Ricardo Rivero-H.

About me:

I am currently a research assistant and Master's student at Universidad de Córdoba - Colombia, where I am working in developing mathematical models that disentangle the mechanisms that drive arboviral co-transmission and co-infection in mosquitoes and Humans.
To do this, we are collecting mosquito samples from 5 states of the Colombian Caribbean and blood samples from humans with admitted to hospitals with febrile syndromes and using meta-transcriptomics to uncover RNA virus diversity and study the co-transmission potential from and to human hosts. My research goal is to combine genomics, epidemiology and ecology to construct precise mathematical models that can predict and prevent the pandemic potential of known and novel RNA viruses in aims to inform public health decision-making.

Bioinformatics + Genomic Epidemiology

I am interested in studying how climate change affects the Ecological, evolutionary and epidemiological dynamics of infectious diseases. To do this I use genomics data generated from infected hosts and vectors to understand the epidemiological links between cases using computational tools. This data can tell us a story of the pathogen's evolution through time, and we can model it's spread by using mathematical frameworks.

Virology

Since 2018, when I started my research career I quickly became fascinated by the world of viruses and its extense diversity. Tropical Viruses such as Dengue, Zika, Chikungunya, Hantavirus, among others, caused high-burden in my country and other tropical countries around the world. But it was when the COVID-19 pandemic hit that I started working in designing, developing an validating molecular and serological assays that would allow low-to-middle income countries to carry accurate and fast diagnostics for viral diseases.
As a part of my experience at Professor Mattar's lab, I developed RT-qPCR assays for the detection of Hantaviruses and SARS-CoV-2 as well as ELISA and LFA tests for detecting anti-Hantavirus IgG antibodies in humans and rodents. During the early stages of the pandemic, I voluntereed to carry out viral isolation for diagnostic of hospitalized patients in my region.
Nowadays, my research is coming back to it's Arboviral ways, with research interests on studying the effect of climate on the transmission and evolution of these viruses in aims to inform policies that shape an estrategy of public health preparedness.

Data Science

I am passionate about extracting and deciphering the stories that data has to tell us, and since first learning how to code basic statistical analyses in R programming has become an important part of my life, from Bash to Python, from R to Julia and now combining data analysis and model fitting in R with geospatial visualization in QGIS.
There is an ever-growing passion in me to extract insights from data and inform my colleagues, professors and public towards powerful decision-making. And may it be an ecological or microbiome dataset in all of it high dimensionality or a simple map of the incidence of an infectious agent. Data science has the power to enlighten the way we do science... And that is one of my missions. Please find my code on Github

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

Cinthy Jimenez-Silva, Ricardo Rivero, et al, 2022. Communications Medicine

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.
To provide a better understanding of the epidemiology of SARS-Cov-2 variants in Colombia, we used 14,049 complete SARS-CoV-2 genomes from the 32 states of Colombia, and 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.
We detected a total of 188 SARS-CoV-2 Pango lineages circulating in Colombia since the start of the pandemic. We showed 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).
Our results reinforce that genomic surveillance programs are essential for countries to make evidence-driven interventions towards the emergence and circulation of novel SARS-CoV-2 variants

Human-to-dog transmission of SARS-CoV-2, Colombia

Ricardo Rivero, Evelin Garay, Yesica Botero, et al, 2022. Scientific Reports

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of the current COVID-19 pandemic, has evolved to have a wide range of hosts, including non-human primates, wild and domestic animals. The ACE2 protein has a high level of conservation and is the common receptor in vertebrate species for a viral infection to occur; this receptor could give rise to anthroponotic events.
This article describes the first event of symptomatic transmission in Latin America from a human to a dog by the B.1.625 lineage of SARS-CoV-2. We found 21 shared mutations in the complete genomes of viral sequences from owners and dogs. Further phylogenetic and molecular analysis showed that 100% co-localization of the clade helps to understand human-animal transmission.
Prediction of the Spike protein structure of the sequenced virus and docking analyzes showed that the E484K mutation in the receptor-binding domain (RBD) could contribute to the viral affinity of dACE2. Therefore, close contact between SARS-CoV-2-infected humans and pets should be avoided to prevent the emergence of novel mutations of public health importance from anthroponotic events.

