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Households are a significant source of SARS-CoV-2 transmission, even during periods of low community-level spread. Comparing household transmission rates by SARS-CoV-2 variant may provide relevant information about current risks and prevention strategies. This investigation aimed to estimate differences in household transmission risk comparing the SARS-CoV-2 Delta and Omicron variants using data from contact tracing and interviews conducted from November 2021 through February 2022 in five U.S. public health jurisdictions (City of Chicago, Illinois; State of Connecticut; City of Milwaukee, Wisconsin; State of Maryland; and State of Utah). Generalized estimating equations were used to estimate attack rates and relative risks for index case and household contact characteristics. Data from 848 households, including 2,622 individuals (median household size = 3), were analyzed. Overall transmission risk was similar in households with Omicron (attack rate = 47.0%) compared to Delta variant (attack rate = 48.0%) circulation. In the multivariable model, a pattern of increased transmission risk was observed with increased time since a household contact’s last COVID-19 vaccine dose in Delta households, although confidence intervals overlapped (0–3 months relative risk = 0.8, confidence interval: 0.5–1.2; 4–7 months relative risk = 1.3, 0.9–1.8; ≥8 months relative risk = 1.2, 0.7–1.8); no pattern was observed in Omicron households. Risk for household contacts of symptomatic index cases was twice that of household contacts of asymptomatic index cases (relative risk = 2.0, 95% confidence interval: 1.4–2.9), emphasizing the importance of symptom status, regardless of variant. Uniquely, this study adjusted risk estimates for several index case and household contact characteristics and demonstrates that few characteristics strongly dictate risk, likely reflecting the complexity of the biological and social factors which combine to impact SARS-CoV-2 transmission.

BackgroundThe complex nature of obesity increasingly requires a comprehensive approach that includes the role of environmental factors. For understanding contextual determinants, the resources provided by technological advances could become a key factor in obesogenic environment research. This study aims to identify different sources of non-traditional data and their applications, considering the domains of obesogenic environments: physical, sociocultural, political and economic.MethodsWe conducted a systematic search in PubMed, Scopus and LILACS databases by two independent groups of reviewers, from September to December 2021. We included those studies oriented to adult obesity research using non-traditional data sources, published in the last 5 years in English, Spanish or Portuguese. The overall reporting followed the PRISMA guidelines.ResultsThe initial search yielded 1583 articles, 94 articles were kept for full-text screening, and 53 studies met the eligibility criteria and were included. We extracted information about countries of origin, study design, observation units, obesity-related outcomes, environment variables, and non-traditional data sources used. Our results revealed that most of the studies originated from high-income countries (86.54%) and used geospatial data within a GIS (76.67%), social networks (16.67%), and digital devices (11.66%) as data sources. Geospatial data were the most utilised data source and mainly contributed to the study of the physical domains of obesogenic environments, followed by social networks providing data to the analysis of the sociocultural domain. A gap in the literature exploring the political domain of environments was also evident.ConclusionThe disparities between countries are noticeable. Geospatial and social network data sources contributed to studying the physical and sociocultural environments, which could be a valuable complement to those traditionally used in obesity research. We propose the use of information available on the Internet, addressed by artificial intelligence-based tools, to increase the knowledge on political and economic dimensions of the obesogenic environment.

No net loss (NNL) biodiversity policies mandating the application of a mitigation hierarchy (avoid, minimize, remediate, offset) to the ecological impacts of built infrastructure are proliferating globally. However, little is known about their effectiveness at achieving NNL outcomes. We reviewed the English‐language peer‐reviewed literature (capturing 15,715 articles), and identified 32 reports that observed ecological outcomes from NNL policies, including >300,000 ha of biodiversity offsets. Approximately one‐third of NNL policies and individual biodiversity offsets reported achieving NNL, primarily in wetlands, although most studies used widely criticized area‐based outcome measures. The most commonly cited reason for success was applying high offset multipliers (large offset area relative to the impacted area). We identified large gaps between the global implementation of offsets and the evidence for their effectiveness: despite two‐thirds of the world's biodiversity offsets being applied in forested ecosystems, we found none of four studies demonstrated successful NNL outcomes for forested habitats or species. We also found no evidence for NNL achievement using avoided loss offsets (impacts offset by protecting existing habitat elsewhere). Additionally, we summarized regional variability in compliance rates with NNL policies. As global infrastructural expansion accelerates, we must urgently improve the evidence‐base around efforts to mitigate development impacts on biodiversity.

