BACKGROUND: Artemether-lumefantrine (AL) and artesunate-amodiaquine (AS-AQ) are the first-line treatments against malaria in Mozambique. Dihydroartemisinin-piperaquine (DP) has been used in-country for mass drug administration campaigns, and artesunate-pyronaridine (AS-PY) is considered an alternative drug to delay AL resistance in the country. To assess whether AL and AS-AQ remain efficacious and to confirm that DP and AS-PY are potential alternatives for uncomplicated malaria treatment, an in vivo therapeutic efficacy study was conducted in Mozambique at five sentinel sites. METHODS: This study was conducted in the districts of Montepuez (AL), Dondo (AL and AS-AQ), Mopeia (AL and AS-PY), Moatize (AL and AS-AQ), and Massinga (AL and DP) following the 2009 World Health Organization (WHO)-recommended protocol. Patients aged 6 months to 11 years with uncomplicated Plasmodium falciparum malaria (1000-200,000 parasites/µl) were enrolled, followed, and assessed for 28 days (AL and AS-AQ) or 42 days (DP and AS-PY). Genotyping for msp1/msp2/poly-α markers and match counting via the WHO/Medicines for Malaria Venture (MMV) 3/3 algorithm were used to differentiate recrudescences from new infections. The primary outcome was polymerase chain reaction corrected efficacy for each drug. RESULTS: In total, 828 participants were enrolled in the four study arms: AL (462), AS-AQ (183), DP (91), and AS-PY (92). Among the recruited participants, 10.2% (85/828) were lost to follow-up or withdrew, and 60 had recurrent malaria infections, 55 of which were considered new infections and five recrudescences. Day 28 corrected AL efficacy was 100% (95% CI 94.3-100) in Massinga, 100% in Dondo, 100% (95% CI 95.5-100) in Moatize, 97.63% (95% CI 94.4-100) in Mopeia, and 98.68% (95% CI 96.2-100) in Montepuez. Day 28 corrected AS-AQ efficacy was 100% in Dondo and 100% (95% CI 95.4-100) in Moatize. For DP, the corrected efficacy on day 42 was 100% (95% CI 94.1-100) in Massinga, and that on day 42 was 97.75% (95% CI 94.7-100) in Mopeia. All drugs were well tolerated, with adverse events reported in less than 2% of the participants. CONCLUSION: AL and AS-AQ remain effective, as their efficacy remained above the 90% WHO-recommended cut-off. DP and AS-PY also showed therapeutic efficacy above the WHO-acceptable cut-off and could be used as first-line treatments when needed. All four artemisinin-based combinations were well tolerated, with minimal safety concerns. TRIAL REGISTRATION: Clinicaltrials.gov: NCT05343312.

BACKGROUND: Despite the availability of highly effective HIV pre-exposure prophylaxis (PrEP), uptake and adherence to PrEP among young men who have sex with men (YMSM) remains low, limiting its impact on the prevention of HIV infection. Strategies that incorporate an array of prevention options and provide YMSM and their providers with tailored education and support tools, including tools to support shared decision-making, are needed. OBJECTIVE: The goals of the Centers for Disease Control and Prevention (CDC)-funded PrEP Choice study include the development and deployment of CDC guideline-consistent PrEP provider training and the implementation of evidence-based provider- and client-facing PrEP education and support tools. Under this initiative, the CDC funded 2 research projects, Florida State University (the Expanding PrEP in Communities of Color [EPICC] project), and Columbia University (the mChoice project). METHODS: Providers from both projects will complete the PrEP Choice online training, which was developed to educate providers on PrEP options and how to engage clients in open discussions around sexual health and PrEP options. EPICC project providers will also attend online tailored motivational interviewing (TMI) training sessions, and mChoice project providers will view a training video on cultural competency and humility in PrEP care. Following training, each project will enroll a cohort of 400 participants receiving care from study providers and follow them for 12-18 months. Participants will complete online surveys every 3 months and provide biomarkers to assess PrEP adherence. Electronic health record (EHR) data will be collected every 6 months to provide additional information on clinic attendance, PrEP prescriptions, and HIV/sexually transmitted infection (STI) testing. Each project will provide cohort participants with a unique digital health tool to support the PrEP choice and ongoing adherence. The study will assess the effectiveness of training and educational and support tools in practice and the critical factors associated with the successful uptake of and adherence to PrEP by participants. The study will also monitor patterns of PrEP use among YMSM, including types of PrEP and switching between types. RESULTS: Formative work to develop and prepare the tools for implementation was completed in 2023. The EPICC project began provider training in early 2024, and the mChoice project began in spring 2024. Cohort enrollment for both projects began after provider training began. CONCLUSIONS: Given the changing PrEP landscape, implementation of provider education and tools to maximize uptake and adherence is needed. By delivering culturally competent and interactive provider training on PrEP options, the study will help providers counsel and guide participants on the effective and safe use of PrEP. The digital health tools created will support participant adherence to help them optimize PrEP benefits. Through the cohort design, the PrEP Choice study will provide real-world data about PrEP use that will be critical for informing future guidelines and tools. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/64186.

