What to consider when developing a new molecular HIV surveillance tool: Perspectives of key stakeholders working in HIV prevention and treatment.

Developing and validating novel molecular HIV surveillance (MHS) tools capable of predicting the growth and trajectory of localized outbreaks driven by specific transmission clusters is key to the . This study explored stakeholders' perspectives on HIV prevention and treatment regarding a developing deep-learning framework, and its ability to predict HIV transmission cluster trajectories and inform decision-making on HIV prevention and treatment scale-up approaches in Florida. We conducted five virtual focus group discussions with 16 clinical health professionals and state and local public health personnel.

A comparative analysis of the role of containment policies, vaccination strategies and virus variants in the COVID-19 pandemic across nine European countries.

The COVID-19 pandemic disrupted public health, economies, and societies worldwide, with lasting effects still visible today. Containment policies were implemented to reduce viral transmission, but their effectiveness varied across geographic regions. Understanding the interplay between policies, epidemiological variables, vaccines, and variants is crucial for optimizing future epidemic responses.

SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein.

Background: The COVID-19 pandemic has caused over 776 million infections and 7 million deaths globally between December 2019 and November 2024. Since the emergence of the original Wuhan strain, SARS-CoV-2 has evolved into multiple variants-including Alpha, Delta, and Omicron-primarily through mutations in the Spike glycoprotein. The S1 subunit, which binds the human angiotensin-converting enzyme 2 (ACE2) receptor, mutates frequently and plays a key role in infectivity and immune escape, while the more conserved S2 subunit mediates membrane fusion.

Behavioral and Demographic Profiles of HIV Transmission and Exposure Networks in Florida: Network Analysis of HIV Contact Tracing Data.

Background: To complete the Ending the HIV Epidemic initiative in areas with high HIV incidence, there needs to be a greater understanding of the demographic, behavioral, and geographic factors that influence the rate of new HIV diagnoses. This information will aid the creation of targeted prevention and intervention efforts.

Objective: This study aims to identify the geographic distribution of risk groups and their role within potential transmission networks in Florida.

Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022-2023.

In the aftermath of 2 extreme weather events in 2022, Malawi experienced a severe cholera outbreak; 59,325 cases and 1,774 deaths were reported by March 31, 2024. We generated 49 Vibrio cholerae full genomes from isolates collected during December 2022-March 2023. Phylogenetic and phylogeographic methods confirmed that the Malawi outbreak strains originated from Pakistan's 2022 cholera outbreak.

Dynamic Networks of Methicillin-Resistant in Communities Drive Hospital Transmission.

Background: Although methicillin-resistant (MRSA) transmission has traditionally been viewed separately in hospital and community settings, this distinction is increasingly blurred. We used whole-genome sequencing and epidemiologic analyses to characterize the movement of MRSA across these interfaces in a rural-urban population.

Methods: Serial cross-sectional sampling of MRSA isolates occurred at a tertiary care hospital between 2010 and 2019.

A case-cluster of aseptic meningitis associated with a newly identified recombinant echovirus6/CoxsackievirusB1 enterovirus.

A daycare teacher presented with complaints of headache, neck stiffness, and fever. Because of initial concerns about meningococcal meningitis, families of daycare attendees were notified and 10 children from the daycare presented for evaluation. CSF from the teacher and nasal swabs from four febrile children were RT-PCR positive for enterovirus.

Dengue and Other Arbovirus Infections among Schoolchildren, Haiti, 2021.

In 2021, we screened 91 children in Haiti with acute undifferentiated febrile illness for arbovirus infections. We identified a major outbreak of dengue virus type 2, with 67% of the children testing positive. Two others were positive for chikungunya East/Central/South African IIa subclade, and 2 were positive for Zika virus.

Phylogenetic-informed graph deep learning to classify dynamic transmission clusters in infectious disease epidemics.

Motivation: In the midst of an outbreak, identification of groups of individuals that represent risk for transmission of the pathogen under investigation is critical to public health efforts. Dynamic transmission patterns within these clusters, whether it be the result of changes at the level of the virus (e.g.

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders.

The COVID-19 pandemic is marked by the successive emergence of new SARS-CoV-2 variants, lineages, and sublineages that outcompete earlier strains, largely due to factors like increased transmissibility and immune escape. We propose DeepAutoCoV, an unsupervised deep learning anomaly detection system, to predict future dominant lineages (FDLs). We define FDLs as viral (sub)lineages that will constitute >10% of all the viral sequences added to the GISAID, a public database supporting viral genetic sequence sharing, in a given week.

Coronavirus Disease 2019 Lineages in a Minimally Vaccinated Island Population: Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 in Haiti.

We monitored severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in Haiti from 2020 to 2023. Despite Haitian coronavirus disease 2019 (COVID-19) travel restrictions and in the setting of a vaccination rate of 2.7%, the timing and lineage evolution of the Haiti epidemic mirrored what was occurring in the rest of the world.

Novel insights on unraveling dynamics of transmission clusters in outbreaks using phylogeny-based methods.

Molecular data analysis is invaluable in understanding the overall behavior of a rapidly spreading virus population when epidemiological surveillance is problematic. It is also particularly beneficial in describing subgroups within the population, often identified as clades within a phylogenetic tree that represent individuals connected via direct transmission or transmission via differing risk factors in viral spread. However, transmission patterns or viral dynamics within these smaller groups should not be expected to exhibit homogeneous behavior over time.

