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. Objective: The overarching objectives of this study were to: 1) describe the distribution of enteroviruses in Arizona during the late summer and fall of 2022, the time of year when they are thought to be most abundant, and 2) demonstrate the utility of viral pan-assay approaches for semi-agnostic discovery that can be followed up by more targeted assays and phylogenomics. Methods: This study utilizes pooled nasal samples collected from school-aged children and long-term care facility residents, and wastewater from multiple locations in Arizona during July-October of 2022. We used PCR to amplify and sequence a region common to all enteroviruses, followed by species-level bioinformatic characterization using the QIIME 2 platform. For Enterovirus-D68 (EV-D68), detection was carried out using RT-qPCR, followed by confirmation using near-complete whole EV-D68 genome sequencing using a newly designed tiled amplicon approach. Results: In the late summer and early fall of 2022, multiple enterovirus species were identified in Arizona wastewater, with Coxsackievirus A6, EV-D68, and Coxsackievirus A19 composing 86% of the characterized reads sequenced. While EV-D68 was not identified in pooled human nasal samples, and the only reported acute flaccid myelitis case in Arizona did not test positive for the virus, an in-depth analysis of EV-D68 in wastewater revealed that the virus was circulating from August through mid-October. A phylogenetic analysis on this relatively limited dataset revealed just a few importations into the state, with a single clade indicating local circulation. Significance: This study further supports the utility of wastewater-based epidemiology to identify potential public health threats. Our further investigations into EV-D68 shows how these data might help inform healthcare diagnoses for children presenting with concerning neurological symptoms.

Large Clusters of Invasive emm49 Group A Streptococcus Identified within and across Arizona Healthcare 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 1,046 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). Phylogenetic analysis initially identified an emm49 genomic cluster of four isolates that rapidly expanded over subsequent months (June 2019-February 2020). Public health investigations identified epidemiologic links with three different long-term care facilities, resulting in specific interventions. Unbiased genomic surveillance allowed for identification and response to clusters that would have otherwise remained undetected.

"Sniffing" out SARS-CoV-2 in Arizona working dogs: an exploratory serosurvey.

Susceptibility to and infection with SARS-CoV-2 in companion animals has been well-documented throughout the COVID-19 pandemic. Surveillance for the virus in dogs has largely been focused on household pets; however, other canine populations may also be impacted. We partnered with a local veterinary hospital with a high working dog patient volume to conduct viral and neutralizing antibody testing in working dogs and identify potential risk factors in the dog's work and home environments. Surveillance of SARS-CoV-2 in law enforcement and security working dogs in Arizona found 24.81% (32/129) of dogs to be seropositive. Thirteen dogs presenting with clinical signs or with reported exposure to COVID-19 in the 30 days prior to sample collection were also tested by PCR; all samples were negative. 90.7% (n = 117) of dogs were reported to be asymptomatic or have no change in performance at the time of sampling. Two dogs (1.6%) had suspected anosmia as reported by their handlers; one of which was seropositive. Known exposure to the dog's COVID-19 positive handler or household member was identified as a significant risk factor. Demographics factors including sex, altered status, and type of work were not associated with canine seropositivity. Further work is warranted to understand the impact of SARS-CoV-2 and other infectious diseases in working dogs.

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. The timing and space-limited nature of the outbreaks validate the public health tracing efforts involved, which were illustrated by multiple short transmission chains over a period of several weeks, eventually resulting in extinction of the lineages. Comprehensive sampling and successful infection control efforts are illustrated in both the effective population size analyses and the limited mortality outcomes. The rapid spread and high attack rates of the two lineages may be due to a combination of sociological determinants of the WMAT and a seemingly enhanced transmissibility. The SARS-CoV-2 genomic epidemiology of the WMAT demonstrates a unique local history of the pandemic and highlights the extraordinary and successful efforts of their public health response. IMPORTANCE This article discusses the introduction and spread of two unique viral lineages of SARS-CoV-2 within the White Mountain Apache Tribe in Arizona. Both genomic sequencing and traditional epidemiological strategies (e.g., contract tracing) were used to understand the nature of the spread of both lineages. Beyond providing a robust genomic analysis of the epidemiology of the outbreaks, this work also highlights the successful efforts of the local public health response.

Variant-specific SARS-CoV-2 shedding rates in wastewater.