There is a pressing need for innovative strategies to control arboviruses transmitted by Aedes aegypti. The modification of indoor residual spraying to target Ae. aegypti is one such strategy. A clinical trial quantifying the epidemiologic impact of targeted indoor residual spraying for Ae. aegypti control used a product with pirimiphos-methyl as the active ingredient in the city of Mérida, Mexico. To monitor the susceptibility of local Ae. aegypti populations over the course of the trial, we calculated a diagnostic dose for pirimiphos-methyl using the Centers for Disease Control and Prevention bottle assay. Two independent laboratories tested a series of 8 concentrations of pirimiphos-methyl, eliciting a range of mortality between 0% and 100% in an insecticide-susceptible reference strain of Ae. aegypti. The results suggested a diagnostic dose of 25 μg/ml at a diagnostic time of 30 min. This diagnostic dose of pirimiphos-methyl was used to monitor pirimphos-methyl susceptibility in Ae. aegypti throughout the trial.

Medically important pathogenic fungi invade vertebrate tissue and are considered primary when part of their nature life cycle is associated with an animal host and are usually able to infect immunocompetent hosts. Opportunistic fungal pathogens complete their life cycle in environmental habitats or occur as commensals within or on the vertebrate body, but under certain conditions can thrive upon infecting humans. The extent of host damage in opportunistic infections largely depends on the portal and modality of entry as well as on the host's immune and metabolic status. Diseases caused by primary pathogens and common opportunists, causing the top approximately 80% of fungal diseases [D. W. Denning, Lancet Infect Dis, 24:e428-e438, 2024, https://doi.org/10.1016/S1473-3099(23)00692-8], tend to follow a predictive pattern, while those by occasional opportunists are more variable. For this reason, it is recommended that diseases caused by primary pathogens and the common opportunists are named after the etiologic agent, for example, histoplasmosis and aspergillosis, while this should not be done for occasional opportunists that should be named as [causative fungus] [clinical syndrome], for example, Alternaria alternata cutaneous infection. The addition of a descriptor that identifies the location or clinical type of infection is required, as the general name alone may cover widely different clinical syndromes, for example, "rhinocerebral mucormycosis." A list of major recommended human and animal disease entities (nomenclature) is provided in alignment with their causative agents. Fungal disease names may encompass several genera of etiologic agents, consequently being less susceptible to taxonomic changes of the causative species, for example, mucormycosis covers numerous mucormycetous molds.

OBJECTIVES: To describe sudden unexpected infant deaths (SUIDs) occurring in safe sleep environments and explore differences in selected characteristics. METHODS: We examined SUID from 22 jurisdictions from 2011 to 2020 and classified them as unexplained, no unsafe sleep factors (U-NUSF). Data were derived from the Sudden Unexpected Infant Death and Sudden Death in the Young Case Registry, a population-based Centers for Disease Control and Prevention surveillance system built on the National Center for Fatality Review and Prevention's child death review program. SUID classified as U-NUSF included infants who were (1) awake, under supervision, and witnessed to become unresponsive or (2) found unresponsive in a safe sleep environment after sleep (unwitnessed). We calculated frequencies and percentages for demographics, birth and environmental characteristics, medical history, and death investigation findings. RESULTS: Most of the 117 U-NUSF SUID occurred before 4 months of age. Witnessed deaths most commonly occurred at <1 month of age (28%), whereas unwitnessed deaths most commonly occurred at ages 2 to 3 months (44%) Among all U-NUSF, 69% occurred in the infant's home (62% witnessed, 77% unwitnessed). All unwitnessed deaths occurred in a crib; most witnessed deaths occurred while being held (54%) or in a car seat traveling (18%). Most infants (84%) had no history of abuse or neglect. Abnormal autopsy findings were reported in 46% of deaths (49% witnessed, 42% unwitnessed). CONCLUSIONS: Characterizing these deaths is key to advancing our knowledge of SUID etiology. Our study revealed a heterogeneous group of infants, suggesting physiologic, genetic, or environmental etiologies.

Aedes mosquito-borne viruses (ABVs) place a substantial strain on public health resources in the Americas. Vector control of Aedes mosquitoes is an important public health strategy to decrease or prevent spread of ABVs. The ongoing Targeted Indoor Residual Spraying (TIRS) trial is an NIH-sponsored clinical trial to study the efficacy of a novel, proactive vector control technique to prevent dengue virus (DENV), Zika virus (ZIKV), and chikungunya virus (CHIKV) infections in the endemic city of Merida, Yucatan, Mexico. The primary outcome of the trial is laboratory-confirmed ABV infections in neighborhood clusters. Despite the difficulties caused by the COVID-19 pandemic, by early 2021 the TIRS trial completed enrollment of 4,792 children aged 2-15 years in 50 neighborhood clusters which were allocated to control or intervention arms via a covariate-constrained randomization algorithm. Here, we describe the makeup and ABV seroprevalence of participants and mosquito population characteristics in both arms before TIRS administration. Baseline surveys showed similar distribution of age, sex, and socio-economic factors between the arms. Serum samples from 1,399 children were tested by commercially available ELISAs for presence of anti-ABV antibodies. We found that 45.1% of children were seropositive for one or more flaviviruses and 24.0% were seropositive for CHIKV. Of the flavivirus-positive participants, most were positive for ZIKV-neutralizing antibodies by focus reduction neutralization testing which indicated a higher proportion of participants with previous ZIKV than DENV infections within the cohort. Both study arms had statistically similar seroprevalence for all viruses tested, similar socio-demographic compositions, similar levels of Ae. aegypti infestation, and similar observed mosquito susceptibility to insecticides. These findings describe a population with a high rate of previous exposure to ZIKV and lower titers of neutralizing antibodies against DENV serotypes, suggesting susceptibility to future outbreaks of flaviviruses is possible, but proactive vector control may mitigate these risks.

