Modeling neutral viral mutations in the spread of SARS-CoV-2 epidemics
ARTIGO
Inglês
Agradecimentos: This work was supported by the Sao Paulo Research Foundation (FAPESP - https://fapesp.br/), grants 2019/13341-7 (VMM), 2019/20271-5 and 2016/01343-7 (MAMA), and by Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq - https://www.gov.br/cnpq/ptbr), grant 301082/2019-7...
Agradecimentos: This work was supported by the Sao Paulo Research Foundation (FAPESP - https://fapesp.br/), grants 2019/13341-7 (VMM), 2019/20271-5 and 2016/01343-7 (MAMA), and by Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq - https://www.gov.br/cnpq/ptbr), grant 301082/2019-7 (MAMA). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We are greatful to Dr. Débora Princepe, Dr. Flávia D. Marquitti and Luis F.P.P.F. Salles for critical readings and suggestions. We also thank the anonymous reviewers for the many valuable comments and suggestions
Abstract: Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an individual-based model for epidemic spreading on networks...
Abstract: Although traditional models of epidemic spreading focus on the number of infected, susceptible and recovered individuals, a lot of attention has been devoted to integrate epidemic models with population genetics. Here we develop an individual-based model for epidemic spreading on networks in which viruses are explicitly represented by finite chains of nucleotides that can mutate inside the host. Under the hypothesis of neutral evolution we compute analytically the average pairwise genetic distance between all infecting viruses over time. We also derive a mean-field version of this equation that can be added directly to compartmental models such as SIR or SEIR to estimate the genetic evolution. We compare our results with the inferred genetic evolution of SARS-CoV-2 at the beginning of the epidemic in China and found good agreement with the analytical solution of our model. Finally, using genetic distance as a proxy for different strains, we use numerical simulations to show that the lower the connectivity between communities, e.g., cities, the higher the probability of reinfection
FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP
2016/01343-7; 2019/13341-7; 2019/20271-5
CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQ
301082/2019-7
Aberto
Modeling neutral viral mutations in the spread of SARS-CoV-2 epidemics
Modeling neutral viral mutations in the spread of SARS-CoV-2 epidemics
Fontes
PLos one Vol. 16, n. 7 (July, 2021), n. art. e0255438, p. 1-18 |