Genomic epidemiology of SARS-CoV-2 variants during the first two years of the pandemic in Colombia.

BACKGROUND: The emergence of highly transmissible SARS-CoV-2 variants has led to surges in cases and the need for global genomic surveillance. While some variants rapidly spread worldwide, other variants only persist nationally. There is a need for more fine-scale analysis to understand transmission dynamics at a country scale. For instance, the Mu variant of interest, also known as lineage B.1.621, was first detected in Colombia and was responsible for a large local wave but only a few sporadic cases elsewhere. METHODS: To better understand the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia. We performed Bayesian phylodynamic analyses to estimate the time of variants' introduction, their respective effective reproductive number, and effective population size, and the impact of disease control measures. RESULTS: Here, we detect a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the pandemic's start. We show that the effective reproduction number oscillated drastically throughout the first two years of the pandemic, with Mu showing the highest transmissibility (Re and growth rate estimation). CONCLUSIONS: Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions toward the emergence and circulation of novel SARS-CoV-2 variants.

Colombia reported its first COVID-19 case on 6th March 2020. By April 2022, the country had reported over 6 million infections and over 135,000 deaths. Here, we aim to understand how SARS-CoV-2, the virus that causes COVID-19, spread through Colombia over this time and how the predominant version of the virus (variant) changed over time. We found that there were multiple introductions of different variants from other countries into Colombia during the first two years of the pandemic. The Gamma variant was dominant earlier in 2021 but was replaced by the Delta variant. The Mu variant had the highest potential to be transmitted. Our findings provide valuable insights into the pandemic in Colombia and highlight the importance of continued surveillance of the virus to guide the public health response.

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. However, an adequate analysis of the dynamics of the variants of concern and interest (VOCIs) is missing. We investigated the dynamics of the COVID-19 pandemic in Peru with a focus on the second wave, which had the greatest case fatality rate. The second wave in Peru was dominated by Lambda and Gamma. Analysis of the origin of Lambda shows that it most likely emerged in Peru before the second wave (June-November, 2020). After its emergence it reached Argentina and Chile from Peru where it was locally transmitted. During the second wave in Peru, we identify the coexistence of two Lambda and three Gamma sublineages. Lambda sublineages emerged in the center of Peru whereas the Gamma sublineages more likely originated in the north-east and mid-east. Importantly, it is observed that the center of Peru played a prominent role in transmitting SARS-CoV-2 to other regions within Peru.

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. This is achieved by constraining a set of gene trees within a species tree and jointly inferring both under a Bayesian framework. However, this approach comes at the cost of increased computational demand. Here, we introduce StarBeast3-a software package for efficient Bayesian inference under the MSC model via Markov chain Monte Carlo. We gain efficiency by introducing cutting-edge proposal kernels and adaptive operators, and StarBeast3 is particularly efficient when a relaxed clock model is applied. Furthermore, gene-tree inference is parallelized, allowing the software to scale with the size of the problem. We validated our software and benchmarked its performance using three real and two synthetic data sets. Our results indicate that StarBeast3 is up to one-and-a-half orders of magnitude faster than StarBeast2, and therefore more than two orders faster than *BEAST, depending on the data set and on the parameter, and can achieve convergence on large data sets with hundreds of genes. StarBeast3 is open-source and is easy to set up with a friendly graphical user interface. [Adaptive; Bayesian inference; BEAST 2; effective population sizes; high performance; multispecies coalescent; parallelization; phylogenetics.].

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. We compared these results to transmission clusters identified by the New Zealand Ministry of Health by contact tracing strategies. We estimated the effective reproduction number of COVID-19 as 1-1.4 during early stages of the pandemic and show that it declined below 1 as human movement was restricted. We also showed that this disease was introduced many times into each country and that introductions slowed down markedly following the reduction of international travel in mid-March 2020. Finally, we confirmed that New Zealand transmission clusters identified via standard health surveillance strategies largely agree with those defined by genomic data. We have demonstrated how the use of genomic data and computational biology methods can assist health officials in characterising the epidemiology of viral epidemics and for contact tracing.

