Tetyana I. Vasylyeva

Background: In 2013, chikungunya virus (CHIKV), a re-emerging Aedes -borne virus, was introduced into the Americas. This led to synchronous epidemics across the region associated mainly with the Asian lineage, which eventually subsided. Resurgent outbreaks have been recorded since, principally in South America, largely driven by the East-Central-South-African (ECSA) lineage. In 2025, more than 300,000 CHIKV suspected cases were reported in Brazil and Cuba. Case Summary: In November 2025, a healthy adult male traveling from Cuba arrived in Merida, Mexico, and shortly after presented febrile symptoms consistent with an arboviral infection. CHIKV infection was diagnosed by RT-qPCR. Though the infection was mild, the patient developed a rash on the abdomen and neck that persisted for up to a month, with further inflammation of the joints of the left leg. Phylogenetic analysis of the viral genome indicated placement within the ECSA lineage, clustering with other contemporaneous virus genomes sampled from Brazil that belong to a recently described clade II within the country, in which viral genomes from Cuba also cluster. Conclusion: We identify a travel-associated ECSA lineage CHIKV case in Mexico. This viral lineage has not previously been detected in the country. This finding highlights the risk for subsequent local transmission and is consistent with reports of the presence of this lineage in Cuba. Ten years since the last CHIKV epidemic in Mexico, strengthened surveillance is required to anticipate potential local outbreaks within the region.

Background: Conducting longitudinal infectious disease research during armed conflicts is important for understanding transmission dynamics and preventing outbreaks. War in Ukraine started in 2014, with the escalation to full-scale invasion in 2022, resulting in massive population displacement, infrastructure destruction, mobility restriction for men, and reduced access to healthcare. The ANCHOR (Analysis of Network Composition, Health Outcomes, and Resilience) study, launched in November 2024, examines how war- and displacement-driven changes affect social networks, HIV risks, and HIV care engagement. Here, we report implementation challenges and adaptations as practical lessons that may inform infectious disease surveillance and research in conflict settings. Methods: ANCHOR is a cohort study conducted in Kyiv and Lviv in 2024–2026 that enrolled sexual minority men (SMM) using respondent-driven sampling, with 6- and 12-month follow up of participants testing positive for HIV. Data collection included structured behavioral and social network interviews, HIV rapid testing, viral load (VL) assessment, and HIV genetic sequencing. Results: A total of 1,199 SMM were enrolled; of those, 87 tested positive for HIV. Challenges of conducting a research study in an ongoing conflict were identified during the first month of recruitment and prompted protocol revision, incorporating online screening, oral consent, remote interviews, video-assisted HIV self-testing, flexible biospecimen collection. These changes enabled safe completion of study recruitment ahead of the anticipated schedule (within 8 instead of 18 months). Interview follow-up rate was 94% (82/87) at both 6-and 12-month, accompanied by successful biospecimen collection in 61/87 and 45/87 cases at 6-month and 12-month follow-up, respectively. Conclusions: Flexible adaptations in response to the war conditions preserved study integrity and safety of study participants and staff. Availability of various modes of biospecimen collection allowed successful completion of clinical and genomic components of the study, including VL testing and HIV molecular epidemiology analyses despite logistical, infrastructural, and security constraints. Longitudinal biospecimen collection remained challenging due to the ongoing migration and displacement. Lessons from the ANCHOR study can support continuity of infectious disease research in conflict settings and among populations facing barriers to participation. Some of these adaptations may also be applicable to routine infectious disease surveillance, although their utility requires further evaluation.