A majority of children admitted to a single hospital in late 2021–early 2022 with acute hepatitis of unknown cause tested positive for adenovirus. This report describes the children’s illnesses and outcomes.

Despite the success of rotavirus vaccines over the last decade, rotavirus remains a leading cause of severe diarrheal disease among young children. Further progress in reducing the burden of disease is inhibited, in part, by vaccine underperformance in certain settings. Early trials suggested that oral poliovirus vaccine (OPV), when administered concomitantly with rotavirus vaccine, reduces rotavirus seroconversion rates after the first rotavirus dose with modest or nonsignificant interference after completion of the full rotavirus vaccine course. Our study aimed to identify a range of individual-level characteristics, including concomitant receipt of OPV, that affect rotavirus vaccine immunogenicity in high- and low-child-mortality settings, controlling for individual- and country-level factors. Our central hypothesis was that OPV administered concomitantly with rotavirus vaccine reduced rotavirus vaccine immunogenicity. Pooled, individual-level data from GlaxoSmithKline's Phase II and III clinical trials of the monovalent rotavirus vaccine (RV1), Rotarix, were analyzed, including 7,280 vaccinated infants (5-17 weeks of age at first vaccine dose) from 22 trials and 33 countries/territories (5 countries/territories with high, 13 with moderately low, and 15 with very low child mortality). Two standard markers for immune response were examined including antirotavirus immunoglobulin A (IgA) seroconversion (defined as the appearance of serum antirotavirus IgA antibodies in subjects initially seronegative) and serum antirotavirus IgA titer, both collected approximately 4-12 weeks after administration of the last rotavirus vaccine dose. Mixed-effect logistic regression and mixed-effect linear regression of log-transformed data were used to identify individual- and country-level predictors of seroconversion (dichotomous) and antibody titer (continuous), respectively. Infants in high-child-mortality settings had lower odds of seroconverting compared with infants in low-child-mortality settings (odds ratio [OR] = 0.48, 95% confidence interval [CI] 0.43-0.53, p < 0.001). Similarly, among those who seroconverted, infants in high-child-mortality settings had lower IgA titers compared with infants in low-child-mortality settings (mean difference [β] = 0.83, 95% CI 0.77-0.90, p < 0.001). Infants who received OPV concomitantly with both their first and their second doses of rotavirus vaccine had 0.63 times the odds of seroconverting (OR = 0.63, 95% CI 0.47-0.84, p = 0.002) compared with infants who received OPV but not concomitantly with either dose. In contrast, among infants who seroconverted, OPV concomitantly administered with both the first and second rotavirus vaccine doses was found to be positively associated with antirotavirus IgA titer (β = 1.28, 95% CI 1.07-1.53, p = 0.009). Our findings may have some limitations in terms of generalizability to routine use of rotavirus vaccine because the analysis was limited to healthy infants receiving RV1 in clinical trial settings. Our findings suggest that OPV given concomitantly with RV1 was a substantial contributor to reduced antirotavirus IgA seroconversion, and this interference was apparent after the second vaccine dose of RV1, as with the original clinical trials that our reanalysis is based on. However, our findings do suggest that the forthcoming withdrawal of OPV from the infant immunization schedule globally has the potential to improve RV1 performance.

