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1. Longitudinal Active Avian Influenza Surveillance in Bangladesh From 2017–2022 Reveals Differential IAV and H5 Infection and Viral Burden Associated With Bird Species, Sex, and Age

   https://doi.org/10.1155/tbed/5569836  

   Harrington, Walter N; Turner, Jasmine_C M; Barman, Subrata; Feeroz, Mohammed M; Hasan, Md Kamrul; Akhtar, Sharmin; Jeevan, Trushar; Mukherjee, Nabanita; Seiler, Patrick; Franks, John; et al (January 2024, Transboundary and Emerging Diseases)

   Wang, Leyi (Ed.)

   Influenza viruses are a major global health burden with up to 650,000 associated deaths annually. Beyond seasonal illness, influenza A viruses (IAVs) pose a constant pandemic threat due to novel emergent viruses that have evolved the ability to jump from their natural avian hosts to humans. Because of this threat, active surveillance of circulating IAV strains in wild and domestic bird populations is vital to our pandemic preparedness and response strategies. Here, we report on IAV surveillance data collected from 2017 to 2022 from wild and domestic birds in Bangladesh. We note evidence to suggest that male birds show a higher risk of IAV, including highly pathogenic avian influenza (HPAI) A(H5) virus, positivity than female birds. The data was stratified to control for selection bias and confounding variables to test the hypothesis that male birds are at a higher risk of IAV positivity relative to female birds. The association of IAV and A(H5) largely held in each stratum, and double stratification suggested that the phenomena was largely specific to ducks. Finally, we show that chickens, male birds, and juvenile birds generally have higher viral loads compared to their counterparts. These observations warrant further validation through active surveillance across various populations. Such efforts could significantly contribute to the enhancement of pandemic prediction and risk assessment models. 

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2. Using test positivity and reported case rates to estimate state-level COVID-19 prevalence and seroprevalence in the United States

   https://doi.org/10.1371/journal.pcbi.1009374  

   Chiu, Weihsueh A.; Ndeffo-Mbah, Martial L. (September 2021, PLOS Computational Biology)

   Althouse, Benjamin Muir (Ed.)

   Accurate estimates of infection prevalence and seroprevalence are essential for evaluating and informing public health responses and vaccination coverage needed to address the ongoing spread of COVID-19 in each United States (U.S.) state. However, reliable, timely data based on representative population sampling are unavailable, and reported case and test positivity rates are highly biased. A simple data-driven Bayesian semi-empirical modeling framework was developed and used to evaluate state-level prevalence and seroprevalence of COVID-19 using daily reported cases and test positivity ratios. The model was calibrated to and validated using published state-wide seroprevalence data, and further compared against two independent data-driven mathematical models. The prevalence of undiagnosed COVID-19 infections is found to be well-approximated by a geometrically weighted average of the positivity rate and the reported case rate. Our model accurately fits state-level seroprevalence data from across the U.S. Prevalence estimates of our semi-empirical model compare favorably to those from two data-driven epidemiological models. As of December 31, 2020, we estimate nation-wide a prevalence of 1.4% [Credible Interval (CrI): 1.0%-1.9%] and a seroprevalence of 13.2% [CrI: 12.3%-14.2%], with state-level prevalence ranging from 0.2% [CrI: 0.1%-0.3%] in Hawaii to 2.8% [CrI: 1.8%-4.1%] in Tennessee, and seroprevalence from 1.5% [CrI: 1.2%-2.0%] in Vermont to 23% [CrI: 20%-28%] in New York. Cumulatively, reported cases correspond to only one third of actual infections. The use of this simple and easy-to-communicate approach to estimating COVID-19 prevalence and seroprevalence will improve the ability to make public health decisions that effectively respond to the ongoing COVID-19 pandemic. 

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3. Excess mortality in the United States during the first three months of the COVID-19 pandemic

   https://doi.org/10.1017/S0950268820002617  

   Rivera, R.; Rosenbaum, J. E.; Quispe, W. (January 2020, Epidemiology and Infection)

   null (Ed.)

   Abstract Deaths are frequently under-estimated during emergencies, times when accurate mortality estimates are crucial for emergency response. This study estimates excess all-cause, pneumonia and influenza mortality during the coronavirus disease 2019 (COVID-19) pandemic using the 11 September 2020 release of weekly mortality data from the United States (U.S.) Mortality Surveillance System (MSS) from 27 September 2015 to 9 May 2020, using semiparametric and conventional time-series models in 13 states with high reported COVID-19 deaths and apparently complete mortality data: California, Colorado, Connecticut, Florida, Illinois, Indiana, Louisiana, Massachusetts, Michigan, New Jersey, New York, Pennsylvania and Washington. We estimated greater excess mortality than official COVID-19 mortality in the U.S. (excess mortality 95% confidence interval (CI) 100 013–127 501 vs. 78 834 COVID-19 deaths) and 9 states: California (excess mortality 95% CI 3338–6344) vs. 2849 COVID-19 deaths); Connecticut (excess mortality 95% CI 3095–3952) vs. 2932 COVID-19 deaths); Illinois (95% CI 4646–6111) vs. 3525 COVID-19 deaths); Louisiana (excess mortality 95% CI 2341–3183 vs. 2267 COVID-19 deaths); Massachusetts (95% CI 5562–7201 vs. 5050 COVID-19 deaths); New Jersey (95% CI 13 170–16 058 vs. 10 465 COVID-19 deaths); New York (95% CI 32 538–39 960 vs. 26 584 COVID-19 deaths); and Pennsylvania (95% CI 5125–6560 vs. 3793 COVID-19 deaths). Conventional model results were consistent with semiparametric results but less precise. Significant excess pneumonia deaths were also found for all locations and we estimated hundreds of excess influenza deaths in New York. We find that official COVID-19 mortality substantially understates actual mortality, excess deaths cannot be explained entirely by official COVID-19 death counts. Mortality reporting lags appeared to worsen during the pandemic, when timeliness in surveillance systems was most crucial for improving pandemic response. 

