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Human Health & Evolution - Coggle Diagram
Human Health & Evolution
Introduction
Viruses are extremely abundant and genetically diverse
They possess different replication strategies and genome organisations
SARS-CoV-2 highlighted the importance of understanding viral evolution
RNA viruses are able to evolve within a very short time
This can be exploited by humans
Allows for better understanding of previous evolutionary events
Predict the occurrence of viral evolution
Predict, vaccine escape, drug resistance and virulence evolution
Evolution is complex
Many conclusions obtained about evolution in one context is not applicable in another setting.
There are 3 main challenges
Predictability, consistency and comprehensiveness
Summary
The problem
Viral diversity & evolution
Vital in disease emergence, vaccine failure and drug resistances
5 challenges in combatting viral diversity
Predicting viral evolution
developing relevant evolutionary systems
integrating viral dynamics and evolution at different scales
systematic appraisal of the virosphere
deepening our understanding of virus-virus interactions
Intensify research in these areas to best combat viral diseases.
Exploit newfound knowledge of viral diversity in new biotechnology
Anticipating viral evolution
Problems
The ability to predict new variants is limited
Will require additional tools for further improvement
Experimental evaluation of mutational pathways
RNA viruses useful due to simple genomes, susceptible to manipulation, rapid mutations
Animal to human transmission is the largest source of new viral strains
It is difficult to predict when a virus will mutate cross-species transmission.
Risk factors have been identified
Advancements
There are constant vaccine updates for the anticipated dominant influenza virus strain of the following year
High-throughput sequencing allows for real time predictions during epidemics
Useful in Ebola, Zika and Covid epidemics
Linking epidemiology with sequence data has allowed for tracking of new variants
Developing evolution systems
Lab experiments can provide information on the repeatability and predictability of viral evolution. However, there are issues
Strong directional selection in lab can create parallel evolution at sequence level
Can be used to identify candidate adaptive mutations
Simple cell cultures in lab may not be indicative of what is happening in nature
Tumoral cells are usually used,
Non-tumoral cells are more suitable
Must combine lab virus evolution with sequencing
Has allowed for categorization of mutational fitness effects in detail.
The effect of every possible mutation can now be predicted.
Integrating viral dynamics and evolution at different scales
Major issue
Phylogenetic inferences on viral evolution rates are dependent on timescales
Rates caused by seasonal outbreaks have higher rates than seen in longer periods
Few studies link evolutionary processes at multiple levels
Intra-host
Inter-host
Community levels
Challenging to measure and define fitness at these levels
Different traits confer different effects on fitness depending on the level; even though, it is the same organism.
Characterizing and understanding the virosphere
Less than 1% of viruses have been discovered
90% of known viruses are phylogenetic dark matter as they lead to no known biological entities
New tools that do not rely on nucleic acid sequencing are needed
Could use artificial neural netwroks
Address how different groups evolved from one another .
How phylogenetic trees map to different organisms and hosts
Would result in a better understanding of viral-cross-species transmission
Improving our understanding of virus-virus interactions
The interactions between viruses, other virus and other microorganisms presents a unique problem
Viruses of the same species can cooperate
Example: Emergence of high multiplicities of infection
Viruses can undergo inter-host transmission or intra-host dissemination which causes aggregation of virions and promotion of coinfections
Horizontal gene transfer in viruses promote coinfections
Difficult to combat because most viral taxa do not have closely related genomes
Indirect interactions
One virus could modify the immune system of the host
Direct interactions
Satellite viruses
Conclusion
The challenges presented in the paper are interconnected
Improving system of experimental evolution should improve predictions and viral evolution in nature and better categorizing the virosphere
Citation
Sanjuán R, Illingworth CJR, Geoghegan JL, Iranzo J, Zwart MP, Ciota AT, Moratorio G, Gago-Zachert S, Duffy S, Vijaykrishna D. 2021. Five Challenges in the Field of Viral Diversity and Evolution. FrontVirol. 1:684949. doi:10.3389/fviro.2021.684949.