Biology subjects

Ferres, M.

Publications and source records attributed to Ferres, M..

5 recordsLinked to original sources

bioRxiv2026

A historical cross-border Andes virus lineage reveals the origin of a cruise ship hantavirus pulmonary syndrome outbreak

Andes virus (ANDV) caused a multi-country outbreak of hantavirus pulmonary syndrome among passengers and crew of a cruise ship in 2026. To investigate the origin and evolutionary history of the virus responsible for the outbreak, we analyzed complete ANDV small (S), medium (M), and large (L) genome segment sequences from Chile alongside outbreak-associated and publicly available genome sequences. Across all three segment-specific phylogenies, the outbreak virus clustered within an ANDV Clade III cluster spanning southern Chile and northern Patagonia in Argentina and were most closely related to a human-derived ANDV (p1236) collected in Los Rios Region of Chile in 2012, representing the closest known historical relative of the outbreak-associated virus. Phylogeographic analysis showed that the genetically distinct ANDV Clade V lineage circulating in central Chile was not closely related to the cruise ship outbreak-associated genomes, thereby reducing the likelihood that the index cases acquired infection through zoonotic spillover while traveling through the Maule Region. These findings trace the geographic origin of the outbreak-associated virus to a defined corridor, the Hua Hum Pass, a cross-border zone connecting Province of Neuquen in Argentina with the Los Rios and La Araucania Regions of Chile.

evolutionary biology↗

bioRxiv2026

Epistasis between SARS-CoV-2 M and N Proteins Balances Particle Assembly and Immune Evasion

Since its emergence in the human population, SARS-CoV-2 has continuously evolved to evade immune responses and robustly establish global circulation. In this process, the structural viral membrane (M) protein has accumulated amino acid changes whose impact on viral particle assembly and innate immune evasion remains incompletely understood. Here, we designed a SARS-CoV-2 replicon system lacking M that assesses the influence of transiently transfected M protein variants on viral particle production independently of viral RNA replication. We found that M protein variants have reduced particle assembly while innate immune antagonism functions are strengthened. Notably, the assembly defect is rescued by co-evolving N protein variants, highlighting how SARS-CoV-2 evolution coordinates between two of its structural proteins to optimize viral infection. Our work underscores the complex evolutionary trajectories of SARS-CoV-2 variants across different viral proteins and informs future therapeutic strategies targeting viral assembly and limiting infection. Author summarySince the onset of the COVID-19, SARS-CoV-2 has been changing continuously in ways that help it spread efficiently and evade human defenses. The viral membrane (M) protein is a key structural component required to form new viral particles. Nevertheless, it has accumulated changes over time with overlooked functions. In this study, we developed an experimental system to examine the impact of these changes on virus assembly and host immune system. We found that recent M variants are better than older variants at suppressing immune responses but less efficient at forming viral particles. This defect seems to be compensated for by coordinated changes in another structural protein, nucleocapsid (N). These findings reveal that SARS-CoV-2 evolution involves trade-offs between different viral characteristics, with changes in one protein balancing changes in another. Understanding these trade-offs provides new insight into how the virus adapts to humans and may help guide therapeutic strategies to limit infection.

microbiology↗

bioRxiv2020

A simple RNA preparation method for SARS-CoV-2 detection by RT-qPCR

The technique RT-qPCR for viral RNA detection is the current worldwide strategy used for early detection of the novel coronavirus SARS-CoV-2. RNA extraction is a key pre-analytical step in RT-qPCR, often achieved using commercial kits. However, the magnitude of the COVID-19 pandemic is causing disruptions to the global supply chains used by many diagnostic laboratories to procure the commercial kits required for RNA extraction. Shortage in these essential reagents is even more acute in developing countries with no means to produce kits locally. We sought to find an alternative procedure to replace commercial kits using common reagents found in molecular biology laboratories. Here we report a method for RNA extraction that takes about 40 min to complete ten samples, and is not more laborious than current commercial RNA extraction kits. We demonstrate that this method can be used to process nasopharyngeal swab samples and yields RT-qPCR results comparable to those obtained with commercial kits. Most importantly, this procedure can be easily implemented in any molecular diagnostic laboratory. Frequent testing is crucial for individual patient management as well as for public health decision making in this pandemic. Implementation of this method could maintain crucial testing going despite commercial kit shortages.

molecular biology↗

bioRxiv2018

Single nucleotide variant at the alphaVbeta3 integrin associated to Andes virus infection susceptibility.