Background: Diagnoses of sexually transmitted infections (STIs), such as Neisseria gonorrhoeae (NG), are key entry points to HIV services, including linkage to pre-exposure prophylaxis. Understanding whether bacterial STI-associated clinical encounters effectively interrupt onward HIV transmission is crucial for evaluating the robustness of integrated prevention systems. Methods: We analyzed 1,866 HIV-1 subtype B pol sequences collected in a high HIV and NG prevalence setting of Miami-Dade County, Florida (2015-2022), and linked them with NG diagnosis records. A time-scaled maximum-likelihood phylogeny was reconstructed, and “young” clades (<2 years old) were identified as proxies for recent HIV transmissions. We evaluated whether any of the “young” clades included at least one individual diagnosed with NG within one year prior to the clade’s time to the most recent common ancestor (clade origination event), and compared annual proportions of such clades to permutation-based “expected” distributions derived from randomizing NG diagnoses across the HIV phylogeny. Results: Among 49 “young” clades, 14 (28.6%) included a recent NG diagnosis. Whereas most years showed no difference from null expectations, 2020 had a higher proportion of “young” clades with a recent NG diagnosis (p = 0.01), coinciding with COVID-19-related service disruptions. In 2021, no “young” clades had recent NG diagnoses (p = 0.04), consistent with reduced STI testing during 2020. “Young” clades with recent NG diagnoses also had a higher than expected proportion of Hispanic individuals (p = 0.02). Conclusions: By linking HIV molecular data with routine STI diagnoses, we observed a temporal pattern consistent with disruption of STI-linked HIV prevention services during the height of the COVID-19 epidemic and the associated healthcare disruption. Integrating molecular epidemiology with routine STI surveillance provides a scalable public health approach to monitoring the performance and robustness of linked STI prevention systems.

We deployed the VANTAGE (VAN for Transmissible Agent Genomic Epidemiology) mobile system in Lviv, Ukraine, demonstrating end-to-end sequencing of dried blood spot samples within a clinic van usually serving de-occupied and frontline regions. HIV-1 pol sequences were obtained from 50% of samples, all subtype A6. Median time to 100× coverage was 38 min. Phylogenetic analysis revealed a local transmission cluster including a displaced person and the non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance mutation E138A, supporting real-time HIV genomic surveillance in humanitarian crises.

While advances in molecular epidemiology and computational modeling have enhanced our capacity to track pathogen evolution, the accurate reconstruction of spatiotemporal transmission dynamics remains essential for developing epidemic preparedness frameworks and implementing outbreak response measures. Structured coalescent models offer a phylogeographic framework by restricting lineage coalescence events to geographically proximate host populations. Although the Bayesian structured coalescent approximation (BASTA) provides a tractable approach, contemporary phylogeographic analyses involving dozens of geographic localities and hundreds to thousands of viral genomes substantially exceed the computational capacity of existing implementations. The BASTA likelihood scales cubically with deme count and quadratically with sequence count due to matrix exponentiation and pairwise coalescent probability calculations. Here, we introduce a comprehensive algorithmic restructuring of the structured coalescent likelihood that eliminates redundancies, optimizes memory access, and exposes parallelization opportunities. Our approach reorganizes computations along three dimensions: (i) independent calculation of deme–transition probability matrices across time intervals; (ii) simultaneous evaluation of partial likelihood vectors within temporal slices; and (iii) concurrent aggregation of coalescent probabilities. Algorithmic restructuring cuts average coalescent likelihood computation by 7 to 8 fold, and parallelization further boosts performance to 10 to 26 fold, enabling joint phylogeographic analyses of dengue virus across 10 South American countries and H5N1 avian influenza across 20 Eurasian regions to finish in a fraction of prior time. This computational efficiency also enables comparison between backward–in–time structured coalescent approximations and forward–in–time phylogeographic methods, revealing that the former provides appropriately conservative posterior estimates, particularly at intermediate phylogenetic depths. We integrate our implementation into the popular BEAST X and BEAGLE software packages, with an accompanying interface in BEAUti X to easily set up the analyses, providing researchers with an accessible and scalable tool for real–time phylogeographic surveillance of rapidly evolving pathogens.