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4. Function and evolution of the aquaporin IsAQP1 in the Lyme disease vector Ixodes scapularis

   https://doi.org/10.1111/imb.12833  

   Tsujimoto, Hitoshi; Metz, Hillery C.; Smith, Alexis A.; Sakamoto, Joyce M.; Pal, Utpal; Rasgon, Jason L. (February 2023, Insect Molecular Biology)

   Abstract Ticks are important vectors of pathogenic viruses, bacteria, and protozoans to humans, wildlife, and domestic animals. Due to their life cycles, ticks face significant challenges related to water homeostasis. When blood‐feeding, they must excrete water and ions, but when off‐host (for stretches lasting several months), they must conserve water to avoid desiccation. Aquaporins (AQPs), a family of membrane‐bound water channels, are key players in osmoregulation in many animals but remain poorly characterized in ticks. Here, we bioinformatically identified AQP‐like genes from the deer tickIxodes scapularisand used phylogenetic approaches to map the evolution of the aquaporin gene family in arthropods. Most arachnid AQP‐like sequences (including those ofI. scapularis) formed a monophyletic group clustered within aquaglycerolporins (GLPs) from bacteria to vertebrates. This gene family is absent from insects, revealing divergent evolutionary paths for AQPs in different hematophagous arthropods. Next, we sequenced the full‐length cDNA ofI. scapularisaquaporin 1 (IsAQP1) and expressed it heterologously inXenopusoocytes to functionally characterize its permeability to water and solutes. Additionally, we examinedIsAQP1expression across different life stages and adult female organs. We foundIsAQP1is an efficient water channel with high expression in salivary glands prior to feeding, suggesting it plays a role in osmoregulation before or during blood feeding. Its functional properties are unique: unlike most GLPs,IsAQP1has low glycerol permeability, and unlike most AQPs, it is insensitive to mercury. Together, our results suggestIsAQP1plays an important role in tick water balance physiology and that it may hold promise as a target of novel vector control efforts. 

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5. Comparison of Antimicrobial-Resistant Escherichia coli Isolates from Urban Raccoons and Domestic Dogs

   https://doi.org/10.1128/AEM.00484-21  

   Worsley-Tonks, Katherine E.; Gehrt, Stanley D.; Miller, Elizabeth A.; Singer, Randall S.; Bender, Jeff B.; Forester, James D.; McKenzie, Shane C.; Travis, Dominic A.; Johnson, Timothy J.; Craft, Meggan E. (July 2021, Applied and Environmental Microbiology)

   Elkins, Christopher A. (Ed.)

   ABSTRACT Wildlife can be exposed to antimicrobial-resistant bacteria (ARB) via multiple pathways. Spatial overlap with domestic animals is a prominent exposure pathway. However, most studies of wildlife-domestic animal interfaces have focused on livestock and little is known about the wildlife-companion animal interface. Here, we investigated the prevalence and phylogenetic relatedness of extended-spectrum cephalosporin-resistant (ESC-R) Escherichia coli from raccoons ( Procyon lotor ) and domestic dogs ( Canis lupus familiaris ) in the metropolitan area of Chicago, IL, USA. To assess the potential importance of spatial overlap with dogs, we explored whether raccoons sampled at public parks (i.e., parks where people and dogs could enter) differed in prevalence and phylogenetic relatedness of ESC-R E. coli to raccoons sampled at private parks (i.e., parks where people and dogs could not enter). Raccoons had a significantly higher prevalence of ESC-R E. coli (56.9%) than dogs (16.5%). However, the richness of ESC-R E. coli did not vary by host species. Further, core single-nucleotide polymorphism (SNP)-based phylogenetic analyses revealed that isolates did not cluster by host species, and in some cases displayed a high degree of similarity (i.e., differed by less than 20 core SNPs). Spatial overlap analyses revealed that ESC-R E. coli were more likely to be isolated from raccoons at public parks than raccoons at private parks, but only for parks located in suburban areas of Chicago, not urban areas. That said, ESC-R E. coli isolated from raccoons did not genetically cluster by park of origin. Our findings suggest that domestic dogs and urban/suburban raccoons can have a diverse range of ARB, some of which display a high degree of genetic relatedness (i.e., differ by less than 20 core SNPs). Given the differences in prevalence, domestic dogs are unlikely to be an important source of exposure for mesocarnivores in urbanized areas. IMPORTANCE Antimicrobial-resistant bacteria (ARB) have been detected in numerous wildlife species across the globe, which may have important implications for human and animal health. Wildlife can be exposed to ARB via numerous pathways, including via spatial overlap with domestic animals. However, the interface with domestic animals has mostly been explored for livestock and little is known about the interface between wild animals and companion animals. Our work suggests that urban and suburban wildlife can have similar ARB to local domestic dogs, but local dogs are unlikely to be a direct source of exposure for urban-adapted wildlife. This finding is important because it underscores the need to incorporate wildlife into antimicrobial resistance surveillance efforts, and to investigate whether certain urban wildlife species could act as additional epidemiological pathways of exposure for companion animals, and indirectly for humans. 

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