A5024545469- SARS-CoV-2 and COVID-19 Research
- Plant Virus Research Studies
- Viral gastroenteritis research and epidemiology
- Viral Infections and Vectors
- Influenza Virus Research Studies
- Respiratory viral infections research
- Animal Disease Management and Epidemiology
- Animal Virus Infections Studies
- COVID-19 epidemiological studies
- Zoonotic diseases and public health
- Rabies epidemiology and control
- Evolution and Genetic Dynamics
- Bat Biology and Ecology Studies
- Bacteriophages and microbial interactions
- RNA and protein synthesis mechanisms
- vaccines and immunoinformatics approaches
- Virology and Viral Diseases
- Genomics and Phylogenetic Studies
- Mosquito-borne diseases and control
- CRISPR and Genetic Engineering
- Herpesvirus Infections and Treatments
- SARS-CoV-2 detection and testing
- Yersinia bacterium, plague, ectoparasites research
- Data-Driven Disease Surveillance
- Cytomegalovirus and herpesvirus research
University of Oxford
2018-2024
University College London
2024
Consejo Nacional de Ciencia y Tecnología
2024
Asociación Mexicana de Psicología y Desarrollo Comunitario
2021-2023
Leibniz Institute for Zoo and Wildlife Research
2015-2019
Universidad Autónoma del Estado de Morelos
2019
Universidad Nacional Autónoma de México
2009-2014
Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach the common vampire bat (Desmodus rotundus), one of only three obligate blood-feeding (sanguivorous) mammals, study evolution its complex dietary adaptation. Specifically, we assembled high-quality reference genome (scaffold N50 = 26.9 Mb, contig 36.6 kb) gut metagenome, compared them against those insectivorous, frugivorous carnivorous bats. Our analyses...
Although recombination is a feature of coronavirus evolution, previously detected recombinant lineages SARS-CoV-2 have shown limited circulation thus far. Here, we present detailed phylogenetic analysis four to investigate the possibility virus among them. Our analyses reveal well-supported differences between Orf1ab region encoding viral non-structural proteins and rest genome, including Spike (S) protein remaining reading frames. By accounting for several deletions in NSP6, Orf3a, S,...
Nipah virus (NiV) is a highly pathogenic paramyxovirus that causes frequent outbreaks of severe neurologic and respiratory disease in humans with high case fatality rates. The 2 glycoproteins displayed on the surface virus, NiV-G NiV-F, mediate host-cell attachment membrane fusion, respectively, are targets host antibody response. Here, we provide molecular basis for neutralization NiV through antibody-mediated targeting NiV-F. Structural characterization neutralizing (nAb) complex trimeric...
During the coronavirus disease 2019 (COVID-19) pandemic, emergence and rapid increase of B.1.1.7 (Alpha) lineage severe acute respiratory syndrome 2 (SARS-CoV-2), first identified in United Kingdom September 2020, was well documented different areas world became a global public health concern because its increased transmissibility. The detected Mexico during December showing slow progressive circulation frequency, which reached maximum May 2021 but never predominant. In this work, we...
Abstract We characterized the nucleic acid‐sensing Toll‐like receptors ( TLR ) of a New World bat species, common vampire Desmodus rotundus ), and through comparative molecular evolutionary approach searched for general adaptation patterns among s eight different bats species belonging to three families Pteropodidae, Vespertilionidae Phyllostomidae ). found that are evolving slowly mostly under purifying selection divergence pattern such is overall congruent with tree, consistent evolution...
Abstract Quantifying how the environment shapes host immune defense is important for understanding which wild populations may be more susceptible or resistant to pathogens. Spatial variation in parasite risk, food and predator abundance, abiotic conditions can each affect immunity, these factors also manifest at both local biogeographic scales. Yet identifying predictors spatial scale of their effects limited by rarity studies that measure immunity across many broadly distributed species. We...
Understanding the introduction, spread, and establishment of SARS-CoV-2 within distinct human populations as well evolution pandemics is crucial to implement effective control strategies. In this work, we report that initial virus strains introduced in Mexico came from Europe United States was circulating locally country early mid-March. We also found evidence for local transmission with a H49Y mutation Spike protein, which could be further used molecular marker follow viral spread region.
<title>Abstract</title> Since the emergence of SARS-CoV-2 in late 2019, highly divergent variants with novel constellations mutations have periodically emerged to displace previously co-circulating virus lineages. The evolutionary mechanisms behind this process remain unclear, but prevailing hypothesis supports through single events followed by a rapid accumulation individual long-term infections. In July 2023, Omicron-descending BA.2.86 Variant Interest (VOI) outcompete other lineages,...
