Oldest Known Human Viruses Discovered In 50,000-Year-Old Neanderthal Bones

It might add weight to the theory that viruses contributed to the extinction of the species.

Author HOLLY LARGE
Jr Copy Editor & Staff Writer

Edited by Maddy Chapman

Did viruses play a role in the extinction of Neanderthals? That’s what researchers from the Federal University of São Paulo have been trying to figure out, and in doing so, ended up uncovering the oldest known human viruses in a set of Neanderthal bones from over 50,000 years ago.

To make this finding, the team combed through the raw DNA sequencing data of two sets of Neanderthal remains recovered from Chagyrskaya cave in Russia. Within those raw sequences, they were looking for the remnants of the genomes – the entirety of an organism’s genetic information – of three types of DNA viruses: adenovirus, herpesvirus, and papillomavirus.

And they found them – remnants of all three groups, in fact. This makes the viruses the oldest human viruses ever discovered, taking the title away from those found in 31,600-year-old Homo sapiens remains.

This, the authors suggest in a preprint that’s yet to be peer-reviewed, demonstrated that not only was it feasible to identify bits of viral genomes in archaeological samples, but that Neanderthals could’ve been afflicted with the same viruses that affect humans today.

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[H/T: New Scientist]

Reconstructing prehistoric viral genomes from Neanderthal sequencing data

Renata C. Ferreira, Gustavo V. Alves, Marcello Ramon, Fernando Antoneli, Marcelo R. S. Briones

doi: https://doi.org/10.1101/2023.03.16.532919

This article is a preprint and has not been certified by peer review [what does this mean?].

Abstract

DNA viruses that produce persistent infections have been proposed as potential causes for the extinction of Neanderthals and therefore, the identification of viral genome remnants in Neanderthal sequencing reads is an initial step to address this hypothesis. Here, as proof of concept, we searched for viral remnants in sequencing reads of Neanderthal genome data by mapping to adenovirus, herpesvirus and papillomavirus, which are double stranded DNA viruses that may establish lifelong latency and can, produce persistent infections. The reconstructed ancient viral genomes of adenovirus, herpesvirus and papillomavirus revealed conserved segments, with nucleotide similarity to extant viral genomes, and variable regions in coding regions with substantial divergence to extant close relatives. Sequencing reads mapped to extant viral genomes showed deamination patterns of ancient DNA and that these ancient viral genomes showed divergence consistent with the age of these samples (≈50,000 years) and viral evolutionary rates (10−5 to 10−8 substitutions/site/year). Analysis of random effects shows that the Neanderthal mapping to genomes of extant persistent viruses is above the expected by random similarities of short reads. Also, negative control with a nonpersistent DNA virus does not yield statistically significant assemblies. This work demonstrates the feasibility of identifying viral genome remnants in archaeological samples with signal-to-noise assessment.

Competing Interest Statement

The authors have declared no competing interest.

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