Phylodynamic of SARS-CoV-2 during the second wave of COVID-19 in Peru.

At over 0.6% of the population, Peru has one of the highest SARS-CoV-2 mortality rate in the world. Much effort to sequence genomes has been done in this country since mid-2020.

StarBeast3: Adaptive Parallelized Bayesian Inference under the Multispecies Coalescent.

As genomic sequence data become increasingly available, inferring the phylogeny of the species as that of concatenated genomic data can be enticing. However, this approach makes for a biased estimator of branch lengths and substitution rates and an inconsistent estimator of tree topology. Bayesian multispecies coalescent (MSC) methods address these issues.

Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations.

New Zealand, Australia, Iceland, and Taiwan all saw success in controlling their first waves of Coronavirus Disease 2019 (COVID-19). As islands, they make excellent case studies for exploring the effects of international travel and human movement on the spread of COVID-19. We employed a range of robust phylodynamic methods and genome subsampling strategies to infer the epidemiological history of Severe acute respiratory syndrome coronavirus 2 in these four countries.

Dengue in Santander State, Colombia: fluctuations in the prevalence of virus serotypes are linked to dengue incidence and genetic diversity of the circulating viruses.

Objective: To investigate the link between fluctuations in the prevalence of dengue virus (DENV) serotypes and the number of dengue cases in the metropolitan area of Bucaramanga, Santander State, Colombia, in the 2007-2010 and 2014-2017 periods.

Method: Viruses were isolated from febrile patient samples by direct application to C6/36-HT cells and typed using monoclonal antibodies. We performed autocorrelation and cross-correlation analyses to determine whether fluctuations in the prevalence of DENV serotypes and dengue cases were correlated.

Evolutionary history and spatio-temporal dynamics of dengue virus serotypes in an endemic region of Colombia.

Dengue is a prevalent disease in Colombia and all dengue virus serotypes (DENV-1 to -4) co-circulate in the country since 2001. However, the relative impact of gene flow and local diversification on epidemic dynamics is unknown due to heterogeneous sampling and lack of sufficient genetic data. The region of Santander is one of the areas with the highest incidence of dengue in Colombia.