural proteins have markedly different evolutionary histories, and evolve at different rates. Despite all of these differences, analyses of both structural and non-structural protein coding regions consistently suggested that the most recent common ancestor of FMDV could be dated back to the Middle Age, ~ 200 to 300 years earlier than previously thought. The ancestors of the Euro-Asiatic and SAT strains could be dated back to the mid-seventeenth century, and to the mid-fifteenth to mid-sixteenth century, respectively. Our results implicated Mediterranean counties as an early geographical origin of FMDV before spreading to Europe and subsequently to Asia and South America.
    MeSH term(s) Animals ; Asia ; Europe ; Evolution, Molecular ; Foot-and-Mouth Disease/virology ; Foot-and-Mouth Disease Virus/genetics ; Genomics ; Molecular Epidemiology/methods ; Open Reading Frames/genetics ; Phylogeny ; South America ; Viral Nonstructural Proteins/genetics
    Chemical Substances Viral Nonstructural Proteins
    Language English
    Publishing date 2020-09-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-72246-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: SARS-CoV-2 genetic variations associated with COVID-19 pathogenicity.

    Aiewsakun, Pakorn / Nilplub, Patrawee / Wongtrakoongate, Patompon / Hongeng, Suradej / Thitithanyanont, Arunee

    Microbial genomics

    2021  Volume 7, Issue 12

    Abstract: In this study, we performed genome-wide association analyses on SARS-CoV-2 genomes to identify genetic mutations associated with pre-symptomatic/asymptomatic COVID-19 cases. Various potential covariates and confounding factors of COVID-19 severity, ... ...

    Abstract In this study, we performed genome-wide association analyses on SARS-CoV-2 genomes to identify genetic mutations associated with pre-symptomatic/asymptomatic COVID-19 cases. Various potential covariates and confounding factors of COVID-19 severity, including patient age, gender and country, as well as virus phylogenetic relatedness were adjusted for. In total, 3021 full-length genomes of SARS-CoV-2 generated from original clinical samples and whose patient status could be determined conclusively as either 'pre-symptomatic/asymptomatic' or 'symptomatic' were retrieved from the GISAID database. We found that the mutation 11 083G>T, located in the coding region of non-structural protein 6, is significantly associated with asymptomatic COVID-19. Patient age is positively correlated with symptomatic infection, while gender is not significantly correlated with the development of the disease. We also found that the effects of the mutation, patient age and gender do not vary significantly among countries, although each country appears to have varying baseline chances of COVID-19 symptom development.
    MeSH term(s) COVID-19/pathology ; COVID-19/virology ; Databases, Genetic ; Female ; Genetic Variation/genetics ; Humans ; Male ; Odds Ratio ; Open Reading Frames/genetics ; Phylogeny ; Risk Factors ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Severity of Illness Index
    Language English
    Publishing date 2021-12-06
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2835258-0
    ISSN 2057-5858 ; 2057-5858
    ISSN (online) 2057-5858
    ISSN 2057-5858
    DOI 10.1099/mgen.0.000734
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification.

    Aiewsakun, Pakorn / Simmonds, Peter

    Microbiome

    2018  Volume 6, Issue 1, Page(s) 38

    Abstract: Background: The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments ...