Previous studies show that SARS-CoV-2 waste shedding rates vary by community and are influenced by multiple factors; however, differences in shedding rates across multiple variants have yet to be evaluated. The purpose of this work is to build on previous research that evaluated waste shedding rates for early SARS-CoV-2 and the Delta variant, and update population level waste shedding rates for the more-recent Omicron variant in six communities. Mean SARS-CoV-2 waste shedding rates were found to increase with the predominance of the Delta variant and subsequently decrease with Omicron infections. Interestingly, the Delta stage had the highest mean shedding rates and was associated with the most severe disease symptoms reported in other clinical studies, while Omicron, exhibiting reduced symptoms, had the lowest mean shedding rates. Additionally, shedding rates were most consistent across communities during the Omicron stage. This is the first paper to identify waste shedding rates specific to the Omicron variant and fills a knowledge gap critical to disease prevalence modeling.

Morbidity and Functional Outcomes Following Rocky Mountain Spotted Fever Hospitalization-Arizona, 2002-2017.

Background: Rocky Mountain spotted fever (RMSF) is a deadly tickborne disease disproportionately affecting Arizona tribal communities. While the acute clinical effects of RMSF are well-documented, more complete understanding of the long-term health consequences is needed to provide guidance for providers and patients in highly impacted areas. Methods: We performed a retrospective review of hospitalized RMSF cases from 2 tribal communities in Arizona during 2002-2017. Medical records from acute illness were abstracted for information on clinical presentation, treatment, and status at discharge. Surviving patients were interviewed about disease recovery, and patients reporting incomplete recovery were eligible for a neurologic examination. Results: Eighty hospitalized cases of RMSF met our inclusion criteria and were reviewed. Of these, 17 (21%) resulted in a fatal outcome. Among surviving cases who were interviewed, most (62%) reported full recovery, 15 (38%) reported ongoing symptoms or reduced function following RMSF illness, and 9 (23%) had evidence of neurologic sequelae at the time of examination. Sequelae included impaired cognition, weakness, decreased deep tendon reflexes, seizures, and cranial nerve dysfunction. Longer hospitalization (25.5 days vs 6.2 days, P < .001), a higher degree of disability at discharge (median modified Rankin score 1 vs 0, P = .03), and delayed doxycycline administration (6.2 days vs 4.1 days, P = .12) were associated with long-term sequelae by logistic regression. Conclusions: Although the etiology of sequelae is not able to be determined using this study design, life-altering sequelae were common among patients surviving severe RMSF illness. Delayed administration of the antibiotic doxycycline after day 5 was the strongest predictor of morbidity.

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.25 identified through ongoing phylogenomic analyses. Continued phylogenetic analyses were conducted to further describe the AY.25 outbreak. Wastewater collected twice weekly from sites across campus was tested for SARS-CoV-2 by RT-qPCR, and subsequently sequenced to identify variants. The AY.25 outbreak was defined by a single mutation (C18804T) and comprised 379 genomes from SARS-CoV-2 positive cases associated with the university and community. Several undergraduate student gatherings and congregate living settings on campus likely contributed to the rapid spread of COVID-19 across the university with secondary transmission into the community. The clade defining mutation was also found in wastewater samples collected from around student dormitories a week before the semester began, and 9 days before cases were identified. Genomic, epidemiologic, and wastewater surveillance provided evidence that an AY.25 clone was likely imported into the university setting just prior to the onset of the Fall 2021 semester, rapidly spread through a subset of the student population, and then subsequent spillover occurred in the surrounding community. The university and local public health department worked closely together to facilitate timely reporting of cases, identification of close contacts, and other necessary response and mitigation strategies. The emergence of new SARS-CoV-2 variants and potential threat of other infectious disease outbreaks on university campuses presents an opportunity for future comprehensive One Health genomic data driven, targeted interventions.

Rickettsiosis subcommittee report to the tick-borne disease working group.

Tick-borne rickettsial infections are serious, common, and difficult to diagnose. Among the most important factors leading to failure to diagnose and treat tick-borne rickettsioses effectively is a lack of consideration of the potential diagnosis by primary caregivers and emergency department physicians in patients presenting with undifferentiated acute febrile illness during tick season. This situation exists because of insufficient primary and continuing medical education of medical students, primary care and emergency medicine residents, and practicing physicians regarding tick-borne rickettsioses specific to the region where they practice. Delayed initiation of treatment with an appropriate antibiotic is associated with adverse outcomes including increased rates of hospitalization, admission to an intensive care unit, and mortality. The earliest symptoms are nonspecific, consisting of fever, headache, myalgias, and nausea and/or vomiting. Laboratory abnormalities are typically absent at this time when the therapeutic response to an appropriate antibiotic would be optimal. There is a mistaken idea among a substantial portion of physicians that the best antibiotic available, doxycycline, should not be administered to children 8 years of age or younger or during pregnancy. For all of the above reasons, there is unnecessary morbidity and mortality caused by tick-borne rickettsioses. This report proposes measures to address these critical issues regarding tick-borne rickettsioses.

