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Reconstructing Prehistoric Viral Genomes from Neanderthal Sequencing Data.

Renata C Ferreira1,2, Gustavo V Alves1, Marcello Ramon3

  • 1Center for Medical Bioinformatics, Escola Paulista de Medicina, Federal University of São Paulo (UNIFESP), São Paulo, SP 04039-032, Brazil.

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Summary
This summary is machine-generated.

Researchers identified ancient viral DNA fragments in Neanderthal genomes, supporting the hypothesis that persistent viruses may have contributed to their extinction. This study demonstrates a method for detecting viral remnants in ancient samples.

Keywords:
Neanderthal genomeadenovirusancient virusesgenome assemblyherpesviruspapillomavirussequence data

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Area of Science:

  • Paleovirology
  • Ancient DNA analysis
  • Neanderthal genomics

Background:

  • Persistent DNA viruses are hypothesized to have impacted Neanderthal populations.
  • Identifying viral remnants in ancient genomes is crucial for testing this hypothesis.

Purpose of the Study:

  • To demonstrate the feasibility of detecting viral genome remnants in Neanderthal DNA sequence data.
  • To investigate the presence of adenovirus, herpesvirus, and papillomavirus in Neanderthal samples.

Main Methods:

  • Mapping Neanderthal genome sequence reads to known persistent DNA virus genomes (adenovirus, herpesvirus, papillomavirus).
  • Analyzing sequence read characteristics, including deamination patterns indicative of ancient DNA.
  • Comparing reconstructed viral genome segments to extant relatives and assessing statistical significance against random similarity.

Main Results:

  • Conserved segments and divergent coding regions were identified in reconstructed ancient viral genomes.
  • Sequence reads exhibited ancient DNA deamination patterns.
  • Mapping results were statistically significant, exceeding random similarity expectations, and negative controls were non-significant.

Conclusions:

  • The study successfully demonstrates the feasibility of identifying viral genome remnants in archaeological samples.
  • The findings provide a methodological basis for investigating the role of persistent viruses in Neanderthal extinction.
  • The identified viral signatures are consistent with the age of Neanderthal samples and viral evolutionary rates.