Gammaherpesviruses (γHVs) are generally considered host specific and to have codiverged with their hosts over millions of years. This tenet is challenged here by broad-scale phylogenetic analysis two viral genes using the largest sample mammalian γHVs date, integrating for first time bat γHV sequences available from public repositories newly generated vampire species (Desmodus rotundus Diphylla ecaudata). Bat primate viruses frequently represented deep branches within supported phylogenies...
The emergence and reemergence of pathogens such as Zika virus, chikungunya yellow fever virus have drawn attention toward other cocirculating arboviruses in South America. Oropouche (OROV) is a poorly studied pathogen responsible for over dozen outbreaks since the early 1960s represents public health burden to countries Brazil, Panama, Peru. OROV likely underreported its symptomatology can be easily confounded with febrile illnesses (e.g., dengue leptospirosis) point-of-care testing still...
Abstract Parallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here, we exploit parallel to understand virulence avian influenza viruses (AIV). Highly-pathogenic AIVs evolve independently from low-pathogenic ancestors via acquisition of polybasic cleavage sites. Why some AIV lineages but not others this way is unknown. We hypothesise that the emergence highly-pathogenic may be facilitated by permissive or compensatory mutations occurring across...
Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation domestic circulation permit the exploration questions regarding early transmission dynamics. Here, we present a detailed description SARS-CoV-2 genomic epidemiology Ecuador, one hardest hit countries during stages coronavirus-19 pandemic. We generated analysed 160 whole genome sequences sampled from all provinces Ecuador 2020....
Over 200 different SARS-CoV-2 lineages have been observed in Mexico by November 2021. To investigate lineage replacement dynamics, we applied a phylodynamic approach and explored the evolutionary trajectories of five dominant that circulated during first year local transmission. For most lineages, peaks sampling frequencies coincided with epidemiological waves infection Mexico. Lineages B.1.1.222 B.1.1.519 exhibited similar constituting clades likely originated persisted for >12 months....
ABSTRACT The Desmodus rotundus endogenous betaretrovirus (DrERV) is fixed in the vampire bat D. population and other phyllostomid bats but not present all species from this family. DrERV phylogenetically related to Old World betaretroviruses rodents New primates, suggesting recent cross-species transmission. A integration age estimation of provirus some taxa indicates that an exogenous counterpart might have been circulation.
Pandemic type A (H1N1) influenza arose in early 2009, probably Mexico and the United States, reappeared North America September for seven more months. An amino acid substitution hemagglutinin (HA), D222G, has been reported a significant proportion of patients with severe fatal outcome. We studied prevalence HA222 substitutions during second wave its association clinical outcome pathogenicity mouse model.The nucleotide sequences (HA) from viruses collected 77 were determined including 50...
Background Aedes-borne arboviruses cause both seasonal epidemics and emerging outbreaks with a significant impact on global health. These viruses share mosquito vector species, often infecting the same host population within overlapping geographic regions. Thus, comparative analyses of virus evolutionary epidemiological dynamics across spatial temporal scales could reveal convergent trends. Methodology/Principal findings Focusing Mexico as case study, we generated novel chikungunya dengue...
Abstract Comparing the evolution of distantly related viruses can provide insights into common adaptive processes to shared ecological niches. Phylogenetic approaches, coupled with other molecular tools, help identify mutations informative on adaptation, although structural contextualization these functional sites proteins may gain insight their biological properties. Two zoonotic betacoronaviruses capable sustained human-to-human transmission have caused pandemics in recent times...
ABSTRACT Throughout the evolutionary history of SARS-CoV-2, divergent variants with an unusually high number novel mutations have repeatedly emerged and displaced other lineages in co- circulation. The latest example is BA.2.86 Variant Of Interest (VOI), which rapidly outcompeted all following its detection late July 2023. Descending sublineages dominated globally by 2024, at time writing this study. mechanisms highly-divergent viral tend to emerge remain unclear, most strongly supported...
Abstract During outbreaks of emerging infectious diseases, internationally connected cities often experience large and early outbreaks, while rural regions follow after some delay. This hierarchical structure disease spread is influenced primarily by the multiscale human mobility. However, during COVID-19 epidemic, public health responses typically did not take into consideration explicit spatial mobility when designing nonpharmaceutical interventions (NPIs). NPIs were applied at national or...
Predicting the fitness of mutations in evolution pathogens is a long-standing and important, yet largely unsolved problem. In this study, we used SARS-CoV-2 as model system to explore whether intrahost diversity viral infections could provide clues on relative single amino acid variants (SAVs). To do so, analysed ~15 million complete genomes nearly ~8000 sequencing libraries generated from infections, which were collected at various timepoints during COVID-19 pandemic. Across timepoints,...