Detection of Ancient Viruses and Long-Term Viral Evolution

Abstract

The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.

Keywords: NGS; PCR; TDRP; ancient DNA; ancient RNA; ancient virome; ancient virus; bioinformatics; viral evolution.

Figure 1

History of ancient viral studies. Yellow and pink dots indicate studies or events related to polymerase chain reaction (PCR) and next-generation sequencing (NGS) techniques, respectively.

Figure 2

Overview of the experiments and bioinformatic analyses of ancient viral genomes. Ancient DNA can be extracted from historical specimens such as bones and teeth. The extracted DNA is derived from human, microbial, and viral genomes. Those mixed sequences can be determined by Sanger sequencing, whole genome sequencing (WGS), or capture-based sequencing based on next-generation sequencing (NGS) platforms. WGS can sequence untargeted DNA from humans, microbes, and viruses, and capture-based methods use biotinylated specific bait libraries and magnetic beads to enrich the target sequences. Following the preprocessing steps, contigs can be constructed by de novo assembly. Then, those contigs and preprocessed reads can be utilized for sequence binning to cluster the sequences into individual groups and obtain ancient viral sequences. Simultaneously, all contigs, preprocessed reads, and polymerase chain reaction (PCR) amplicons can be aligned to known viral sequences to detect candidate ancient viral sequences. Finally, the ancient viral sequences can be applied for downstream analyses: metagenomic profiling, the reconstruction of ancient viral genomes, DNA authenticity testing, and phylogenetic analyses.