infection disparities among Hispanics and non-Hispanics in Yuma, Arizona.

infection patterns in Yuma, Arizona show a 2.25x higher infection rate in non-Hispanics. Males had higher infection rates in most age classes.

A framework for integrating wastewater-based epidemiology and public health.

Wastewater-based epidemiology (WBE) is an environmental approach to monitor community health through the analysis of sewage. The COVID-19 pandemic catalyzed scientists and public health professionals to revisit WBE as a tool to optimize resource allocation to mitigate disease spread and prevent outbreaks. Some studies have highlighted the value of WBE programs that coordinate with public health professionals; however, the details necessary for implementation are not well-characterized.

An inaugural forum on epidemiological modeling for public health stakeholders in Arizona.

Epidemiological models-which help us understand and forecast the spread of infectious disease-can be valuable tools for public health. However, barriers exist that can make it difficult to employ epidemiological models routinely within the repertoire of public health planning. These barriers include technical challenges associated with constructing the models, challenges in obtaining appropriate data for model parameterization, and problems with clear communication of modeling outputs and uncertainty.

Correlates of Co-Infection with Coccidiosis and Avian Malaria in House Finches (Haemorhous mexicanus).

Pathogens have traditionally been studied in isolation within host systems; yet in natural settings they frequently coexist. This raises questions about the dynamics of co-infections and how host life-history traits might predict co-infection versus single infection. To address these questions, we investigated the presence of two parasites, a gut parasite (Isospora coccidians) and a blood parasite (Plasmodium spp.

Pan-Enterovirus Characterization Reveals Cryptic Circulation of Clinically Relevant Subtypes in Arizona Wastewater.

Background: Most seasonally circulating enteroviruses result in asymptomatic or mildly symptomatic infections. In rare cases, however, infection with some subtypes can result in paralysis or death. Of the 300 subtypes known, only poliovirus is reportable, limiting our understanding of the distribution of other enteroviruses that can cause clinical disease.

Large Clusters of Invasive emm49 Group A Streptococcus Identified Within Arizona Health Care Facilities Through Statewide Genomic Surveillance System, 2019-2021.

A statewide genomic surveillance system for invasive Group A Streptococcus was implemented in Arizona in June 2019, resulting in 1046 isolates being submitted for genomic analysis to characterize emm types and identify transmission clusters. Eleven of the 32 identified distinct emm types comprised >80% of samples, with 29.7% of all isolates being typed as emm49 (and its genetic derivative emm151).

Lyssa excreta: Defining parameters for fecal samples as a rabies virus surveillance method.

It is not possible to systematically screen the environment for rabies virus (RABV) using current approaches. We sought to determine under what conditions RABV is detectable from feces and other accessible samples from infected wildlife to broaden the number of biological samples that could be used to test for RABV. We employed a recently-developed quantitative RT-PCR assay called the "LN34 panlyssavirus real-time RT-PCR assay", which is highly sensitive and specific for all variants of RABV.

Knockdown resistance mutations are common and widely distributed in Xenopsylla cheopis fleas that transmit plague in Madagascar.

Background: Plague, caused by the bacterium Yersinia pestis, remains an important disease in Madagascar, where the oriental rat flea, Xenopsylla cheopis, is a primary vector. To control fleas, synthetic pyrethroids (SPs) have been used for >20 years, resulting in resistance in many X. cheopis populations.

Biting midges (Diptera: Ceratopogonidae) as putative vectors of zoonotic (Nematoda: Onchocercidae) in northern Arizona and New Mexico, southwestern United States.

(Rodonaja, 1967) is an understudied, vector-borne, filarioid nematode that causes ocular onchocercosis in dogs, cats, coyotes, wolves, and is also capable of infecting humans. Onchocercosis in dogs has been reported with increasing incidence worldwide. However, despite the growing number of reports describing canine cases as well as zoonotic infections globally, the disease prevalence in endemic areas and vector species of this parasite remains largely unknown.

A sliding window approach to optimize the time-varying parameters of a spatially-explicit and stochastic model of COVID-19.

The implementation of non-pharmaceutical public health interventions can have simultaneous impacts on pathogen transmission rates as well as host mobility rates. For instance, with SARS-CoV-2, masking can influence host-to-host transmission, while stay-at-home orders can influence mobility. Importantly, variations in transmission rates and mobility patterns can influence pathogen-induced hospitalization rates.

Unique Genomic Epidemiology of COVID-19 in the White Mountain Apache Tribe, April to August 2020, Arizona.

The first case of coronavirus disease 2019 (COVID-19) within the White Mountain Apache Tribe (WMAT) in Arizona was diagnosed almost 1 month after community transmission was recognized in the state. Aggressive contact tracing allowed for robust genomic epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and subsequent phylogenetic analyses implicated only two virus introductions, which resulted in the spread of two unique viral lineages on the reservation. The phylogenies of these lineages reflect the nature of the introductions, the remoteness of the community, and the extraordinarily high attack rates.

Application of Phylodynamic Tools to Inform the Public Health Response to COVID-19: Qualitative Analysis of Expert Opinions.

Background: In the wake of the SARS-CoV-2 pandemic, scientists have scrambled to collect and analyze SARS-CoV-2 genomic data to inform public health responses to COVID-19 in real time. Open source phylogenetic and data visualization platforms for monitoring SARS-CoV-2 genomic epidemiology have rapidly gained popularity for their ability to illuminate spatial-temporal transmission patterns worldwide. However, the utility of such tools to inform public health decision-making for COVID-19 in real time remains to be explored.

