| Full text | |
| Author(s): |
Total Authors: 3
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| Affiliation: | [1] Univ Sao Paulo, Biomed Sci Inst, Dept Microbiol, Lab Mol Evolut & Bioinformat, Sao Paulo - Brazil
[2] UFSCar Fed Univ Sao Carlos, Dept Genet & Evolut, Sao Carlos, SP - Brazil
Total Affiliations: 2
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| Document type: | Journal article |
| Source: | PLoS One; v. 13, n. 1 JAN 31 2018. |
| Web of Science Citations: | 4 |
| Abstract | |
Codon adaptation index (CAI) is a measure of synonymous codon usage biases given a usage reference. Through mutation, selection, and drift, viruses can optimize their replication efficiency and produce more offspring, which could increase the chance of secondary transmission. To evaluate how higher CAI towards the host has been associated with higher viral titers, we explored temporal trends of several historic and extensively sequenced zoonotic flaviviruses and relationships within the genus itself. To showcase evolutionary and epidemiological relationships associated with silent, adaptive synonymous changes of viruses, we used codon usage tables from human housekeeping and antiviral immune genes, as well as tables from arthropod vectors and vertebrate species involved in the flavivirus maintenance cycle. We argue that temporal trends of CAI changes could lead to a better understanding of zoonotic emergences, evolutionary dynamics, and host adaptation. CAI appears to help illustrate historically relevant trends of well-characterized viruses, in different viral species and genetic diversity within a single species. CAI can be a useful tool together with in vivo and in vitro kinetics, phylodynamics, and additional functional genomics studies to better understand species trafficking and viral emergence in a new host. (AU) | |
| FAPESP's process: | 13/22136-1 - Discovering novel viruses in communities encroaching tropical hotspots via a metagenomics approach |
| Grantee: | Nicholas Di Paola |
| Support Opportunities: | Scholarships in Brazil - Doctorate (Direct) |