The Global Specialized Polio Laboratory at CDC supports the Global Poliovirus Laboratory Network with environmental surveillance (ES) to detect the presence of vaccine strain polioviruses, vaccine-derived polioviruses, and wild polioviruses in high-risk countries. Environmental sampling provides valuable supplementary information, particularly in areas with gaps in surveillance of acute flaccid paralysis (AFP) mainly in children less than 15 years. In collaboration with Guatemala's National Health Laboratory (Laboratorio Nacional de Salud Guatemala), monthly sewage collections allowed screening enterovirus (EV) presence without incurring additional costs for sample collection, transport, or concentration. Murine recombinant fibroblast L-cells (L20B) and human rhabdomyosarcoma (RD) cells are used for the isolation of polioviruses following a standard detection algorithm. Though non-polio-Enteroviruses (NPEV) can be isolated, the algorithm is optimized for the detection of polioviruses. To explore if other EV's are present in sewage not found through standard methods, five additional cell lines were piloted in a small-scale experiment, and next-generation sequencing (NGS) was used for the identification of any EV types. Human lung fibroblast cells (HLF) were selected based on their ability to isolate EV-A genus. Sewage concentrates collected between 2020-2021 were isolated in HLF cells and any cytopathic effect positive isolates used for NGS. A large variety of EVs, including echoviruses 1, 3, 6, 7, 11, 13, 18, 19, 25, 29; coxsackievirus A13, B2, and B5, EV-C99, EVB, and polioviruses (Sabin 1 and 3) were identified through genomic typing in NGS. When the EV genotypes were compared by phylogenetic analysis, it showed many EV's were genomically like viruses previously isolated from ES collected in Haiti. Enterovirus occurrence did not follow a seasonality, but more diverse EV types were found in ES collection sites with lower populations. Using the additional cell line in the existing poliovirus ES algorithm may add value by providing data about EV circulation, without additional sample collection or processing. Next-generation sequencing closed gaps in knowledge providing molecular epidemiological information on multiple EV types and full genome sequences of EVs present in wastewater in Guatemala.

BACKGROUND: Mexico has experienced a significant reduction in malaria cases over the past two decades. Certification of localities as malaria-free areas (MFAs) has been proposed as a steppingstone before elimination is achieved throughout the country. The Mexican state of Quintana Roo is a candidate for MFA certification. Monitoring the status of insecticide susceptibility of major vectors is crucial for MFA certification. This study describes the susceptibility status of Anopheles albimanus, main malaria vector, from historically important malaria foci in Quintana Roo, using both phenotypic and genotypic approaches. METHODS: Adult mosquito collections were carried out at three localities: Palmar (Municipality of Othon P. Blanco), Buenavista (Bacalar) and Puerto Morelos (Puerto Morelos). Outdoor human-landing catches were performed by pairs of trained staff from 18:00 to 22:00 during 3-night periods at each locality during the rainy season of 2022. Wild-caught female mosquitoes were exposed to diagnostic doses of deltamethrin, permethrin, malathion, pirimiphos-methyl or bendiocarb using CDC bottle bioassays. Mortality was registered at the diagnostic time and recovery was assessed 24 h after exposure. Molecular analyses targeting the Voltage-Gated Sodium Channel (vgsc) gene and acetylcholinesterase (ace-1) gene were used to screen for target site polymorphisms. An SNP analysis was carried out to identify mutations at position 995 in the vgsc gene and at position 280 in the ace-1 gene. RESULTS: A total of 2828 anophelines were collected. The main species identified were Anopheles albimanus (82%) and Anopheles vestitipennis (16%). Mortalities in the CDC bottle bioassay ranged from 99% to 100% for all the insecticides and mosquito species. Sequence analysis was performed on 35 An. albimanus across the three localities; of those, 25 were analysed for vgsc and 10 for ace-1 mutations. All individuals showed wild type alleles. CONCLUSION: The results demonstrated that An. albimanus populations from historical malaria foci in Quintana Roo are susceptible to the main insecticides used by the Ministry of Health.

