TRAVEL-ASSOCIATED CHIKUNGUNYA VIRUS INFECTION, MEXICO, 2025

medRxiv · 2026-01-15

Abstract In November 2025, a traveler from Cuba tested positive for chikungunya virus upon arrival to Mexico. The virus belonged to the East-Central-South-African lineage, clustering with a clade prevalent in Brazil. Ten years after the last chikungunya epidemic in Mexico, strengthened surveillance is required to anticipate transmission of this emergent lineage.

Nighttime lights as a proxy for conflict intensity and infrastructure recovery in Yemen and Ukraine

Conflict and Health · 2026-05-11

INTRODUCTION: Quantifying the impacts of armed conflict on civilians and infrastructure remains a major challenge, particularly where reporting is limited. Most conflict measurement tools require affected populations to report events and are limited by short time series, under-reporting, and varying methods. These tools do not capture infrastructural rebuilding, which has important health implications. Given this, we demonstrate the utility of nighttime lights (NTL) as a complementary tool for measuring conflict dynamics and infrastructure recovery with an epidemiological application. METHODS: We used monthly NASA Black Marble data to analyze NTL patterns in Yemen (2012-2022) and Ukraine (2019-2024) before and after the onset of large-scale military operations. We calculated month-specific NTL ratios relative to pre-event baselines and assessed the alignment of structural breakpoints, identified using BFAST methods, with aerial attack onset. Generalized additive models were used to measure the relationship between NTL and aerial attacks while accounting for the built environment, population, diesel price (Yemen), and spatiotemporal factors. Finally, we applied NTL to an existing model on the association between conflict, measured via air raids, and cholera in Yemen by replacing the original conflict categories with ones defined by NTL and included a variable for NTL recovery. RESULTS: Mean NTL declined by 53.3% in Yemen and 21.0% in Ukraine following conflict escalation, with detected breakpoints aligning with aerial attack onset in 85.7% of Yemeni governorates and 51.9% of Ukrainian oblasts. Generalized additive models showed that attacks were significantly associated with NTL reductions, independent of built environment factors. Incorporating NTL-based conflict measures into a cholera transmission model for Yemen produced results consistent with attack-based models and found that light recovery was associated with reduced disease risk. DISCUSSION: NTL is a viable tool for measuring conflict and can offer insights on dynamics that are not present in standard tools while avoiding many of these tools' limitations. These data have epidemiological applications and can be a proxy for important events affecting transmission dynamics. While event-based tools have vast utility, NTL can complement them with specific strengths and means of application.

Synonymous substitution rate slowdown preceding the emergence of SARS-CoV-2 variants and during persistent infections

medRxiv · 2026-01-28

The emergence of variants has shaped the COVID-19 pandemic. The lack of directly observed precursors to these variants has led to proposals that variants emerge from either persistent infections, transmission in non-human animal populations after reverse-zoonosis, or cryptic transmission in the human population. We investigated the origin of variants by analyzing the molecular clock and rate of nonsynonymous and synonymous substitutions in SARS-CoV-2 circulating in human population, persistently infected individuals, non-human animals, and along variant stems: the branches preceding emergence of SARS-CoV-2 variants (Alpha, Beta, Gamma, Delta, Epsilon, Iota, B.1.637, Mu, and Omicron: BA.1, BA.2/BA.4/BA.5). Along the variant stems we find evidence for an acceleration in the non-synonymous substitution rate, as compared with non-synonymous substitution rate along the branches that represent the genetic diversity of circulating virus. We also find evidence for a slowdown in the synonymous substitution rate preceding the emergence of multiple named variants (e.g., Beta, Delta, Iota, Mu, Omicron BA.1); a similar pattern was observed in some individuals with persistent infections, suggesting that the viral replication rate can slow down during persistent infection. However, the synonymous rate slowdown was not observed for all variants, with some exhibiting an increase in synonymous substitution rates preceding their emergence compared with typical viral transmission (e.g., Alpha, Epsilon). The similarity in evolutionary dynamics preceding some variant emergence and during persistent infections supports the hypothesis that persistent infections were the likely source of many COVID-19 variants.

Nighttime lights as a proxy for conflict intensity and infrastructure recovery in Yemen and Ukraine

Research Square · 2026-02-06

Transmission dynamics of the 2022 mpox epidemic in New York City

Nature Medicine · 2025-03-25 · 15 citations

The 2022 global mpox epidemic was caused by transmission of MPXV clade IIb, lineage B.1 through sexual contact networks, with New York City (NYC) experiencing the first and largest outbreak in the United States. By performing phylogeographic analysis of MPXV genomes sampled from 757 individuals in NYC between April 2022 and April 2023, and 3,287 MPXV genomes sampled around the world, we identify over 200 introductions of MPXV into NYC with at least 84 leading to onward transmission. These infections primarily occurred among men who have sex with men, transgender women and nonbinary individuals. Through a comparative analysis with HIV in NYC, we find that both MPXV and HIV genomic cluster sizes are best fit by scale-free distributions, and that people in MPXV clusters are more likely to have previously received an HIV diagnosis and be a member of a recently growing HIV transmission cluster. We model MPXV transmission through sexual contact networks and show that highly connected individuals would be disproportionately infected at the start of an epidemic, which would likely result in the exhaustion of the most densely connected parts of the network, and, therefore, explain the rapid expansion and decline of the NYC outbreak. By coupling the genomic epidemiology of MPXV and HIV with epidemic modeling, we demonstrate that the transmission dynamics of MPXV in NYC can be understood by general principles of sexually transmitted pathogens.