CSF1R inhibition depletes brain macrophages and reduces brain virus burden in SIV-infected macaques.

Perivascular macrophages (PVMs) and, to a lesser degree, microglia are targets and reservoirs of HIV and simian immunodeficiency virus (SIV) in the brain. Previously, we demonstrated that colony-stimulating factor 1 receptor (CSF1R) in PVMs was upregulated and activated in chronically SIV-infected rhesus macaques with encephalitis, correlating with SIV infection of PVMs. Herein, we investigated the role of CSF1R in the brain during acute SIV infection using BLZ945, a brain-penetrant CSF1R kinase inhibitor.

Phylodynamic Insights into Global Emergence and Diversification of the Tomato Pathogen pv. .

The emergence of plant pathogens is often associated with waves of unique evolutionary and epidemiological events. pv. is one of the major pathogens causing bacterial spot disease of tomatoes.

DeepDynaForecast: Phylogenetic-informed graph deep learning for epidemic transmission dynamic prediction.

In the midst of an outbreak or sustained epidemic, reliable prediction of transmission risks and patterns of spread is critical to inform public health programs. Projections of transmission growth or decline among specific risk groups can aid in optimizing interventions, particularly when resources are limited. Phylogenetic trees have been widely used in the detection of transmission chains and high-risk populations.

Bacterial DnaK reduces the activity of anti-cancer drugs cisplatin and 5FU.

Background: Chemotherapy is a primary treatment for cancer, but its efficacy is often limited by cancer-associated bacteria (CAB) that impair tumor suppressor functions. Our previous research found that Mycoplasma fermentans DnaK, a chaperone protein, impairs p53 activities, which are essential for most anti-cancer chemotherapeutic responses.

Methods: To investigate the role of DnaK in chemotherapy, we treated cancer cell lines with M.

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders.

The coronavirus disease of 2019 (COVID-19) pandemic is characterized by sequential emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants, lineages, and sublineages, outcompeting previously circulating ones because of, among other factors, increased transmissibility and immune escape. We propose DeepAutoCoV, an unsupervised deep learning anomaly detection system to predict future dominant lineages (FDLs). We define FDLs as viral (sub)lineages that will constitute more than 10% of all the viral sequences added to the GISAID database on a given week.

Seafood-Associated Outbreak of ctx-Negative Vibrio mimicus Causing Cholera-Like Illness, Florida, USA.

Vibrio mimicus caused a seafood-associated outbreak in Florida, USA, in which 4 of 6 case-patients were hospitalized; 1 required intensive care for severe diarrhea. Strains were ctx-negative but carried genes for other virulence determinants (hemolysin, proteases, and types I-IV and VI secretion systems). Cholera toxin-negative bacterial strains can cause cholera-like disease.

Ancestral Origin and Dissemination Dynamics of Reemerging Toxigenic Vibrio cholerae, Haiti.

The 2010 cholera epidemic in Haiti was thought to have ended in 2019, and the Prime Minister of Haiti declared the country cholera-free in February 2022. On September 25, 2022, cholera cases were again identified in Port-au-Prince. We compared genomic data from 42 clinical Vibrio cholerae strains from 2022 with data from 327 other strains from Haiti and 1,824 strains collected worldwide.

ARCA: the interactive database for arbovirus reported cases in the Americas.

Background: Accurate case report data are essential to understand arbovirus dynamics, including spread and evolution of arboviruses such as Zika, dengue and chikungunya viruses. Giving the multi-country nature of arbovirus epidemics in the Americas, these data are not often accessible or are reported at different time scales (weekly, monthly) from different sources.

Results: We developed a publicly available and user-friendly database for arboviral case data in the Americas: ARCA.

Network typologies predict future molecular linkages in the network of HIV transmission.

Objective: HIV molecular transmission network typologies have previously demonstrated associations to transmission risk; however, few studies have evaluated their predictive potential in anticipating future transmission events. To assess this, we tested multiple models on statewide surveillance data from the Florida Department of Health.

Design: This was a retrospective, observational cohort study examining the incidence of new HIV molecular linkages within the existing molecular network of persons with HIV (PWH) in Florida.

Diversity and Genetic Reassortment of Keystone Virus in Mosquito Populations in Florida.

Keystone orthobunyavirus (KEYV), a member of the genus Orthobunyavirus, was first isolated in 1964 from mosquitoes in Keystone, Florida. Although data on human infections are limited, the virus has been linked to a fever/rash syndrome and, possibly, encephalitis, with early studies suggesting that 20% of persons in the Tampa, Florida, region had antibodies to KEYV. To assess the distribution and diversity of KEYV in other regions of Florida, we collected > 6,000 mosquitoes from 43 sampling sites in St.

Infectivity of three Mayaro Virus geographic isolates in human cell lines.

Mayaro virus (MAYV) is an emergent arthropod-borne virus that causes an acute febrile illness accompanied by arthralgia, similar to chikungunya virus. Increasing urbanization of MAYV outbreaks in the Americas has led to concerns for geographic expansion and spillover. Given the potential importance of this pathogen, we sought to fill critical gaps in knowledge regarding MAYV infectivity and geographic variation.