INTRODUCTION: In the USA each year, there are approximately 3400 sudden unexpected infant (<1 year of age) deaths (SUID) which occur without an obvious cause before an investigation. SUID includes the causes of death (COD) undetermined/unknown, sleep-related suffocation/asphyxia and sudden infant death syndrome (SIDS); these are often called SUID subtypes. Three common ways SUID subtypes are grouped (SUID subtype groups) include International Classification of Diseases (ICD) Codes, SUID Case Registry Categories or Child Death Review (CDR)-Assigned Causes. These groups are often used to monitor SUID trends and characteristics at the local, state and national levels. We describe and compare the characteristics of these three SUID subtype groups. DISCUSSION: SUID subtype groups are distinct and not directly interchangeable. They vary in purpose, strengths, limitations, uses, history, data years available, population coverage, assigning entity, guidance documentation and information available to assign subtypes. CONCLUSION: Making informed decisions about which SUID subtype group to use is important for reporting statistics, increasing knowledge of SUID epidemiology and informing prevention strategies.

OBJECTIVES: Describe characteristics of sudden unexpected infant deaths (SUID) occurring on shared or nonshared sleep surfaces. METHODS: We examined SUID among residents of 23 US jurisdictions who died during 2011 to 2020. We calculated frequencies and percentages of demographic, sleep environment, and other characteristics by sleep surface sharing status and reported differences of at least 5% between surface sharing and nonsharing infants. RESULTS: Of 7595 SUID cases, 59.5% were sleep surface sharing when they died. Compared with nonsharing infants, sharing infants were more often aged 0 to 3 months, non-Hispanic Black, publicly insured, found supine, found in an adult bed or chair/couch, had a higher number of unsafe sleep factors present, were exposed to maternal cigarette smoking prenatally, were supervised by a parent at the time of death, or had a supervisor who was impaired by drugs or alcohol at the time of death. At least 76% of all SUID had multiple unsafe sleep factors present. Among surface-sharing SUID, most were sharing with adults only (68.2%), in an adult bed (75.9%), and with 1 other person (51.6%). Surface sharing was more common among multiples than singletons. CONCLUSIONS: Among SUID, surface sharing and nonsharing infants varied by age at death, race and ethnicity, insurance type, presence of unsafe sleep factors, prenatal smoke exposure, and supervisor impairment. Most SUID, regardless of sleep location, had multiple unsafe sleep factors present, demonstrating the need for comprehensive safe sleep counseling for every family at every encounter.

Vaginal inserts that can be used on demand before or after sex may be a desirable HIV prevention option for women. We recently showed that inserts containing tenofovir alafenamide fumarate (TAF/20mg) and elvitegravir (EVG/16mg) were highly protective against repeated SHIV vaginal exposures when administered to macaques 4h before or after virus exposure (93% and 100%, respectively). Here, we show in the same macaque model that insert application 8h or 24h after exposure maintains high efficacy (94.4% and 77.2%, respectively). These data extend the protective window by TAF/EVG inserts and inform their clinical development for on-demand prophylaxis in women.

Farmed mink are one of few animals in which infection with SARS-CoV-2 has resulted in sustained transmission among a population and spillback from mink to people. In September 2020, mink on a Michigan farm exhibited increased morbidity and mortality rates due to confirmed SARS-CoV-2 infection. We conducted an epidemiologic investigation to identify the source of initial mink exposure, assess the degree of spread within the facility's overall mink population, and evaluate the risk of further viral spread on the farm and in surrounding wildlife habitats. Three farm employees reported symptoms consistent with COVID-19 the same day that increased mortality rates were observed among the mink herd. One of these individuals, and another asymptomatic employee, tested positive for SARS-CoV-2 by real-time reverse transcription PCR (RT-qPCR) 9 days later. All but one mink sampled on the farm were positive for SARS-CoV-2 based on nucleic acid detection from at least one oral, nasal, or rectal swab tested by RT-qPCR (99%). Sequence analysis showed high degrees of similarity between sequences from mink and the two positive farm employees. Epidemiologic and genomic data, including the presence of F486L and N501T mutations believed to arise through mink adaptation, support the hypothesis that the two employees with SARS-CoV-2 nucleic acid detection contracted COVID-19 from mink. However, the specific source of virus introduction onto the farm was not identified. Three companion animals living with mink farm employees and 31 wild animals of six species sampled in the surrounding area were negative for SARS-CoV-2 by RT-qPCR. Results from this investigation support the necessity of a One Health approach to manage the zoonotic spread of SARS-CoV-2 and underscores the critical need for multifaceted public health approaches to prevent the introduction and spread of respiratory viruses on mink farms.

Anopheles stephensi is a major vector of malaria in Asia and the Arabian Peninsula, and its recent invasion into Africa poses a major threat to malaria control and elimination efforts on the continent. The mosquito is well adapted to urban environments, and its presence in Africa could potentially lead to an increase in malaria transmission in cities. Most of the knowledge about An stephensi ecology in Africa has been generated from studies conducted during the rainy season, when vectors are most abundant. Here, we provide evidence from the peak of the dry season in the city of Jigjiga in Ethiopia, and report An stephensi immature stages infesting predominantly in water reservoirs made to support construction operations (ie, in construction sites or associated with brick-manufacturing businesses). Political and economic changes in Ethiopia (particularly the Somali Region) have fuelled an unprecedented construction boom since 2018 that, in our opinion, has been instrumental in the establishment, persistence, and propagation of An stephensi via the year-round availability of perennial larval habitats associated with construction. We argue that larval source management during the dry season might provide a unique opportunity for focused control of An stephensi in Jigjiga and similar areas.