Background The direct effectiveness of infant rotavirus vaccination implemented in 2006 in the United States has been evaluated extensively, however, understanding of population-level vaccine effectiveness (VE) is still incomplete. Methods We analyzed time series data on rotavirus gastroenteritis (RVGE) and all-cause acute gastroenteritis (AGE) hospitalization rates in the United States from the MarketScan® Research Databases for July 2001–June 2016. Individuals were grouped into ages 0–4, 5–9, 10–14, 15–24, 25–44, and 45–64 years. Negative binomial regression models were fitted to monthly RVGE and AGE data to estimate the direct, indirect, overall, and total VE. Results A total of 9211 RVGE and 726,528 AGE hospitalizations were analyzed. Children 0–4 years of age had the largest declines in RVGE hospitalizations with direct VE of 87% (95% CI: 83, 90%). Substantial indirect effects were observed across age groups and generally declined in each older group. Overall VE against RVGE hospitalizations for all ages combined was 69% (95% CI: 62, 76%). Total VE was highest among young children; a vaccinated child in the post-vaccine era has a 95% reduced risk of RVGE hospitalization compared to a child in the pre-vaccine era . We observed higher direct VE in odd post-vaccine years and an opposite pattern for indirect VE. Conclusions Vaccine benefits extended to unvaccinated individuals in all age groups, suggesting infants are important drivers of disease transmission across the population. Imperfect disease classification and changing disease incidence may lead to bias in observed direct VE. Trial registration Not applicable.

Background Blood-feeding insects are important vectors for an array of zoonotic pathogens. While previous efforts toward generating molecular resources have largely focused on major vectors of global medical and veterinary importance, molecular data across a large number of hematophagous insect taxa remain limited. Advancements in long-read sequencing technologies and associated bioinformatic pipelines provide new opportunities for targeted sequencing of insect mitochondrial (mt) genomes. For engorged hematophagous insects, such technologies can be leveraged for both insect mitogenome genome assembly and identification of vertebrate blood-meal sources. Methods We used nanopore adaptive sampling (NAS) to sequence genomic DNA from four species of field-collected, blood-engorged mosquitoes ( Aedes and Culex spp. ) and one deer fly ( Chrysops sp.). NAS was used for bioinformatical enrichment of mtDNA reads of hematophagous insects and potential vertebrate blood-meal hosts using publically available mt genomes as references. We also performed an experimental control to compare results of traditional non-NAS nanopore sequencing to the mt genome enrichment by the NAS method. Results Complete mitogenomes were assembled and annotated for all five species sequenced with NAS: Aedes trivittatus, Aedes vexans , Culex restuans , Culex territans and the deer fly, Chrysops niger . In comparison to data generated during our non-NAS control experiment, NAS yielded a substantially higher proportion of reference-mapped mtDNA reads, greatly streamlining downstream mitogenome assembly and annotation. The NAS-assembled mitogenomes ranged in length from 15,582 to 16,045 bp, contained between 78.1% and 79.0% A + T content and shared the anticipated arrangement of 13 protein-coding genes, two ribosomal RNAs, and 22 transfer RNAs. Maximum likelihood phylogenies were generated to further characterize each insect species. Additionally, vertebrate blood-meal analysis was successful in three samples sequenced, with mtDNA-based phylogenetic analyses revealing that blood-meal sources for Chrysops niger , Culex restuans and Aedes trivittatus were human, house sparrow ( Passer domesticus ) and eastern cottontail rabbit ( Sylvilagus floridanus ), respectively. Conclusions Our findings show that NAS has dual utility to simultaneously molecularly identify hematophagous insects and their blood-meal hosts. Moreover, our data indicate NAS can facilitate a wide array of mitogenomic systematic studies through novel ‘phylogenetic capture’ methods. We conclude that the NAS approach has great potential for broadly improving genomic resources used to identify blood-feeding insects, answer phylogenetic questions and elucidate complex pathways for the transmission of vector-borne pathogens. Graphical Abstract

