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Copy_of_KHN_ICU_bed_county_analysis_2 for Rural America’s Hospitals are Not Prepared to Protect Older Adults From a Surge in COVID-19 Cases by Natalie M. Davoodi, Margaret Healy and Elizabeth M. Goldberg in Gerontology and Geriatric Medicine

Seasonal reproduction is a period of extreme physiological and behavioral changes, yet we know little about how it may affect host microbial communities (i.e. microbiota) and pathogen transmission. Here, we investigated shifts of the bacterial microbiota in saliva, urine and faeces during the seasonal reproduction of bats in South Africa, and test for an interaction in shedding patterns of both bacterial (Leptospira) and viral (adeno- and herpes-viruses) agents. Based on a comparative approach in two cave-dwelling bat species and high-throughput sequencing of the 16S rRNA gene, we demonstrated a clear signature in microbiota changes over the reproduction season, consistent across the multiple body habitats investigated, and associated with sex, age and reproductive condition of bats. We observed in parallel highly dynamic shedding patterns for both bacteria and viruses, but did not find a significant association between viral shedding and bacterial microbiota composition. Indeed, only Leptospira shedding was associated with alterations in both the diversity and composition of the urinary microbiota. These results illustrate how seasonal reproduction in bats substantially affects microbiota composition and infection dynamics, and have broad implications for the understanding of disease ecology in important reservoir hosts, such as bats. Rousettus_SampleList_SalivaList and details of Rousettus samples.Miniopterus_SampleList_Saliva-Urine-FaecesList and details of Miniopterus samples.Rousettus fasta DryadA zip folder with fasta files for Rousettus.Miniopterus fasta dryadA zip folder with fasta files for Miniopterus.Rousettus_Saliva_OTUsOTU table for Rousettus saliva samples.Miniopterus_Saliva_OTUsOTU table for Miniopterus saliva samples.Miniopterus_Faeces_OTUsOTU table for Miniopterus faeces samples.Miniopterus_Urine_OTUsOTU table for Miniopterus urine samples.

Upregulated DEGs in hypothalamus. Raw DEG data for upregulated genes in hypothalamus. (XLSX 344 kb)

Additional file 5 Maximum likelihood inference of masked sequence location from genomes (left) and GP sequences (right) via a CTMC model implemented in TreeTime. Horizontal bars indicate the posterior distribution of masked tip locations coloured by country (Sierra Leone in blue, Liberia in red, Guinea in green) and location (lighter colours indicate administrative divisions lying towards west of the country). The correct location of each tip is outlined in white with the smaller plot to the right showing only the probability of the correct location. Bars marked with an open circle indicate cases where the correct location is within the 95% credible set and solid circles indicate cases where the location with the most probability is also the correct location. Genomes still perform better in terms of correct guess (0.432 probability that best guess location is true location for genomes versus 0.259 for GP), cross entropy (12012.800 nats for genome versus 24397.109 nats for GP) and mean probability-weighted great circle distance between true location population centroid and estimated location population centroid (87.568 km for genome versus 124.909 km for GP).

To estimate the fatality rate upon infection with SARS-CoV-2 in unvaccinated subjects carrying auto-Abs against type I IFNs across age groups and sexes

Bartonella spp. are globally distributed bacteria that cause endocarditis in humans and domestic animals. Recent work has suggested bats as zoonotic reservoirs of some human Bartonella infections; however, the ecological and spatiotemporal patterns of infection in bats remain largely unknown. Here we studied the genetic diversity, prevalence of infection across seasons and years, individual risk factors, and possible transmission routes of Bartonella in populations of common vampire bats (Desmodus rotundus) in Peru and Belize, for which high infection prevalence has previously been reported. Phylogenetic analysis of the gltA gene for a subset of PCR-positive blood samples revealed sequences that were related to Bartonella described from vampire bats from Mexico, other Neotropical bat species, and streblid bat flies. Sequences associated with vampire bats clustered significantly by country but commonly spanned Central and South America, implying limited spatial structure. Stable and nonzero Bartonella prevalence between years supported endemic transmission in all sites. The odds of Bartonella infection for individual bats was unrelated to the intensity of bat flies ectoparasitism, but nearly all infected bats were infested, which precluded conclusive assessment of support for vector-borne transmission. While metagenomic sequencing found no strong evidence of Bartonella DNA in pooled bat saliva and fecal samples, we detected PCR positivity in individual saliva and feces, suggesting the potential for bacterial transmission through both direct contact (i.e., biting) and environmental (i.e., fecal) exposures. Further investigating the relative contributions of direct contact, environmental, and vector-borne transmission for bat Bartonella is an important next step to predict infection dynamics within bats and the risks of human and livestock exposures. Becker et al PLoS NTD_dataIndividual-level data on Bartonella infection status as determined by PCR targeting gltA and relevant vampire bat covariates.

Currently, the entire globe is affected by the COVID-19 pandemic caused by the novel coronavirus, SARS-CoV-2(SCV2). The ability to detect, monitor and assess the spread of the virus is imperative to controlling the effects of the pandemic. In order to meet the need for global testing, several methods have been developed. As a complement to individual testing, wastewater-based epidemiology represents a low-cost way to estimate the prevalence of the virus in a community. This information can be used to influence public policy regarding viral mitigation measures. This thesis documents our efforts at implementing wastewater testing in Santa Cruz County over the past 18 months. We sampled from the Watsonville Wastewater Treatment Plant on a weekly basis and quantified the presence of SCV2 using reverse transcriptase digital PCR normalized to Pepper Mild Mottle Virus (PMMV). Our data showed a large discrepancy between reported case counts and SCV2 in wastewater. This data also revealed seasonal variation in PMMV, potentially hindering it as a reliable normalizer. In addition to our sewage work, we performed masked-based sampling for Pacific Elementary School and documented a probable positive. This work demonstrates the potential of sewage sampling for SARS-CoV-2 and some of the current unmet challenges in both sewage sampling and pandemic response as a whole.