During the COVID-19 pandemic, many public schools across the United States shifted from fully in-person learning to alternative learning modalities such as hybrid and fully remote learning. In this study, data from 14,688 unique school districts from August 2020 to June 2021 were collected to track changes in the proportion of schools offering fully in-person, hybrid and fully remote learning over time. These data were provided by Burbio, MCH Strategic Data, the American Enterprise Institute's Return to Learn Tracker and individual state dashboards. Because the modalities reported by these sources were incomplete and occasionally misaligned, a model was needed to combine and deconflict these data to provide a more comprehensive description of modalities nationwide. A hidden Markov model (HMM) was used to infer the most likely learning modality for each district on a weekly basis. This method yielded higher spatiotemporal coverage than any individual data source and higher agreement with three of the four data sources than any other single source. The model output revealed that the percentage of districts offering fully in-person learning rose from 40.3% in September 2020 to 54.7% in June of 2021 with increases across 45 states and in both urban and rural districts. This type of probabilistic model can serve as a tool for fusion of incomplete and contradictory data sources in order to obtain more reliable data in support of public health surveillance and research efforts.

Guatemala implemented wastewater-based poliovirus surveillance in 2018, and three genetically unrelated vaccine-derived polioviruses (VDPVs) were detected in 2019. The Ministry of Health (MoH) response included event investigation through institutional and community retrospective case searches for acute flaccid paralysis (AFP) during 2018-2020 and a bivalent oral polio/measles, mumps, and rubella vaccination campaign in September 2019. This response was reviewed by an international expert team in July 2021. During the campaign, 93% of children 6 months <7 years of age received a polio-containing vaccine dose. No AFP cases were detected in the community search; institutional retrospective searches found 37% of unreported AFP cases in 2018‒2020. No additional VDPV was isolated from wastewater. No evidence of circulating VDPV was found; the 3 isolated VDPVs were classified as ambiguous VDPVs by the international team of experts. These detections highlight risk for poliomyelitis reemergence in countries with low polio vaccine coverage.

OBJECTIVE: From May 2016 through September 2017, the Zika Contraception Access Network (Z-CAN) program increased access to contraception during the Zika virus outbreak in Puerto Rico by providing no-cost client-centered contraceptive counseling and (same-day) access to the full range of US Food and Drug Administration-approved reversible contraceptives to women desirous of not becoming pregnant. The purpose of this study was to identify areas for programmatic improvement and enhance the sustainability of services from the perspectives of participating Z-CAN physicians and other staff. METHODS: From April through July 2017, 49 in-depth key-informant interviews were conducted with Z-CAN physicians and clinic staff. Twenty-five clinics participating in the Z-CAN program were selected through a cluster randomization process. A semi-structured interview guide was developed to explore the participants' perceptions of the Z-CAN program and examine facilitators of and barriers to said implementation. A thematic analysis of the emerging topics was conducted. RESULTS: Our analysis encountered 4 common overarching themes: facilitators of the Z-CAN program; barriers to Z-CAN implementation; the perceived impact of Z-CAN on providers and communities; and the sustainability of contraception access after the Z-CAN program ended. The key findings were that provider training, mentor support, and communication campaigns facilitated program implementation and that delays in the acquisition and distribution of contraceptives were obstacles. CONCLUSION: Lessons learned from the implementation of Z-CAN from the perspective of physicians and other staff can be used to work towards sustainable contraceptive services in Puerto Rico and inform other contraception-access programs' design and implementation strategies.

In the past decade, distributed acoustic sensing (DAS) has enabled many new monitoring applications in diverse fields including hydrocarbon exploration and extraction; induced, local, regional, and global seismology; infrastructure and urban monitoring; and several others. However, to date, the open-source software ecosystem for handling DAS data is relatively immature. Here we introduce DASCore, a Python library for analyzing, visualizing, and managing DAS data. DASCore implements an object-oriented interface for performing common data processing and transformations, reading and writing various DAS file types, creating simple visualizations, and managing file system-based DAS archives. DASCore also integrates with other Python-based tools which enable the processing of massive data sets in cloud environments. DASCore is the foundational package for the broader DAS data analysis ecosystem (DASDAE), and as such its main goal is to facilitate the development of other DAS libraries and applications.