Genomic investigation of a household SARS-CoV-2 disease cluster in Arizona involving a cat, dog, and pet owner.

Arizona's COVID-19 and Pets Program is a prospective surveillance study being conducted to characterize how SARS-CoV-2 impacts companion animals living in households with SARS-CoV-2-positive individuals. Among the enrolled pets, we identified a SARS-CoV-2-infected cat and dog from the same household; both animals were asymptomatic but had close contact with the symptomatic and SARS-CoV-2-positive owner. Whole genome sequencing of animal and owner specimens revealed identical viral genomes of the B.1.575 lineage, suggesting zoonotic transmission of SARS-CoV-2 from human to at least one pet. This is the first report of the B.1.575 lineage in companion animals. Genetically linking SARS-CoV-2 between people and animals, and tracking changes in SARS-CoV-2 genomes is essential to detect any cross-species SARS-CoV-2 transmission that may lead to more transmissible or severe variants that can affect humans. Surveillance studies, including genomic analyses of owner and pet specimens, are needed to further our understanding of how SARS-CoV-2 impacts companion animals.

Applying Genomic Epidemiology to Characterize a COVID-19 Outbreak in a Developmentally Disabled Adult Group Home Setting, Arizona.

Individuals living in congregate settings, including those in group homes, have been disproportionately impacted by COVID-19 and may be at increased risk of exposure or infection due to underlying illness. In mid-May 2020, local public health officials responded to an outbreak of COVID-19 among staff and residents associated with a multi-residential group home that provides care for adults with intellectual and developmental disabilities. Samples were collected at 16 of the homes. In four of the homes all the residents tested positive, and in the remaining 12 houses where samples were collected, all residents tested negative. Of the 152 individuals tested, 15/58 (25.9%) residents and 27/94 (28.7%) staff were positive for SARS-CoV-2, including eight hospitalizations and four deaths. Phylogenetic analysis of genomes from this outbreak in the context of genomes from Northern Arizona shows that very few mutations separate the samples from this outbreak. A potential transmission network was developed to illustrate person-place epidemiologic linkages and further demonstrates the dynamic connections between staff and residents with respect to each group home location. Epidemiologic and genomic evidence correlate, and suggest that asymptomatic infected staff likely introduced and spread COVID-19 in this setting. Implementation of public health prevention measures alongside rapid genomic analysis can help guide policy development and guide management efforts to prevent and mitigate future outbreaks.

Experiences of Military Veterans in a Therapeutic Horseback Riding Program.

Posttraumatic stress disorder commonly occurs among U.S. military veterans. Therapeutic horseback riding (THR) has emerged as an adjunct therapy. We explored 20 veterans' perceived benefits, drawbacks and views of a 6-week THR program. Participants had confirmed diagnoses of posttraumatic stress disorder, traumatic brain injury, or both. Veterans rode the same horse weekly, the same day, at the same time. Data were collected as part of a randomized clinical trial testing the effects of THR on Post-Traumatic Stress Disorder. Veterans responded to an open-ended questionnaire. Content analysis was used for data analysis. Benefits were "Connection to the Horse," "Relaxing," "180 Degree Change," and "Meeting New People." Drawbacks were "None," "Struggle to Get There," "Pain," "Too Short," and "It is Structured." Overall perceptions were "I Absolutely Loved It," "Feel Again," "The Horse," "The People," and "No Worries." Participants viewed THR as positive. Findings may elucidate why THR may be clinically beneficial.

Clinical, diagnostic, and epidemiological features of a community-wide outbreak of canine leptospirosis in a low-prevalence region (Maricopa County, Arizona).

