Detection of Ancient Viruses and Long-Term Viral Evolution

Nishimura, Luca; Fujito, Naoko T.; Sugimoto, Ryota; Inoue, Ituro

doi:10.3390/v14061336

Cited by 9 publications

(8 citation statements)

References 205 publications

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“…Ancient DNAs have been discovered from various kinds of archeological samples such as bones and mummified tissues. Those ancient samples contain ancient viral genomes which existed in ancient organisms’ bodies [ 43 ]. Those ancient viral genomes are useful to elucidate past pandemic events and long-term viral evolution.…”

Section: Scientific Programmentioning

confidence: 99%

The International Virus Bioinformatics Meeting 2023

Hufsky,

Abecasis,

Babaian

et al. 2023

Viruses

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The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24–26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.

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Section: Scientific Programmentioning

confidence: 99%

The International Virus Bioinformatics Meeting 2023

Hufsky,

Abecasis,

Babaian

et al. 2023

Viruses

Self Cite

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“…Despite these difficulties, the number of discovered ancient viruses is constantly increasing (e.g. [60]). With the convenient setting of alignment parameters, the flexibility of our pipeline can potentially allow the reconstruction of ancient viral sequences.…”

Section: Plos Onementioning

confidence: 99%

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

et al. 2022

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The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the project’s GitHub page (https://github.com/laczkol/QVG).

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“…Previous research on ancient virology has mainly focused on the reference-based reconstruction of human pathogens 8 , retroviral elements incorporated in animal genomes 9 , or eukaryotic viruses that have remained dormant since prehistory 10 . However, knowledge about ancient bacteriophages is limited 11 . The first reports on ancient phages described viruses from 14th-century faecal material in Belgium 12 and the gut contents of pre-Columbian Andean mummies 13 .…”

Section: Introductionmentioning

confidence: 99%

Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

Rozwalak,

Barylski,

Wijesekara

et al. 2024

Nat Commun

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Bacteriophages are widely recognised as rapidly evolving biological entities. However, knowledge about ancient bacteriophages is limited. Here, we analyse DNA sequence datasets previously generated from ancient palaeofaeces and human gut-content samples, and identify an ancient phage genome nearly identical to present-day Mushuvirus mushu, a virus that infects gut commensal bacteria. The DNA damage patterns of the genome are consistent with its ancient origin and, despite 1300 years of evolution, the ancient Mushuvirus genome shares 97.7% nucleotide identity with its modern counterpart, indicating a long-term relationship between the prophage and its host. In addition, we reconstruct and authenticate 297 other phage genomes from the last 5300 years, including those belonging to unknown families. Our findings demonstrate the feasibility of reconstructing ancient phage genome sequences, thus expanding the known virosphere and offering insights into phage-bacteria interactions spanning several millennia.

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Detection of Ancient Viruses and Long-Term Viral Evolution

Cited by 9 publications

References 205 publications

The International Virus Bioinformatics Meeting 2023

The International Virus Bioinformatics Meeting 2023

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces

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