Anopheles stephensi is a major vector of malaria in Asia and the Arabian Peninsula, and its recent invasion into Africa poses a significant threat to malaria control and elimination efforts on the continent. The mosquito is well-adapted to urban environments, and its presence in Africa could potentially lead to an increase in malaria transmission in cities. Most of the knowledge about An. stephensi ecology in Africa has been generated from studies conducted during the rainy season, when vectors are most abundant. Here, we provide evidence from the peak of the dry season in the city of Jigjiga, Ethiopia, and report the finding of An. stephensi immature stages infesting predominantly water reservoirs made to support construction operations (in construction sites or associated with brick manufacturing businesses). Political and economic changes in Ethiopia (and particularly the Somali Region) have fueled an unprecedented construction boom since 2018 that, in our opinion, has been instrumental in the establishment, persistence and propagation of An. stephensi via the year-round availability of perennial larval habitats associated with construction. We argue that larval source management during the dry season may provide a unique opportunity for focused control of An. stephensi in Jigjiga and similar areas. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.

As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.

Monkeypox is a viral zoonotic disease endemic in Central and West Africa. In May 2022, dozens of non-endemic countries reported hundreds of monkeypox cases, most with no epidemiological link to Africa. We identified two lineages of Monkeypox virus (MPXV) among nine 2021 and 2022 U.S. monkeypox cases. A 2021 case was highly similar to the 2022 MPXV outbreak variant, suggesting a common ancestor. Analysis of mutations among these two lineages revealed an extreme preference for GA-to-AA mutations indicative of APOBEC3 cytosine deaminase activity that was shared among West African MPXV since 2017 but absent from Congo Basin lineages. Poxviruses are not thought to be subject to APOBEC3 editing; however, these findings suggest APOBEC3 activity has been recurrent and dominant in recent West African MPXV evolution. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.

Genomic surveillance of monkeypox virus (MPXV) during the 2022 outbreak has been mainly focused on single nucleotide polymorphism (SNP) changes. DNA viruses, including MPXV, have a lower SNP mutation rate than RNA viruses due to higher fidelity replication machinery. We identified a large genomic rearrangement in a MPXV sequence from a 2022 case in the state of Minnesota (MN), USA, from an abnormal, uneven MPXV read mapping coverage profile in whole-genome sequencing (WGS) data. We further screened WGS data of 206 U.S. MPXV samples and found seven (3.4 percent) sequenced genomes contained similar abnormal read coverage profiles that suggested putative large deletions or genomic rearrangements. Here, we present three MPXV genomes containing deletions ranging from 2.3 to 15 kb and four genomes containing more complex rearrangements. Five genomic changes were each only seen in one sample, but two sequences from linked cases shared an identical 2.3 kb deletion in the 3' terminal region. All samples were positive using VAC1 and Clade II (formerly West African)-specific MPXV diagnostic tests; however, large deletions and genomic rearrangements like the ones reported here have the potential to result in viruses in which the target of a PCR diagnostic test is deleted. The emergence of genomic rearrangements during the outbreak may have public health implications and highlight the importance of continued genomic surveillance. Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license.

The Costa Rican pygmy rice rat (Oligoryzomys costaricensis) is the primary reservoir of Choclo orthohantavirus (CHOV), the causal agent of hantavirus disease, pulmonary syndrome, and fever in humans in Panama. Since the emergence of CHOV in early 2000, we have systematically sampled and archived rodents from >150 sites across Panama to establish a baseline understanding of the host and virus, producing a permanent archive of holistic specimens that we are now probing in greater detail. We summarize these collections and explore preliminary habitat/virus associations to guide future wildlife surveillance and public health efforts related to CHOV and other zoonotic pathogens. Host sequences of the mitochondrial cytochrome b gene form a single monophyletic clade in Panama, despite wide distribution across Panama. Seropositive samples were concentrated in the central region of western Panama, consistent with the ecology of this agricultural commensal and the higher incidence of CHOV in humans in that region. Hantavirus seroprevalence in the pygmy rice rat was >15% overall, with the highest prevalence in agricultural areas (21%) and the lowest prevalence in shrublands (11%). Host-pathogen distribution, transmission dynamics, genomic evolution, and habitat affinities can be derived from the preserved samples, which include frozen tissues, and now provide a foundation for expanded investigations of orthohantaviruses in Panama.

Updated (bivalent) COVID-19 vaccines were first recommended by CDC on September 1, 2022.* An analysis of case and death rates by vaccination status shortly after authorization of bivalent COVID-19 vaccines showed that receipt of a bivalent booster dose provided additional protection against SARS-CoV-2 infection and associated death (1). In this follow-up report on the durability of bivalent booster protection against death among adults aged ≥65 years, mortality rate ratios (RRs) were estimated among unvaccinated persons and those who received a bivalent booster dose by time since vaccination during three periods of Omicron lineage predominance (BA.5 [September 18–November 5, 2022], BQ.1/BQ.1.1 [November 6, 2022–January 21, 2023], and XBB.1.5 [January 22–April 1, 2023]).† | | During September 18, 2022–April 1, 2023, weekly counts of COVID-19–associated deaths§ among unvaccinated persons and those who received a bivalent booster dose¶ were reported from 20 U.S. jurisdictions** that routinely link case surveillance data to immunization registries and vital registration databases (1). Vaccinated persons who did not receive a bivalent COVID-19 booster dose were excluded. Rate denominators were calculated from vaccine administration data and 2019 U.S. intercensal population estimates,†† with numbers of unvaccinated persons estimated by subtracting numbers of vaccinated persons from the 2019 intercensal population estimates, as previously described§§ (1). Average weekly mortality rates were estimated based on date of specimen collection¶¶ during each variant period by vaccination status and time since bivalent booster dose receipt. RRs were calculated by dividing rates among unvaccinated persons by rates among bivalent booster dose recipients; after detrending the underlying linear changes in weekly rates, 95% CIs were estimated from the remaining variation in rates observed*** (1). SAS (version 9.4; SAS Institute) and R (version 4.1.2; R Foundation) software were used to conduct all analyses. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.†††