LupiQuant: A real-time PCR based assay for determining host-to-parasite DNA ratios of Onchocerca lupi and host Canis lupus from onchocercosis samples.

Onchocerca lupi is a filarial nematode that causes ocular onchocercosis in canines globally including North America and areas of Europe, North Africa, and the Middle East. Reported incidence of this parasite in canines has continued to steadily escalate since the early 21st century and was more recently documented in humans. Whole genome sequencing (WGS) of this parasite can provide insight into gene content, provide novel surveillance targets, and elucidate the origin and range expansion.

A Quantitative Assessment of Staphylococcus aureus Community Carriage in Yuma, Arizona.

Background: Disease control relies on pathogen identification and understanding reservoirs. Staphylococcus aureus infection prevention is based upon decades of research on colonization and infection, but diminishing returns from mitigation efforts suggest significant knowledge gaps. Existing knowledge and mitigation protocols are founded upon culture-based detection, with almost no information about pathogen quantities.

One health genomic surveillance and response to a university-based outbreak of the SARS-CoV-2 Delta AY.25 lineage, Arizona, 2021.

Genomic surveillance and wastewater tracking strategies were used to strengthen the public health response to an outbreak of the SARS-CoV-2 Delta AY.25 lineage associated with a university campus in Arizona. Epidemiologic and clinical data routinely gathered through contact tracing were matched to SARS-CoV-2 genomes belonging to an outbreak of AY.

SPARSEMODr: Rapidly simulate spatially explicit and stochastic models of COVID-19 and other infectious diseases.

Building realistically complex models of infectious disease transmission that are relevant for informing public health is conceptually challenging and requires knowledge of coding architecture that can implement key modeling conventions. For example, many of the models built to understand COVID-19 dynamics have included stochasticity, transmission dynamics that change throughout the epidemic due to changes in host behavior or public health interventions, and spatial structures that account for important spatio-temporal heterogeneities. Here we introduce an R package, SPARSEMODr, that allows users to simulate disease models that are stochastic and spatially explicit, including a model for COVID-19 that was useful in the early phases of the epidemic.

Genome Sequences of Community Carriage Strains of Staphylococcus aureus from Yuma, Arizona.

Staphylococcus aureus exists as a pathogen and commensal. Individuals with asymptomatic carriage serve as a reservoir for transmission and are at increased risk of infecting themselves. In order to characterize the genomic diversity of S.

Complete mitochondrial genome of (Nematoda, Onchocercidae).

Rodonaja 1967, is an emerging, zoonotic filarial nematode parasite that causes ocular disease in dogs, cats, wild canids, and humans. It is the causative agent of ocular onchocercosis in canines with increasing incidence in both North America and the Old World during the early twenty-first century. We report the complete mitochondrial genome of an isolate from a dog from Arizona, southwestern USA, and its genetic differentiation from related species.

St. Louis Encephalitis Virus in the Southwestern United States: A Phylogeographic Case for a Multi-Variant Introduction Event.

Since the reemergence of St. Louis Encephalitis (SLE) Virus (SLEV) in the Southwest United States, identified during the 2015 outbreak in Arizona, SLEV has been seasonally detected within spp. populations throughout the Southwest United States.

Characterization of neonatal opioid withdrawal syndrome in Arizona from 2010-2017.

In this paper, we describe a population of mothers who are opioid dependent at the time of giving birth and neonates exposed to opioids in utero who experience withdrawal following birth. While there have been studies of national trends in this population, there remains a gap in studies of regional trends. Using data from the Arizona Department of Health Services Hospital Discharge Database, this study aimed to characterize the population of neonates with neonatal opioid withdrawal syndrome (NOWS) and mothers who were opioid dependent at the time of giving birth, in Arizona.

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity.

The COVID-19 pandemic has led to a rapid accumulation of SARS-CoV-2 genomes, enabling genomic epidemiology on local and global scales. Collections of genomes from resources such as GISAID must be subsampled to enable computationally feasible phylogenetic and other analyses. We present genome-sampler, a software package that supports sampling collections of viral genomes across multiple axes including time of genome isolation, location of genome isolation, and viral diversity.

Sample pooling methods for efficient pathogen screening: Practical implications.

Due to the large number of negative tests, individually screening large populations for rare pathogens can be wasteful and expensive. Sample pooling methods improve the efficiency of large-scale pathogen screening campaigns by reducing the number of tests and reagents required to accurately categorize positive and negative individuals. Such methods rely on group testing theory which mainly focuses on minimizing the total number of tests; however, many other practical concerns and tradeoffs must be considered when choosing an appropriate method for a given set of circumstances.

Health disparities in jail populations: Mixed methods and multi-disciplinary community engagement for justice and health impacts.

This special issue of Practicing Anthropology presents multidisciplinary and multisectoral views of a community engaged health disparities project titled "Health Disparities in Jail Populations: Converging Epidemics of Infectious Disease, Chronic Illness, Behavioral Health, and Substance Abuse." The overall project incorporated traditional anthropological mixed-methods approaches with theory and methods from informatics, epidemiology, genomics, evolutionary and computational biology, community engagement, and applied/translational science.

An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona.

In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona.

Systematic review: the impact of socioeconomic factors on mosquito distribution in the mainland United States.

mosquitoes are primary vectors of dengue, yellow fever, chikungunya and Zika viruses. is highly anthropophilic and relies nearly exclusively on human blood meals and habitats for reproduction. Socioeconomic factors may be associated with the spread of due to their close relationship with humans.