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. Full envelope (E) gene sequences were employed to examine the genetic diversity of serotypes circulating by using a phylogenetic approach. RESULTS: All four dengue virus serotypes were detected. DENV-1 was the dominant serotype in both periods followed by DENV-3 or DENV-2 depending on the period; DENV-4 was the least prevalent virus in both periods. Cross-correlation analyses suggest a temporal relation between the fluctuations in the prevalence of DENV serotypes, which were almost simultaneous (lag = 0) or related to recent past fluctuations (lag > 1.0) in the number of dengue cases. Data suggest that a sustained predominance of DENV-1, an increase of the DENV-4 prevalence, and a switch from DENV-3 to DENV-2 could be linked to an outbreak. Circulating viruses were grouped into Genotype V, Asia/American III and II for DENV-1, -2, -3 and -4, respectively; intragenotypic diversity was detected. CONCLUSIONS: The present work highlights the need of comprehensive studies on dynamics of DENV in Colombia to understand transmission of dengue and evaluate the effectiveness of a vaccination programme.

OBJECTIF: Etudier le lien entre les fluctuations de la prévalence des sérotypes du virus de la dengue (DENV) et le nombre de cas de dengue dans la région métropolitaine de Bucaramanga, dans l'Etat de Santander, en Colombie, au cours des périodes 2007-2010 et 2014-2017. MÉTHODE: Les virus ont été isolés à partir d'échantillons de patients fébriles par application directe sur des cellules C6/36-HT et typés à l'aide d'anticorps monoclonaux. Nous avons effectué des analyses d'autocorrélation et de corrélation croisée afin de déterminer si les fluctuations de la prévalence des sérotypes du DENV et des cas de dengue étaient corrélées. Des séquences de gènes d'enveloppe complète (E) ont été utilisées pour examiner la diversité génétique des sérotypes en circulation en utilisant une approche phylogénétique. RÉSULTATS: Tous les quatre sérotypes du virus de la dengue ont été détectés. DENV-1 était le sérotype dominant dans les deux périodes, suivi de DENV-3 ou DENV-2, selon la période; le virus DENV-4 était le moins prévalent au cours des deux périodes. Les analyses de corrélation croisée suggèrent une relation temporelle entre les fluctuations de la prévalence des sérotypes de DENV, qui étaient presque simultanées (lag = 0) ou liées aux fluctuations passées récentes (lag > 1,0) du nombre de cas de dengue. Les données suggèrent qu'une prédominance durable de DENV-1, qu'une augmentation de la prévalence de DENV-4 et qu'un passage de DENV-3 à DENV-2 pourraient être liés à une éclosion. Les virus en circulation ont été regroupés dans les génotypes V, Asie/Amérique III et II pour DENV-1, -2, -3 et -4, respectivement; une diversité intra-génotypique a été détectée. CONCLUSIONS: Le présent travail souligne la nécessité d'études approfondies sur la dynamique du DENV en Colombie afin de comprendre la transmission de la dengue et évaluer l'efficacité d'un programme de vaccination.

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. To provide a better understanding of the epidemiology of dengue, we inferred DENV population dynamics using samples collected between 1998 and 2015. We used Bayesian phylogenetic analysis and included 143 new envelope gene sequences from Colombia, mainly from the region of Santander, and 235 published sequences from representative countries in the Americas. We documented one single genotype for each serotype but multiple introductions. Whereas the majority of DENV-1, DENV-2, and DENV-4 strains fell into one single lineage, DENV-3 strains fell into two distinct lineages that co-circulated. The inferred times to the most recent common ancestors for the most recent clades of DENV-1, DENV-2, and DENV-4 fell between 1977 and 1987, and for DENV-3 was around 1995. Demographic reconstructions suggested a gradual increase in viral diversity over time. A phylogeographical analysis underscored that Colombia mainly receives viral lineages and a significant diffusion route between Colombia and Venezuela. Our findings contribute to a better understanding of the viral diversity and dengue epidemiology in Colombia.