BackgroundANDV, agent of hantavirus cardiopulmonary syndrome, enters through integrin cell protein. A change from leucine-to-proline at residues 33 in the PSI-domain (L33P) inhibits ANDV recognition. We assessed the association between this human-variant and ANDV infection.\n\nResultsWe defined susceptible genotype to \"TT\" (coding leucine) and protective \"CC\" (coding proline). TT was in 89.2% (66/74) of a first cohort of ANDV-cases and in 60% (63/105) of exposed close-household contacts who remained unifected (p<0.05). Protective genotype was absent in all 85 ANDV cases in both cohorts and was present at 11.4% in exposed close-household contacts who remained uninfected. Logistic regression modeling to become a case had an OR 6.2-12.6 (p<0.05) in presence of TT and ANDV well-known risk activities. Moreover, OR of 7.3 was obtained when TT condition was analyzed for two groups exposed to the same environmental risk.\n\nConclusionHost genetic background has an important role in ANDV-infection susceptibility in the studied population.\n\nAuthor summaryHantavirus is a worldwide infection known to cause two different diseases: the hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS or HPS), diseases seen in the old world and new world hantaviruses, respectively. Andes orthohantavirus (ANDV), is the etiological agent of HCPS in Chile and South of Argentina, and is the only hantavirus recognized to be transmited person-to-person. It has been suggested that {beta}3-integrin is a cellular receptor for ANDV entry into cells. Here we try to understand the role of one human genetic variant of {beta}3-integrin in susceptibility to ANDV-infection. We compared, exposed infected and non infected subjects, and their genotype differences regarding a {beta}3 integrin variant that change a Leucine to Proline at PSI domain of the receptor. Leucine and proline aminoacids at the PSI domain, turn the cell susceptible or resistant to ANDV-infection, respectively. We were able to show genotype differences in cases and close-household contact that suggest differences in ANDV-infection susceptibility. Our results propose that the TT genotype, that codes to leucine, is a risk factor to become infected with ANDV, and the CC genotype that codes for proline at PSI domain, is a protective factor. (193/200)

microbiology↗

bioRxiv2018

Microbiome disturbance and resilience dynamics of the upper respiratory tract in response to influenza A virus infection in analog hosts

Infection with influenza can be aggravated by bacterial co-infections, which often results in disease exacerbation because of host responses and cellular damage. The native upper respiratory tract (URT) microbiome likely plays a role, yet the effects of influenza infection on the URT microbiome are largely unknown. We performed a longitudinal study to assess the temporal dynamics of the URT microbiomes of uninfected and influenza virus-infected humans and ferrets. Uninfected human patients and ferret URT microbiomes had stable \"heathy ecostate\" communities both within and between individuals. In contrast, infected patients and ferrets exhibited large changes in bacterial community composition over time and between individuals. The \"unhealthy\" ecostates of infected individuals progressed towards the \"healthy ecostate\" over time, coinciding with viral clearance and recovery. Blooms of Pseudomonas were a statistically associated constant in the disturbed microbiomes of infected individuals. The dynamic and resilient nature of the microbiome during influenza virus infection in multiple hosts provides a compelling rationale for the maintenance of the microbiome homeostasis as a potential therapeutic target to prevent IAV associated bacterial co-infections.\n\nOne Sentence SummaryDynamics of the upper respiratory tract microbiome during influenza A virus infection

microbiology↗