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Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest.

ABSTRACT: West Nile Virus (WNV) has been detected annually in Maricopa County, Arizona, since 2003. With this in mind, we sought to determine if contemporary strains are endemic to the county or are annually imported. As part of this effort, we developed a new protocol for tiled amplicon sequencing of WNV to efficiently attain greater than 99% coverage of 14 WNV genomes collected directly from positive mosquito pools distributed throughout Maricopa County between 2014 and 2017. Bayesian phylogenetic analyses revealed that contemporary genomes fall within two major lineages; NA/WN02 and SW/WN03. We found that all of the Arizona strains possessed an amino acid substitution known to be under positive selection, which has arisen independently at least four times in Arizona. The SW/WN03 strains exhibited transient behavior, with at least 10 separate introductions into Arizona when considering both historical and contemporary strains. However, NA/WN02 strains are geographically differentiated and appear to be endemic in Arizona, with two clades that have been circulating for four and seven years. This establishment in Maricopa County provides the first evidence of local overwintering by a WNV strain over the course of several years in Arizona. Within a national context, the placement of eleven contemporary Arizona strains in the NA/WN02 lineage indicates while WNV first entered the northeastern United States in 1999, the most ancestral extant strains of WNV are now circulating in the American southwest.

SUBMITTER: Hepp CM

PROVIDER: S-EPMC6261030 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:On 10 August 2016, the Maricopa County Department of Public Health identified culture-confirmed Salmonella enterica serotype Javiana isolates from two persons who reported eating at a seafood restaurant; seven additional cases were reported by 15 August. We investigated to identify a source and prevent further illness. We interviewed persons with laboratory-reported Salmonella Javiana infection. Pulsed-field gel electrophoresis (PFGE) and whole genome sequencing of isolates were performed. A case was defined as diarrheal illness in a person during July to September 2016; confirmed cases had Salmonella Javiana isolate yielding outbreak-related PFGE patterns; probable cases had diarrheal illness and an epidemiologic link to a confirmed case. Case finding was performed (passive surveillance and identification of ill meal companions). A case-control study assessed risk factors for Salmonella Javiana infection among restaurant diners; control subjects were chosen among meal companions. No restaurant workers reported illness. Foods were reportedly cooked according to the Food Code. Food and environmental samples were collected and cultured; Salmonella Javiana with an indistinguishable PFGE pattern was isolated from portioned repackaged raw shrimp, halibut, and a freezer door handle. We identified 50 Salmonella Javiana cases (40 confirmed and 10 probable); illness onset range was from 22 July to 17 September 2016. Isolates from 40 patients had highly related PFGE patterns. Thirty-three (73%) of 45 patients interviewed reported eating at the restaurant. Among 21 case patients and 31 control subjects, unfried cooked shrimp was associated with illness (odds ratio, 6.7; 95% confidence interval, 1.8 to 24.9; P = 0.004). Among restaurant diners, laboratory and case-control evidence indicated shrimp as the possible outbreak source; poor thermal inactivation of Salmonella on shrimp is theorized as a possible cause. Cross-contamination might have prolonged this outbreak; however, the source was not identified and highlights limitations that can arise during these types of investigations.

Project description:Campylobacter is a leading cause of gastroenteritis across the globe caused by the ingestion of contaminated food, water, or contact with animals carrying Campylobacter bacteria. The resulting disease, campylobacteriosis, is usually self-limiting, but cases may develop post-infectious sequelae (PIS) such as gastrointestinal disorders, neurological disorders, and joint disorders. The objective of this study was to estimate a crude incidence rate for PIS among Campylobacter cases in Maricopa County, Arizona, USA and to determine the feasibility of conducting a larger scale study to understand chronic outcomes from campylobacteriosis and salmonellosis.The pilot study spanned from August 1, 2016, to August 31, 2017. During this time, cases of campylobacteriosis were reported to the Maricopa County Department of Public Health and interviewed by public health students at the University of Arizona. Initial interviews were conducted using a routine enteric surveillance questionnaire, and eligible cases were recruited and consented into the pilot study. Follow-up with a questionnaire occurred 4 to 6 weeks from the date of each case's initial interview. Data analysis was conducted using STATA SE 14 and included chi-squared tests to determine differences in demographics, symptoms, and exposures between those enrolled in the study and those eligible but not enrolled during the study period and feasibility metrics for the study including enrollment rates, response rates, time to interview, and reasons for non-enrollment. Crude rates with 95% confidence intervals were calculated to estimate PIS.Of the routine surveillance cases, 102 (36%) enrolled into the pilot study. Of enrolled participants, 68.6% completed the follow-up questionnaire. Most enrolled participants were non-Hispanic White, male, and aged 60?+?years. Over half (52.8%, 95% CI 41.1%, 64.5%) of cases experienced PIS approximately 4 to 6 weeks after acute onset of campylobacteriosis.Results from this pilot study indicate that a larger study is feasible. The larger study will identify the true incidence of PIS and improve the management of patient health among ethnically diverse populations.

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Phylogenetic analysis of West Nile Virus in Maricopa County, Arizona: Evidence for dynamic behavior of strains in two major lineages in the American Southwest.

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