BACKGROUND: Observational studies have improved our understanding of the risk factors for sudden infant death syndrome, but separate examination of risk for sleep-related suffocation and unexplained infant deaths has been limited. We examined the association between unsafe infant sleep practices and sudden infant deaths (sleep-related suffocation and unexplained causes including sudden infant death syndrome). METHODS: We conducted a population-based case-control study using 2016 to 2017 Centers for Disease Control and Prevention data. Controls were liveborn infants from the Pregnancy Risk Assessment Monitoring System; cases were from the Sudden Unexpected Infant Death Case Registry. We calculated risk factor prevalence among cases and controls and crude and adjusted odds ratios. RESULTS: We included 112 sleep-related suffocation cases with 448 age-matched controls and 300 unexplained infant death cases with 1200 age-matched controls. Adjusted odds for sleep-related suffocation ranged from 18.7 (95% confidence interval [CI]: 6.8-51.3) among infants not sharing a room with their mother or caregiver to 1.9 (95% CI: 0.9-4.1) among infants with nonsupine sleep positioning. Adjusted odds for unexplained death ranged from 7.6 (95% CI: 4.7-12.2) among infants not sharing a room with their mother or caregiver to 1.6 (95% CI: 1.1-2.4) among nonsupine positioned infants. COCLUSIONS: We confirmed previously identified risk factors for unexplained infant death and independently estimated risk factors for sleep-related suffocation. Significance of associations for suffocation followed similar patterns but was of larger magnitude. This information can be used to improve messaging about safe infant sleep.

Bass et al show that SUID differs by age at death. Understanding factors related to age differences informs interventions. SUID rarely occurs in the neonatal period. Of the 4 million US births in 2015, SUID accounted for 108 deaths at 0–6 days and 314 deaths at 7–27 days. Fifty-one deaths were sudden unexpected postnatal collapse (SUPC), born >35 weeks’ gestation, 10-minute APGAR >7, died before 7 days(1). The higher SUID rates in infants 7–27 days compared to infants 0–7 days likely reflect different underlying etiologies. The Centers for Disease Control and Prevention’s SUID Case Registry (2) program works with child death review teams to better document the burden of SUID. Review teams are uniquely positioned to evaluate information about SUID, including SUPC in their jurisdictions. Teams review environmental and clinical factors from scene investigation, autopsy, and medical records for all SUID. Dissemination of review findings and recommendations assists jurisdictions in developing programs to improve infant health and well-being. Review teams collaborate with healthcare providers and parent education programs to encourage uptake of infant safe sleep recommendations (3). Ongoing surveillance of SUID rates by age at death is important to evaluate the impact of infant care interventions, identify new risk factors, and track progress towards reducing SUID mortality.

BACKGROUND: People with a maternal substance use disorder (SUD) may experience a lack of access to necessary healthcare and more specifically, postpartum healthcare. It is not known whether increased insurance coverage introduced by Medicaid expansion has improved postpartum healthcare utilization among this population. METHODS: Oregon 2008-2016 birth certificates and Medicaid claims were used to examine whether continuous insurance enrollment and postpartum healthcare utilization increased post-Medicaid expansion in a population with and without SUD (n = 9,337). International Classification of Diseases codes were used to identify deliveries, SUD, and postpartum healthcare. Univariable and multivariable generalized linear regression with standard errors clustered by individual were used to estimate the association between Medicaid expansion and postpartum healthcare utilization, stratified by maternal SUD. RESULTS: Among the 10.3% with SUD, expansion was not associated with increased continuous enrollment or postpartum healthcare utilization. Among those without SUD, post-expansion deliveries were associated with increased continuous enrollment (+105.0 days; 95% CI=96.9-113.2), total (+4.4; 95% CI=2.9-6.0), postpartum (+0.3; 95% CI=0.2-0.4), inpatient (+0.9; 95% CI=0.7-1.1), outpatient (+2.3; 95% CI=1.4-3.3), office (+0.9; 95% CI=0.2-1.6), and emergency department (+0.3; 95% CI=0.1-0.5) visits. Among deliveries to postpartum people with SUD, 27.2% had opioid use disorder (OUD); expansion was associated with increased OUD medication use (12.0% vs 18.3%) and number of fills (6.7 vs 16.6). CONCLUSIONS: Medicaid expansion in Oregon was only associated with increased Medicaid-financed healthcare utilization for postpartum people without SUD, with the exception of those with OUD, demonstrating the need for assessing various strategies to improve postpartum healthcare utilization.

