Astroviruses affect human public health and present multiple complexities that challenge taxonomic assignment. Human astrovirus infections (HAstV subgenera) present with gastroenteritis and diarrhea with recent reports of expanded pathologies including neurotropic effects, contributing to encephalitis and meningitis in immunocompromised patients, and mild respiratory effects such as cough and...
Through antigenic evolution, viruses like seasonal influenza evade recognition by neutralizing antibodies elicited by previous infection or vaccination. This means that a person with antibodies well-tuned to an initial infection will not be protected against the same virus years later and that vaccine-mediated protection will decay. It is not fully understood which of the many endemic human...
Preexposition prophylaxis (PrEP) was approved for use in the Spanish National Health System in late November 2019. We examined whether PrEP roll-out had an effect on HIV-1 clustering in Spain. For this study, protease-reverse transcriptase sequences from HIV-1 infections diagnosed in 11 Spanish regions in the years before and after PrEP roll-out were analyzed with an approximate maximum...
Protein-unbound antiretroviral (ARV) drugs in the plasma may either diffuse across the walls of high endothelial venules (HEVs) into the lymph node (LN) parenchyma or be taken up by lymphocytes (naïve T cells) in the bloodstream and transported into the lymph node through cell migration via HEVs. To explore the relative contributions of free and cell-mediated drug trafficking, our...
SARS-CoV-2 evolution is shaped by human adaptive immunity, with mutations that allow escape from the B-cell response conferring selective advantage and spreading in the population. Meanwhile, the role of the escape from T-cellular cytotoxic response remains controversial. Here, we study the origin and spread of SARS-CoV-2 variants that allow escape from presentation by the HLA class I alleles...
Geographical spread and spillover events of avian influenza viruses (AIVs) are increasing in recent times. Characterizing the intra-host variation of AIVs is crucial for understanding their evolution. However, existing sequencing methods fall short in detecting rare intra-host sequence variants and reconstructing lengthy genome regions at the single-molecule level. To address this limitation,...
In this study, we studied an HIV-1 infected individual who experienced a 48 month delay between acute infection and seroconversion, and despite undergoing ART, had a viral load more typical of untreated individuals. To investigate the evolution of HIV-1 in this unique individual, we whole-genome, deep-sequenced HIV-1 plasma RNA from four samples taken over 1737 days. We compared evolutionary...
Mpox has evolved from a rare zoonotic disease to a significant human disease of international concern. Several studies have demonstrated the role of APOBEC3-driven hypermutation in enhancing the human adaptability of the virus. However, modelling this substitution process in BEAST has been challenging. We, therefore, develop a novel APOBEC3 substitution process in BEAST that correctly captures...
If two lineages differ by a single mutation, can wastewater lineage abundance estimators (such as Freyja) actually distinguish them? Can the presence of mutations be predicted from previous wastewater samples, possibly with machine learning methods? Can we use clustering algorithms to detect new lineages from wastewater without prior knowledge of any lineage definitions?
These questions are...
Background: Hypermutated proviruses, which arise in a single replication cycle when host antiviral APOBEC proteins introduce G-to-A mutations throughout the HIV genome, persist during ART. But, their within-host origins and longevity are poorly understood because standard phylogenetic analyses, which assume that mutations arise over many replication cycles, cannot accommodate them. We describe...
Dengue virus (DENV) is a significant public health concern in Colombia. Since a large outbreak in 2019, the departments of Risaralda and Valle del Cauca have experienced increased incidence of arboviral disease. Phylogeographic tools are critical to understanding DENV diversity, persistence, and spread across Colombia. Therefore, this study analyzed plasma samples from individuals with...
Host immunity drives the evolution of many pathogens towards antigenic escape. However, the contribution towards this escape may not be uniform across the population: different types of hosts may contribute more or less in terms of both immune pressure and onward transmission. Here we investigate the population-level consequences of this heterogeneity, focussing on vaccine escape.
This...
