The paradox of HBV evolution as revealed from a 16th century mummy.
Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously pale...
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doaj-01450f220a7542fbb9431c6f9f4a77182021-06-19T04:34:15ZengPublic Library of Science (PLoS)PLoS Pathogens1553-73661553-73742018-01-01141e100675010.1371/journal.ppat.1006750The paradox of HBV evolution as revealed from a 16th century mummy.Zoe Patterson RossJennifer KlunkGino FornaciariValentina GiuffraSebastian DuchêneAna T DugganDebi PoinarMark W DouglasJohn-Sebastian EdenEdward C HolmesHendrik N PoinarHepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D), at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen.https://doi.org/10.1371/journal.ppat.1006750 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Zoe Patterson Ross Jennifer Klunk Gino Fornaciari Valentina Giuffra Sebastian Duchêne Ana T Duggan Debi Poinar Mark W Douglas John-Sebastian Eden Edward C Holmes Hendrik N Poinar |
spellingShingle |
Zoe Patterson Ross Jennifer Klunk Gino Fornaciari Valentina Giuffra Sebastian Duchêne Ana T Duggan Debi Poinar Mark W Douglas John-Sebastian Eden Edward C Holmes Hendrik N Poinar The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathogens |
author_facet |
Zoe Patterson Ross Jennifer Klunk Gino Fornaciari Valentina Giuffra Sebastian Duchêne Ana T Duggan Debi Poinar Mark W Douglas John-Sebastian Eden Edward C Holmes Hendrik N Poinar |
author_sort |
Zoe Patterson Ross |
title |
The paradox of HBV evolution as revealed from a 16th century mummy. |
title_short |
The paradox of HBV evolution as revealed from a 16th century mummy. |
title_full |
The paradox of HBV evolution as revealed from a 16th century mummy. |
title_fullStr |
The paradox of HBV evolution as revealed from a 16th century mummy. |
title_full_unstemmed |
The paradox of HBV evolution as revealed from a 16th century mummy. |
title_sort |
paradox of hbv evolution as revealed from a 16th century mummy. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS Pathogens |
issn |
1553-7366 1553-7374 |
publishDate |
2018-01-01 |
description |
Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D), at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen. |
url |
https://doi.org/10.1371/journal.ppat.1006750 |
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