OBJECTIVE: To describe clinical, diagnostic, and epidemiological features of an outbreak of leptospirosis in dogs in Maricopa County, Ariz, from January 2016 through June 2017. ANIMALS: 71 case and 281 control dogs. PROCEDURES: Cases were classified as confirmed, probable, suspect, or not a case on the basis of medical record data that fulfilled clinical, diagnostic, and epidemiological criteria. Potential exposures were assessed by owner survey. For the case-control investigation, control dogs were recruited through owner completion of a July 2017 survey. Summary statistics and ORs for case dog lifestyle factors were reported. RESULTS: 54 dogs were classified as confirmed and 17 as probable cases. For 4 dogs of a household cluster (5 confirmed and 3 probable), the highest microscopic agglutination titer was for serovar Djasiman (Leptospira kirschneri detected by PCR assay), and for 13 dogs of a community outbreak (49 confirmed and 14 probable cases), the highest titer was for serovar Canicola (Leptospira interrogans detected by PCR assay). The 44 case dogs included in the case-control investigation were 7.7 (95% CI, 3.5 to 16.7) and 2.9 times (95% CI, 1.3 to 6.6) as likely as control dogs to have visited dog daycare or to have been kenneled overnight at a boarding facility, respectively, 30 days prior to the onset of clinical signs or diagnosis. CONCLUSIONS AND CLINICAL RELEVANCE: Diagnostic and epidemiological findings indicated 2 outbreaks. Transmission where dogs congregated likely propagated the community outbreak. Outbreaks of leptospiral infections can occur in regions of low prevalence, and a dog's exposure to areas where dogs congregate should be considered when making Leptospira vaccination recommendations.

Distribution and Occurrence of Amblyomma maculatum sensu lato (Acari: Ixodidae) and Rickettsia parkeri (Rickettsiales: Rickettsiaceae), Arizona and New Mexico, 2017-2019.

Amblyomma maculatum Koch sensu lato (s.l.) ticks are the vector of Rickettsia parkeri in Arizona, where nine cases of R. parkeri rickettsiosis have been identified since the initial case in 2014. The current study sought to better define the geographic ranges of the vector and pathogen and to assess the potential public health risk posed by R. parkeri in this region of the southwestern United States. A total of 275 A. maculatum s.l. ticks were collected from 34 locations in four counties in Arizona and one county in New Mexico and screened for DNA of Rickettsia species. Rickettsia parkeri was detected in 20.4% of the ticks, including one specimen collected from New Mexico, the first report of R. parkeri in A. maculatum s.l. from this state. This work demonstrates a broader distribution of A. maculatum s.l. ticks and R. parkeri in the southwestern United States than appreciated previously to suggest that R. parkeri rickettsiosis is underrecognized in this region.

Expanding Recognition of Rickettsia parkeri Rickettsiosis in Southern Arizona, 2016-2017.

Rickettsia parkeri rickettsiosis is an emerging, tick-borne disease in the United States (US), transmitted by the bite of Amblyomma maculatum group ticks. Clinical manifestations include fever, headache, myalgia, maculopapular rash, and a characteristic eschar that forms at the site of the tick bite. Arizona's index case of R. parkeri rickettsiosis was reported in 2014. Seven additional confirmed and probable cases were identified during 2016-2017 through routine investigation of electronic laboratory reports and by self-reporting to public health authorities. Serum samples were evaluated for immunoglobulin G antibodies reactive with antigens of Rickettsia rickettsii (the agent of Rocky Mountain spotted fever [RMSF]) and R. parkeri using indirect immunofluorescence antibody tests. Eschar swab specimens were evaluated using Rickettsia genus-specific and R. parkeri-specific real-time PCR assays. Patients (six male, one female) ranged in age from 29 to 69 years (median of 41 years), and became ill between July 2016 and September 2017. Fever (6/7), myalgia (5/7), and arthralgia (5/7) were most commonly reported and 5/7 patients had a documented eschar. All patients reported a tick bite acquired in southern Arizona within 2-8 days before illness onset. Four patients worked as U.S. Border Patrol agents. Antibodies reactive to R. rickettsii, R. parkeri, or to both antigens were detected in all patients. Seroconversions between acute and convalescent-phase samples were identified for two patients and DNA of R. parkeri was identified in eschar swab samples from two patients. R. parkeri rickettsiosis is endemic to a region of the southwestern United States and presents an occupational risk that could be lessened by prevention messaging to Border Patrol agents. RMSF, a closely related and more severe spotted fever rickettsiosis, is also endemic to Arizona. Public health agencies can assist clinicians in distinguishing these two infections clinically through education and accessing species-specific diagnostic assays that can improve surveillance efforts for both diseases.

Knowledge, attitudes, and practices relevant to zoonotic disease reporting and infection prevention practices among veterinarians - Arizona, 2015.

