An Adagio for Viruses, Played Out on Ancient DNA

Abstract

Studies of ancient DNA have transformed our understanding of human evolution. Palaeogenomics can also reveal historic and prehistoric agents of disease, including endemic, epidemic and pandemic pathogens. Viruses – and in particular those with single or double-stranded DNA genomes – are an important part of the palaeogenomic revolution, preserving within some remains or environmental samples for tens of thousands of years. The results of these studies capture the public imagination, as well as giving scientists a unique perspective on some of the more slowly-evolving viruses which cause disease. In this review, we will revisit the first studies of historical virus genetic material in the 1990s, through to the genomic revolution of recent years. We will look at how palaeogenomics works for viral pathogens, such as the need for careful precautions against modern contamination, and robust computational pipelines to identify and analyse authenticated viral sequences. We will discuss the insights into virus evolution which have been gained through palaeogenomics, concentrating on three DNA viruses in particular: parvovirus B19, herpes simplex virus 1, and smallpox. As we consider recent worldwide transmission of monkeypox and synthetic biology tools that allow the potential reconstruction of extinct viruses, we show that studying historical and ancient virus evolution has never been more topical.

Overview of reemerging mpox infection with a focus on neurological manifestations

“…2 Smallpox-associated encephalitis has a mortality rate of up to 25% after vaccination, with additional neurological complications like headache, seizures, cranial nerve palsy, Guillain-Barre syndrome, hemiplegia, and coma. 34 A confirmed diagnosis of mpox-associated encephalitis involves skin biopsy and encephalopathy examination. The presence of IgM in cerebrospinal fluid (CSF) signifies active central nervous system infection with intrathecal antibody production, serving as a laboratory diagnostic standard.…”

Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past

“…Over the past decade dental calculus, bone tissues, and dentine have been subject to aDNA analysis for identifying ancient protists, and bacterial and viral pathogens (de-Dios et al 2023 ; Enard and Petrov 2018 ; Greenbaum et al 2019 ; Guzmán-Solís et al 2021 ; Margaryan et al 2018 ). However, ancient pathogen DNA from environmental sources remains understudied but presents itself as an important domain for future innovation (Malyarchuk et al 2022 ).…”

Utilizing convolutional neural networks to classify monkeypox skin lesions

“…The clinical symptoms of monkeypox are similar to those of smallpox and can include fever, rash, and pustules. However, monkeypox is generally less severe than smallpox, with a lower mortality rate 3 .…”