    Abstract Background: The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families, genera and species and provides a regulated system for their nomenclature that is universally used in virus descriptions. Virus taxonomic assignments have traditionally been based upon virus phenotypic properties such as host range, virion morphology and replication mechanisms, particularly at family level. However, gene sequence comparisons provide a clearer guide to their evolutionary relationships and provide the only information that may guide the incorporation of viruses detected in environmental (metagenomic) studies that lack any phenotypic data.
    Results: The current study sought to determine whether the existing virus taxonomy could be reproduced by examination of genetic relationships through the extraction of protein-coding gene signatures and genome organisational features. We found large-scale consistency between genetic relationships and taxonomic assignments for viruses of all genome configurations and genome sizes. The analysis pipeline that we have called 'Genome Relationships Applied to Virus Taxonomy' (GRAViTy) was highly effective at reproducing the current assignments of viruses at family level as well as inter-family groupings into orders. Its ability to correctly differentiate assigned viruses from unassigned viruses, and classify them into the correct taxonomic group, was evaluated by threefold cross-validation technique. This predicted family membership of eukaryotic viruses with close to 100% accuracy and specificity potentially enabling the algorithm to predict assignments for the vast corpus of metagenomic sequences consistently with ICTV taxonomy rules. In an evaluation run of GRAViTy, over one half (460/921) of (near)-complete genome sequences from several large published metagenomic eukaryotic virus datasets were assigned to 127 novel family-level groupings. If corroborated by other analysis methods, these would potentially more than double the number of eukaryotic virus families in the ICTV taxonomy.
    Conclusions: A rapid and objective means to explore metagenomic viral diversity and make informed recommendations for their assignments at each taxonomic layer is essential. GRAViTy provides one means to make rule-based assignments at family and order levels in a manner that preserves the integrity and underlying organisational principles of the current ICTV taxonomy framework. Such methods are increasingly required as the vast virosphere is explored.
    MeSH term(s) Eukaryota/virology ; Evolution, Molecular ; Genome, Viral/genetics ; Host Specificity/genetics ; Metagenomics ; Viruses/classification ; Viruses/genetics
    Language English
    Publishing date 2018-02-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2697425-3
    ISSN 2049-2618 ; 2049-2618
    ISSN (online) 2049-2618
    ISSN 2049-2618
    DOI 10.1186/s40168-018-0422-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Virus classification - where do you draw the line?

    Simmonds, Peter / Aiewsakun, Pakorn

    Archives of virology

    2018  Volume 163, Issue 8, Page(s) 2037–2046

    Abstract: High-throughput sequencing (HTS) and its use in recovering and assembling novel virus sequences from environmental, human clinical, veterinary and plant samples has unearthed a vast new catalogue of viruses. Their classification, known by their sequences ...

    Abstract High-throughput sequencing (HTS) and its use in recovering and assembling novel virus sequences from environmental, human clinical, veterinary and plant samples has unearthed a vast new catalogue of viruses. Their classification, known by their sequences alone, sets a major challenge to traditional virus taxonomy, especially at the family and species levels, which have been historically based largely on descriptive taxon definitions. These typically entail some knowledge of their phenotypic properties, including replication strategies, virion structure and clinical and epidemiological features, such as host range, geographical distribution and disease outcomes. Little to no information on these attributes is available, however, for viruses identified in metagenomic datasets. If such viruses are to be included in virus taxonomy, their assignments will have to be guided largely or entirely by metrics of genetic relatedness. The immediate problem here is that the International Committee on Taxonomy of Viruses (ICTV), an organisation that authorises the taxonomic classification of viruses, provides little or no guidance on how similar or how divergent viruses must be in order to be considered members of new species or new families. We have recently developed a method for scoring genomic (dis)similarity between viruses (Genome Relationships Applied to Virus Taxonomy - GRAViTy) among the eukaryotic and prokaryotic viruses currently classified by the ICTV. At the family and genus levels, we found large-scale consistency between genetic relationships and their taxonomic assignments for eukaryotic viruses of all genome configurations and genome sizes. Family assignments of prokaryotic viruses have, however, been made at a quite different genetic level, and groupings currently classified as sub-families are a much better match to the eukaryotic virus family level. These findings support the ongoing reorganisation of bacteriophage taxonomy by the ICTV Phage Study Group. A rapid and objective means to explore metagenomic viral diversity and make evidence-based assignments for such viruses at each taxonomic layer is essential. Analysis of sequences by GRAViTy provides evidence that family (and genus) assignments of currently classified viruses are largely underpinned by genomic relatedness, and these features could serve as a guide towards an evidence-based classification of metagenomic viruses in the future.
    MeSH term(s) Animals ; Bacteriophages/classification ; Bacteriophages/genetics ; Bacteriophages/isolation & purification ; Genome, Viral ; Humans ; Phylogeny ; Virus Diseases/virology ; Viruses/classification ; Viruses/genetics ; Viruses/isolation & purification
    Language English
    Publishing date 2018-07-24
    Publishing country Austria
    Document type Journal Article ; Review
    ZDB-ID 7491-3
    ISSN 1432-8798 ; 0304-8608
    ISSN (online) 1432-8798
    ISSN 0304-8608
    DOI 10.1007/s00705-018-3938-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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