Glycosylation of proteins is a post-translational process where oligosaccharides are attached to proteins, potentially altering their folding, epitope availability, and immune recognition. In Porcine reproductive and respiratory syndrome virus-type 2 (PRRSV-2), positive selection pressure acts on amino acid sites potentially associated with immune escape through glycan shielding. Here, we describe the patterns of potential N-glycosylation sites over time and across different phylogenetic lineages of PRRSV-2 to better understand how these may contribute to patterns of coexistence and emergence of different lineages. We screened 19,179 PRRSV GP5 sequences (2004–2021) in silico for potential N-glycosylated sites. The emergence of novel combinations of N-glycosylated sites coincided with past PRRSV epidemics in the U.S. For lineage L1A, glycosylation at residues 32, 33, 44, 51, and 57 first appeared in 2012, but represented >62% of all L1A sequences by 2015, coinciding with the emergence of the L1A 1-7-4 strain that increased in prevalence from 8 to 86% of all L1A sequences from 2012 to 2015. The L1C 1-4-4 strain that emerged in 2020 also had a distinct N-glycosylation pattern (residues 32, 33, 44, and 51). From 2020 to 2021, this pattern was responsible for 44–47% of the L1C sequences, contrasting to <5% in years prior. Our findings support the hypothesis that antigenic evolution contributes to the sequential dominance of different PRRSV strains and that N-glycosylation patterns may partially account for antigenic differences amongst strains. Further studies on glycosylation and its effect on PRRSV GP5 folding are needed to further understand how glycosylation patterns shape PRRSV occurrence.

Sustainable control of soil-transmitted helminths requires a combination of chemotherapy treatment and environmental interventions, including access to safe drinking water, sufficient water for hygiene, use of clean sanitation facilities, and handwashing (WASH). We quantified associations between home-, school-, and community-level WASH characteristics and hookworm infection-both prevalence and eggs per gram of stool (intensity)-among Togolese school children in the context of community-based chemotherapy treatments administered in the country from 2010 through 2014. We analyzed data from two surveys conducted by the Togo Ministry of Health: a school-based survey of students aged 6-9 years across Togo conducted in 2009 and a follow-up survey in 2015, after four to five years of preventive chemotherapy. Data were available for 16,473 students attending 1,129 schools in 2009 and for 16,890 students from 1,126 schools in 2015. Between surveys, children in study schools received 0 to 8 rounds of deworming chemotherapy treatments. Few WASH conditions (only unimproved drinking water) were found to be significantly associated with the presence or absence of hookworms in an individual; however, quantitative eggs per gram of feces was associated with availability of unimproved drinking water, availability of improved drinking water either on or off school grounds, having a handwashing station with water available, and access to a sex-separate non-private or private latrine. The association between school WASH conditions and hookworm infection or burden often depended on the 2009 prevalence of infection, as more WASH characteristics were found to be significant predictors of infection among schools with high underlying endemicity of hookworm. Our findings emphasize the complex and often inconsistent or unpredictable relationship between WASH and hookworm. Specifically, we found that while preventive chemotherapy appeared to dramatically reduce hookworm infection, WASH was associated with infection intensity.

Abstract Background Rotavirus disease rates dramatically declined among children <5 years of age since the rotavirus vaccine was introduced in 2006; population-level impacts remain to be fully elucidated. Methods Data from the Healthcare Cost and Utilization Project State Inpatient Databases were used to conduct a time-series analysis of monthly hospital discharges across age groups for acute gastroenteritis and rotavirus from 2000 to 2013. Rate ratios were calculated comparing prevaccine and postvaccine eras. Results Following vaccine introduction, a decrease in rotavirus hospitalizations occurred with a shift toward biennial patterns across all ages. The 0-4-year age group experienced the largest decrease in rotavirus hospitalizations (rate ratio, 0.14; 95% confidence interval, .09-.23). The 5-19-year and 20-59-year age groups experienced significant declines in rotavirus hospitalization rates overall; the even postvaccine calendar years were characterized by progressively lower rates, and the odd postvaccine years were associated with reductions in rates that diminished over time. Those aged ≥60 years experienced the smallest change in rotavirus hospitalization rates overall, with significant reductions in even postvaccine years compared with prevaccine years (rate ratio, 0.51; 95% confidence interval, .39-.66). Conclusions Indirect impacts of infant rotavirus vaccination are apparent in the emergence of biennial patterns in rotavirus hospitalizations that extend to all age groups ineligible for vaccination. These observations are consistent with the notion that young children are of primary importance in disease transmission and that the initial postvaccine period of dramatic population-wide impacts will be followed by more complex incidence patterns across the age range in the long term. Indirect impacts of infant rotavirus vaccination are apparent in the emergence of biennial patterns in rotavirus hospitalizations that extend to all ages. The initial postvaccine period of dramatic population-wide impacts is followed by more complex incidence patterns across age groups.