Serological cross-reactivity using a SARS-CoV-2 ELISA test in acute Zika virus infection, Colombia

Alvaro Faccini-Martinez, Ricardo Rivero, et al, 2020. International Journal of Infectious Diseases

We investigated seroreactivity by using a commercial SARS-CoV-2 ELISA test in samples collected from different groups of individuals, including patients diagnosed to have Dengue, Zika, and Chikungunya infection between 2015 and 2019, from an endemic area in the Caribbean Colombian region.
A total of 127 sera samples obtained from six different groups of individuals were included in this study: Group A: patients with confirmed SARS-CoV-2 infection; Group B: patients with symptoms suggestive of COVID-19 or asymptomatic contacts with confirmed patients; Group C: patients with acute or recent dengue virus infection; Group D: patients with acute Zika virus infection; Group E: patients with previous Chikungunya virus infection; and Group F: individuals with exposure to spotted fever group rickettsiae.
Overall, group A, group B, and group D showed seroreactivity to SARS-CoV-2 in 92%, 75%, and 26% of samples, respectively; furthermore, group C, group E, and group F showed 100% seronegativity. Conclusions: We found 26% of serological cross-reactivity in patients with acute Zika virus infection by using a commercial SARS-CoV-2 ELISA test. Further studies are needed to evaluate whether serological cross-reaction is maintained with time in nonacute patients with previous exposure to the Zika virus and its effect in SARS-CoV-2 serosurveys in endemic areas for this arbovirus.

Learn more!

More research on my Scholar, Researchgate and Twitter profiles.

Virome of Bats and Mosquitoes from the Colombian Caribbean

At Universidad de Córdoba, we are currently working on a project funded by Colombia's Science Ministry (Minciencias) with the goal of studying the ecology of RNA viruses present in Mosquitoes and Bats.
To do this, we are doing field-work to collect sylvatic mosquitoes and bucal swabs from bats in several departments of Colombia in order to study the richness and diversity of Colombian Caribbean virome using metagenomics and bioinformatics methods coupled with modeling of the effect that climate variables have in this diversity.
Our work aims to discover new viral species that give answers but also birth to new research questions such as the intra-host and intra-vector interaction of diverse viral communities and its effect on the replication and transmission of viruses of public health importance such as Alpha and Flaviviruses.

Effect of climate, behavioral and epidemiological variables on DENV evolution.

Arboviruses, especially Dengue virus have been causing high burden of disease in tropical countries from Southeastern Asia, Central and South America. With the introduction of control measures such as fumigation, elimination egg-hatching sites and the introduction of vaccines, It is important to predict the impact of these measures on viral evolution.
I aim to integrate genomics, geospatial analysis and mathematical modeling to create epidemiological frameworks that explain the effect of control measures, coupled with epidemiological and metereological variables on the dynamics of Dengue fever.
The non-stopping velocity of global climate change poses a threat to temperate countries, whose population is highly susceptible to arboviruses, and actionable insights are needed to explain, predict and prevent the public health impact of the expansion of vector populations due to increasing global temperature. I dream of a world where we as quantitative researchers can precisely produce insights for our goverments to make informed public health decisions and prevent the next pandemic.

Nextstrain build for Pathogen Evolution

I build and maintain nextstrain builds to track the evolution of SARS-CoV-2 in Colombia, At the moment I have two active builds, one to reconstruct the origin and spread of the Mu variant (B.1.621) which emerged in Colombia and caused a surge in cases and deaths during March-July of 2021.
The second build is kept updated by retrieving the latest sequences generated and deposited to GISAID by Colombia's genomic surveillance network led by National Health Institute.