BACKGROUND: Household food insecurity is associated with poor dietary intake in the general population, but little is known about this association in persons with diabetes. OBJECTIVE: We examined the degree of adherence to the dietary reference intakes and 2020-2025 Dietary Guidelines for Americans overall and according to food security status and diabetes type among youth and young adults (YYA) with youth-onset diabetes. DESIGN: /Participants/Setting: The SEARCH for Diabetes in Youth study includes 1,197 YYA with type 1 diabetes (T1D, mean age: 21 years ± 5) and 319 YYA with type 2 diabetes (T2D, 25 years ± 4). Participants (or parents if <18 years) completed the USDA Household Food Security Survey Module, wherein ≥3 affirmations indicate food insecurity. MAIN OUTCOME MEASURES: Diet was assessed via food frequency questionnaire and compared to age- and sex-specific dietary reference intakes for 10 nutrients and dietary components (calcium, fiber, magnesium, potassium, sodium, vitamins C, D, E, added sugar, saturated fat). STATISTICAL ANALYSES PERFORMED: Median regression models controlled for sex- and type-specific means for age, diabetes duration, and daily energy intake. RESULTS: Prevalence of guideline adherence was overarchingly poor, with <40% of participants meeting recommendations for 8 of 10 nutrients and dietary components; however, higher adherence (>47%) was observed for vitamin C and added sugars. YYA with T1D who were food insecure were more likely to meet recommendations for calcium, magnesium, and vitamin E (p<0.05), and less likely for sodium (p<0.05) than those food secure. In adjusted models, YYA with T1D who were food secure had closer median adherence to sodium (p=0.002) and fiber (p=0.042) guidelines than those food insecure. No associations were observed in YYA with T2D. CONCLUSIONS: Food insecurity is associated with lesser adherence to fiber and sodium guidelines in YYA with T1D, which may lead to diabetes complications, and other chronic diseases.

OBJECTIVE: Although the US infant mortality rate reached a record low in 2020, the sudden infant death syndrome (SIDS) rate increased from 2019. To understand if the increase was related to changing death certification practices or the coronavirus disease 2019 (COVID-19) pandemic, we examined sudden unexpected infant death (SUID) rates as a group, by cause, and by race and ethnicity. METHODS: We estimated SUID rates during 2015 to 2020 using US period-linked birth and death data. SUID included SIDS, unknown cause, and accidental suffocation and strangulation in bed. We examined changes in rates from 2019 to 2020 and assessed linear trends during prepandemic (2015-2019) using weighted least squares regression. We also assessed race and ethnicity trends and quantified COVID-19-related SUID. RESULTS: Although the SIDS rate increased significantly from 2019 to 2020 (P < .001), the overall SUID rate did not (P = .24). The increased SIDS rate followed a declining linear trend in SIDS during 2015 to 2019 (P < .001). Other SUID causes did not change significantly. Our race and ethnicity analysis showed SUID rates increased significantly for non-Hispanic Black infants from 2019 to 2020, widening the disparities between these two groups during 2017 to 2019. In 2020, <10 of the 3328 SUID had a COVID-19 code. CONCLUSIONS: Diagnositic shifting likely explained the increased SIDS rate in 2020. Why the SUID rate increased for non-Hispanic Black infants is unknown, but warrants continued monitoring. Interventions are needed to address persistent racial and ethnic disparities in SUID.

We report healthcare provider attitudes and practices on emergency preparedness counseling for women of reproductive age (WRA), including pregnant, postpartum, and lactating women (PPLW), for disasters and weather emergencies. DocStyles is a web-based panel survey of primary healthcare providers in the United States. During March 17-May 17, 2021, obstetricians-gynecologists, family practitioners, internists, nurse practitioners, and physician assistants were asked about the importance of emergency preparedness counseling, level of confidence, frequency, barriers to providing counseling, and preferred resources to support counseling among WRA and PPLW. We calculated frequencies of provider attitudes and practices, and prevalence ratios with 95% CIs for questions with binary responses. Among 1503 respondents (family practitioners (33%), internists (34%), obstetrician-gynecologists (17%), nurse practitioners (8%), and physician assistants (8%)), 77% thought emergency preparedness was important, and 88% thought counseling was necessary for patient health and safety. However, 45% of respondents did not feel confident providing emergency preparedness counseling, and most (70%) had never talked to PPLW about this topic. Respondents cited not having time during clinical visits (48%) and lack of knowledge (34%) as barriers to providing counseling. Most respondents (79%) stated they would use emergency preparedness educational materials for WRA, and 60% said they were willing to take an emergency preparedness training. Healthcare providers have opportunities to provide emergency preparedness counseling; however, many have not, noting lack of time and knowledge as barriers. Emergency preparedness resources combined with training may improve healthcare provider confidence and increase delivery of emergency preparedness counseling.