Parallel algorithms for phylogenetic inference under a structured coalescent approximation

Proceedings of the National Academy of Sciences · 2025-09-24 · 1 citations

Advances in molecular epidemiology and computational modeling have improved our ability to track pathogen evolution, but accurate reconstruction of spatiotemporal transmission remains essential for epidemic preparedness and response. Structured coalescent models offer a phylogeographic framework by restricting coalescence to lineages within the same deme. Although the Bayesian structured coalescent approximation (BASTA) provides a tractable approach, contemporary phylogeographic analyses involving dozens of localities and hundreds to thousands of genomes 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 partial likelihood vectors update. Here, we introduce an 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 BEAST X and BEAGLE software packages, providing researchers with an accessible and scalable tool for real-time phylogeographic surveillance of rapidly evolving pathogens.

VANTAGE: van-based real-time HIV sequencing for transmission mapping and drug resistance profiling in war-affected Ukraine

AIDS · 2025-12-04

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.

Phylogeographic and genetic network assessment of COVID-19 mitigation protocols on SARS-CoV-2 transmission in university campus residences

EBioMedicine · 2025-05-09 · 1 citations

BACKGROUND: Congregate living provides an ideal setting for SARS-CoV-2 transmission in which many outbreaks and superspreading events occurred. To avoid large outbreaks, universities turned to remote operations during the initial COVID-19 pandemic waves in 2020 and 2021. In late-2021, the University of California San Diego (UC San Diego) facilitated the return of students to campus with comprehensive testing, vaccination, masking, wastewater surveillance, and isolation policies. METHODS: We performed molecular epidemiological and phylogeographic analysis of 4418 SARS-CoV-2 genomes sampled from UC San Diego students during the Omicron waves between December 2021 and September 2022, representing 58% of students with confirmed SARS-CoV-2 infection. We overlaid these analyses across on-campus residential information to assess the spread and persistence of SARS-CoV-2 within university residences. FINDINGS: Within campus residences, SARS-CoV-2 transmission was frequent among students residing in the same room or suite. However, a quarter of pairs of suitemates with concurrent infections had distantly related viruses, suggesting separate sources of infection during periods of high incidence in the surrounding community. Students with concurrent infections residing in the same building were not at substantial increased probability of being members of the same transmission cluster. Genetic network and phylogeographic inference indicated that only between 3.1 and 12.4% of infections among students could be associated with transmission within buildings outside of individual suites. The only super-spreading event we detected was related to a large event outside campus residences. INTERPRETATION: We found little evidence for sustained SARS-CoV-2 transmission within individual buildings, aside from students who resided in the same suite. Even in the face of heightened community transmission during the 2021-2022 Omicron waves, congregate living did not result in a heightened risk for SARS-CoV-2 transmission in the context of the multi-pronged mitigation strategy. FUNDING: SEARCH Alliance: Centers for Disease Control and Prevention (CDC) BAA (75D301-22-R-72097) and the Google Cloud Platform Research Credits Program. J.O.W.: NIH-NIAID (R01 AI135992). T.I.V.: Branco Weiss Fellowship and Newkirk Fellowship. L.L.: University of California San Diego.

Traumatic events exposure in men who have sex with men with and without experience of displacement in Ukraine

BMJ Global Health · 2025-07-01

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.

HIV-1 partial-pol nanopore sequencing protocol v1

2025-07-16

Reverse transcription and amplification of the HIV-1 partial-pol gene were performed using primers and PCR conditions adapted from Zhou et al. (2011), originally optimized for drug resistance surveillance in resource-limited settings. The resulting amplicons (~1.3 kb, covering the protease (PR) and reverse transcriptase (RT) regions) were used for nanopore library preparation. Optionally, a nested PCR can be performed using the second-round primers described in the same study, yielding a product of 1,084 nt. However, we found that a single round of RT-PCR was sufficient for successful amplification, reducing both time and cost. Library preparation followed a modified version of the ARTIC LoCost protocol, adapted for partial-pol amplicons and compatible with the Native Barcoding Kit 96 V14 (SQK-NBD114.96, Oxford Nanopore Technologies). Bioinformatics Workflow Suggestion:RAMPART can be run concurrently with ONT MinKNOW sequencing to provide real-time visualisation of read mapping, coverage, and reference matching to the HXB2 genome for each barcode. The RAMPART configuration protocol is available at https://github.com/AnyaKovalenko/rampart-protocol-HIV-1_partial-pol For reference-based consensus generation, align reads to the HXB2 reference genome (GenBank accession: K03455.1 ), or specifically to the pol region (coordinates: 2030–3400), using Minimap2, followed by polishing with Racon and Medaka. Please cite the associated publications when using or adapting this workflow.