The Russian invasion of Ukraine has displaced millions, potentially exposing them to traumatic events in the process. Potentially traumatic events (PTEs) have been linked to negative health outcomes, including depression, substance abuse and risky sexual behaviours. Men who have sex with men (MSM) are especially vulnerable to the effects of displacement, given widespread MSM stigma in Ukraine. A cross-sectional survey of MSM was conducted as part of a peer-driven intervention between August 2023 and January 2024 across eight cities in Ukraine via respondent-driven sampling. Lifetime PTE exposure responses were grouped into three binary variables: accidental/injury, victimisation and death threat. The relationship between displacement and exposure to PTEs was modelled using multivariate covariance generalized linear models with a logistic link, extending logistic regression to all three PTE responses. n=3617 (mean age 29.8, SD 8.1; 93% of the 3886 surveyed) were analysed. Controlling for sampling structure, participation in military operations, adverse experience of unstable housing in the last 2 years and age, internal displacement was significantly associated (p<0.001) with all three types of PTEs: adjusted ORs for accidental/injury, victimisation and death threat were 2.04, 1.57 and 2.05, respectively. As the war continues, our results highlight the need for trauma-informed care for internally displaced MSM in Ukraine, as many of them have been exposed to various types of PTEs. Those with adverse experiences of unstable housing conditions or participating in military operations particularly need to be considered.

Background: Between 10 - 50% of female PWID in former USSR countries, where HIV epidemics are driven by injecting drug use, are reported to exchange sex for money, drugs or goods. Research in the region shows contradictory data on the association between exchange sex and HIV for PWID, and suggests that this association might be influenced by other factors. Since female PWID who exchange sex might be a bridge population between PWID and other people, it is important to monitor their risks and suggest timely interventions.

Objective: Internally displaced persons (IDPs) can have limited access to HIV and hepatitis C Virus (HCV) treatment and prevention. IDPs comprise > 7% of Georgian population but prevalence and levels of HIV and HCV knowledge in this population remain unknown. We tested 100 IDPs in Georgia for HIV and HCV, many of whom had drug injecting experience, and interviewed them about their migration experience, sexual and drug injecting practices, and HIV/HCV transmission knowledge. Results: The average age of participants was 37.5 years (range 18–63); 31% were women. Almost half (N = 48) of participants reported ever injecting drugs; 17% of those (N = 8) started injecting drugs within the last year. Anti-HCV and HIV prevalence was 11% and 0%, respectively. Fewer people without drug use experience compared to people who inject drugs correctly answered all questions on the HIV knowledge test (13% vs. 35%, p = 0.015) or knew where to get tested for HIV (67% vs 98%, p < 0.001). There was no difference in HCV knowledge between the two groups. HIV and HCV prevalence remains low among Georgian IDPs, but levels of HIV knowledge were much lower than levels of HCV knowledge.

Socio-economic disparities were associated with disproportionate viral incidence between neighborhoods of New York City (NYC) during the first wave of SARS-CoV-2. We investigated how these disparities affected the co-circulation of SARS-CoV-2 variants during the second wave in NYC. We tested for correlation between the prevalence, in late 2020/early 2021, of Alpha, Iota, Iota with E484K mutation (Iota-E484K), and B.1-like genomes and pre-existing immunity (seropositivity) in NYC neighborhoods. In the context of varying seroprevalence we described socio-economic profiles of neighborhoods and performed migration and lineage persistence analyses using a Bayesian phylogeographical framework. Seropositivity was greater in areas with high poverty and a larger proportion of Black and Hispanic or Latino residents. Seropositivity was positively correlated with the proportion of Iota-E484K and Iota genomes, and negatively correlated with the proportion of Alpha and B.1-like genomes. The proportion of persisting Alpha lineages declined over time in locations with high seroprevalence, whereas the proportion of persisting Iota-E484K lineages remained the same in high seroprevalence areas. During the second wave, the geographic variation of standing immunity, due to disproportionate disease burden during the first wave of SARS-CoV-2 in NYC, allowed for the immune evasive Iota-E484K variant, but not the more transmissible Alpha variant, to circulate in locations with high pre-existing immunity.