The evolution of retroviruses

Saakshi Bangera, DY Patil School of Biotechnology and Bioinformatics

The predecessors of modern cetaceans – whales and dolphins, went through an evolutionary transition from terrestrial to aquatic settings more than 50 million years ago. During this transition, cetaceans developed morphological as well as behavioural innovations. Streamlined bodies, echolocation, filter-feeding, and loss of body hair, dermal glands, and hindlimbs are some of the changes that cetaceans underwent. 

Viruses such as adenovirus, astroviruses, coronaviruses, enteroviruses, and herpesviruses have been known to infect cetaceans. How these viruses originated in cetaceans is largely unclear. 

Among viruses, one of the most notable ones is Endogenous retroviruses. Endogenous retroviruses (ERVs) are grouped into three classes, namely Class 1, Class 2, and Class 3. This classification is based on the relationship of ERVs with endogenous retroviruses. ERVs thrive within the host’s genomes through three modes: 

• ERVs in somatic cells produce viral particles to infect somatic cells – reinfection
• Within the cell, they can increase in copy number either by retrotransposition in cis or by complementation in trans ERVs lacking functional env genes (required for reinfection) can infect germline cells by “hitchhiking” env genes of other retroviruses

Reinfection requires three core genes, namely gag, pol, and env. 

This study uses a phylogenomic approach to determine the origin and trace the evolution of ERVs along with the evolution of cetaceans. A total of 8,724 ERVs were identified in 25 genomes of cetaceans. These genes cluster into 315 ERV lineages. This study hypothesizes that cetacean ERVs must have originated from two possible routes, either through land-to-water transition or secondary host switching

Results

1.1 Identification and classification of ERVs in cetaceans

A combined approach of similarity and search and phylogenetic analysis was implemented to explore the evolution of retroviruses in cetaceans. The genomes of 25 cetaceans, including 19 odontocetes and 6 mysticetes were screened. ERVs were found to be present in all cetaceans. A total of 8,724 ERVS were identified. A large-scale phylogenetic analysis of ERVs in cetaceans was also conducted to identify the distinct ERV lineages in cetaceans. The identified ERVs were classified into 315 distinct lineages. It was also found that each lineage represents one or more independent events of invasion. 

1.2 Retrovirus evolution in cetaceans

The two possible scenarios of the origination of retroviruses were studied. 

• In the land-to-water (LTW) scenario, the retrovirus:

1. 1 infected the cetacean ancestor during or before cetacean’s conquest of the aquatic environment
2. Incorporated into its genome 
3. Moved into the water with ancient hosts
4. In this scenario, remnants of ERV should be identified in the genomes of almost all modern cetaceans.

• In the secondary host switching (SHS) scenario, retroviruses:

1. 1 Infected the cetaceans through cross-species transmission after the conquest of the marine environment
2. Became incorporated into the host genome

In this scenario, ERV can be identified only in a sub-lineage of cetaceans and might thrive to a high copy number.

1.3 Retrovirus’ origin through the land-to-water transition

Uniform with the land-to-water scenario, 298 out of 315 lineages was distributed in both odontocetes and mysticetes. This implies that the last common ancestor of modern cetaceans had these ERV lineages. To understand the origin and evolution of distinct ERV lineages, phylogenetic analysis of cetacean ERVs and ERVs that are closely related within the vertebrate genomes of each ERV lineage. It was elucidated that the retrovirus endogenization events had taken place before the last common ancestor of hippopotamuses and cetaceans. 

1.4 Retrovirus’ origin through secondary host switching

17 out of 315 cetacean lineages were found to be distributed in the genomes within a sub-lineage of cetaceans. 

Conclusion

In the study, the evolutionary histories of ERVs in the cetaceans were explored. A total of 315 ERV lineages suggest that diverse retroviruses infected early cetaceans. Two major routes of the evolution of cetacean retroviruses were also discussed. Several DNA viruses, as well as RNA viruses, have been infecting cetaceans. Due to the under-sampling of retroviruses in cetaceans, it is difficult to explicate how these viruses originated in cetaceans. The study holds special significance since it provides unique insights into the evolution of retroviruses during the macroevolutionary shift of cetaceans.

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Source: Zheng, J., Wang, J., Gong, Z., & Han, G.-Z. (2021). Molecular fossils illuminate the evolution of retroviruses following a macroevolutionary transition from land to water. PLOS Pathogens, 17(7), e1009730. https://doi.org/10.1371/journal.ppat.1009730

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About the author: Saakshi is currently pursuing MSc in Biotechnology from DY Patil School of Biotechnology and Bioinformatics. She believes that she doesn’t have a specific area of interest yet. She wishes to explore toxicology and food biotechnology. She’s quite passionate about Biotechnology and aims to grab every opportunity she comes across.