Veterinarians play a crucial role in zoonotic disease detection in animals and prevention of disease transmission; reporting these zoonoses to public health officials is an important first step to protect human and animal health. Evidence suggests veterinarians and their staff are at higher risk for exposure to zoonoses because of possible interactions with infected animals. We examined the knowledge, attitudes, and practices of veterinarians regarding zoonotic disease reporting to public health agencies and associated infection prevention (IP) practices such as personal protective equipment (PPE) use, and the need for targeted education and outreach for veterinarians in Arizona. An online questionnaire was developed and distributed by email in September 2015 and was available through November 2015 to all 1,100 members of the Arizona Veterinary Medical Association. Chi-square and logistic regression analyses were performed. In total, 298 (27%) veterinarians from all 15 Arizona counties completed the survey; the majority (70%) were female, practiced small animal medicine (84%), and reported practicing veterinary medicine for ≥10 years (75%). Only 57% reported they knew when to report a suspected zoonotic disease and 60% reported they knew how to make that type of report. The majority said they would report rabies (97%), plague (96%), and highly pathogenic avian influenza (91%) to a state agency. Most respondents reported using PPE (e.g., masks, face shields, and gloves) when performing a surgical procedure (96%) or necropsy (94%), although fewer reported using PPE for handling clinically ill animals (37%) or healthy animals (17%). Approximately 70% reported always using PPE when in contact with animal birthing fluids, urine, or feces, and 47% for contact with animal blood, saliva, or other body fluids. Veterinarians who agreed that they knew the appropriate actions to protect themselves from zoonotic disease exposures were more likely to report always washing their hands before eating or drinking at work (OR = 3.81, 95% confidence interval (CI) [1.97-7.35], P < 0.01). Responses for when to make a report and how to report were not significantly different by gender, years of practice, or holding additional degrees, but did differ by practice type, age, and number of veterinarians in the practice. Small animal veterinarians were less likely to report knowing when to make a report compared to other veterinarians (P < 0.01). Respondents demonstrated suboptimal zoonotic disease reporting and IP practices, including PPE use. Public health agencies should improve outreach and education to veterinarians to facilitate better zoonotic disease prevention practices and reporting.

USING CITIZEN SCIENCE TO ENHANCE SURVEILLANCE OF AEDES AEGYPTI IN ARIZONA, 2015-17.

Vector surveillance is an essential component of vector-borne disease prevention, but many communities lack resources to support extensive surveillance. The Great Arizona Mosquito Hunt (GAMH) was a collaborative citizen science project conducted during 2015-17 to enhance surveillance for Aedes aegypti in Arizona. Citizen science projects engage the public in scientific research in order to further scientific knowledge while improving community understanding of a specific field of science and the scientific process. Participating schools and youth organizations across the state conducted oviposition trapping for 1-4 wk during peak Ae. aegypti season in Arizona and returned the egg sheets to collaborating entomologists for identification. During the 3-year program, 120 different schools and youth organizations participated. Few participants actually collected Aedes eggs in their traps in 2015 or 2017, but about one-third of participants collected eggs during 2016, including 3 areas that were not previously reported to have Ae. aegypti. While relatively few new areas of Ae. aegypti activity were identified, GAMH was found to be a successful method of engaging citizen scientists. Future citizen science mosquito surveillance projects might be useful to further define the ecology and risk for vector-borne diseases in Arizona.

Tick-Borne Relapsing Fever in the White Mountains, Arizona, USA, 2013-2018.

Tick-borne relapsing fever (TBRF) is a bacterial infection transmitted by tick bites that occurs in several different parts of the world, including the western United States. We describe 6 cases of TBRF acquired in the White Mountains of Arizona, USA, and diagnosed during 2013-2018. All but 1 case-patient had recurrent fever, and some had marked laboratory abnormalities, including leukopenia, thrombocytopenia, hyperbilirubinemia, and elevated aminotransaminases. One patient had uveitis. Diagnosis was delayed in 5 of the cases; all case-patients responded to therapy with doxycycline. Two patients had Jarisch-Herxheimer reactions. The White Mountains of Arizona have not been previously considered a region of high incidence for TBRF. These 6 cases likely represent a larger number of cases that might have been undiagnosed. Clinicians should be aware of TBRF in patients who reside, recreate, or travel to this area and especially for those who sleep overnight in cabins there.

Evidence of Likely Autochthonous Transmission of Chagas Disease in Arizona.

A healthy 16-year-old girl born and raised in Tucson, AZ, had screening and confirmatory testing revealing Chagas disease; clinical evaluation established that she had the indeterminate form of chronic Chagas disease with evidence of likely autochthonous transmission. Trypanosoma cruzi DNA was detected by conventional polymerase chain reaction in Triatoma rubida captured at her home.