Geographic Differences In Prevalence Research Articles

Staphylococcus argenteus bacteremia in the Republic of Korea.

In 2015, Staphylococcus argenteus and Staphylococcus schweitzeri were proposed as new species, distinct from Staphylococcus aureus and collectively referred to as the S. aureus complex. However, no clinical reports of these new species exist in Korea. Upon the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for all bloodstream isolates since September 2022, S. argenteus was identified in one patient. Therefore, we aimed to search for new species among the archives of the S. aureus bacteremia cohort and describe their clinical and microbiological characteristics. Among the 691 archived S. aureus isolates between 2012 and 2018, one was identified as S. argenteus via MALDI-TOF MS. Both S. argenteus isolates (one in 2022) were obtained from patients with extensive pneumonia accompanied by bacteremia and both cases had fatal outcomes. They harbored multiple virulence genes (clfA, clfB, fnbpA, sdrC, sdrD, sdrE, bbp, cna, see, seg, sei, blaZ, fnbpB, and map) but did not harbor mecA and pvl. No matched sequence type (ST) was found in either isolate, and both S. argenteus isolates were closely related to ST1594, ST1593, ST1793, and ST1303, which belonged to S. argenteus. S. argenteus accounted for <1% of the S. aureus complex but had clinical characteristics similar to S. aureus. Therefore, clinicians should be aware of these factors to avoid misidentifying these strains as coagulase-negative staphylococci, and appropriate reporting is required to minimize confusion.IMPORTANCEStaphylococcus argenteus, a member of Staphylococcus aureus complex, has been reported as an important pathogen that causes clinically invasive infections in humans similar to S. aureus. Clinical isolates of S. argenteus have been reported across the world, showing a large geographical difference in prevalence and genomic profile. However, there have been no clinical reports regarding this new species in Korea. This is the first report to investigate the clinical and genetic characteristics of S. argenteus identified in patients with bacteremia, and the proportion of S. argenteus bacteremia among S. aureus bacteremia cohort in Korea.

Global birth prevalence of Robin sequence in live-born infants: a systematic review and meta-analysis.

Robin sequence (RS), a congenital disorder of jaw maldevelopment and glossoptosis, poses a substantial healthcare burden and has long-term health implications if airway obstruction is suboptimally treated. This study describes the global birth prevalence of RS and investigates whether prevalence estimates differ by geographical location, ethnicity or study data source (registry versus non-registry data). The protocol was prospectively registered with PROSPERO.Databases were searched using keywords and subject terms for "Robin sequence", "epidemiology", "incidence" and "birth prevalence". Meta-analysis was performed fitting random effects models with arcsine transformation.From 34 eligible studies (n=2722 RS cases), pooled birth prevalence was 9.5 per 100 000 live births (95% CI 7.1-12.1) with statistical heterogeneity. One third of studies provided a case definition for RS and numerous definitions were used. A total of 22 countries were represented, predominantly from European populations (53% of studies). There was a trend towards higher birth prevalence in European populations and lower prevalence from registry-based studies. Only two studies reported ethnicity.This study indicates that RS occurs globally. To investigate geographical differences in prevalence, additional studies from non-European populations and reporting of ethnicity are needed. Heterogeneity of estimates may be due to variable diagnostic criteria and ascertainment methods. Recently published consensus diagnostic criteria may reduce heterogeneity among future studies.

Prevalence, antibiotic resistance, and molecular epidemiology of Listeria monocytogenes isolated from imported foods in China during 2018 to 2020

A total of 1797 imported food samples collected during 2018 to 2020 were investigated for Listeria monocytogenes. Antibiotic susceptibility tests and whole genome sequencing analysis were performed for the obtained isolates. The overall prevalence of L. monocytogenes was 5.62 %; the highest prevalence was observed for pork (13.65 %), followed by fish (6.25 %), sheep casing (6.06 %), chicken (3.61 %), and beef (2.06 %). Geographical differences in prevalence were also observed for pork. Resistance to oxacillin (39.33 %) and clindamycin (16.85 %) was common, whereas resistance rates for other antibiotics were relatively low, ranging from 0 % to 6.74 %. Pork and fish isolates showed resistance to more antibiotics than beef isolates. Tetracycline and chloramphenicol resistance phenotypes strongly correlated with genotypes. The predominant serogroup was 1/2a, 3a, at 44.44 %, while the percentages of three other serogroups were similar and relatively lower, from 17.28 % to 19.75 %. Significant genetic differences were observed among lineage I and II isolates. LIPI-3 was carried by 19.75 % (16/81) of isolates and LIPI-4 by 6.17 % (5/81); all were lineage I. The stress survival island was present in 31.03 % (9/29) of lineage I and 83.02 % (44/53) of lineage II. Benzalkonium chloride tolerance genes were carried by 10.34 % (3/29) of lineage I and 23.08 % (12/52) of lineage II isolates. A total of 25 sequence types (STs) were identified, among which one was novel; ST9 and ST121 were the most prevalent. Disparate distribution of STs among food types was observed, and geographical and food related characteristics were also found for some STs. Hypervirulent STs, such as ST1, ST4 and ST6, belonged to 4b,4e,4e; carried LIPI-3 and/or LIPI-4; and some even were ECI or ECII; while only one carried SSI or BC tolerance genes. In contrast, hypo-virulent STs such as ST9 and ST121 carried SSI and BC tolerance genes, while none had LIPI-3/LIPI-4. Certain STs were detected frequently from a particular food of a particular country for a long time, indicating more attention should be given to these special persistent isolates. These findings are valuable for source tracking, prevention and control of L. monocytogenes in the global food chain.

CKD Prevalence Among Patients With and Without Type 2 Diabetes: Regional Differences in the United States

Rationale & ObjectiveRegional variation in chronic kidney disease (CKD) prevalence in patients with or without type 2 diabetes mellitus (T2DM) has not been well characterized.Study DesignSpatial and temporal comparative analysis.Setting & ParticipantsMarketScan databases were used to identify patients with CKD overall and subgroups of patients with CKD with and without T2DM in the United States.OutcomesSpatial patterns in CKD prevalence based on year, regional clusters of CKD between years, and characteristics of patients in high-prevalence states.Analytical ApproachGeomapping was used to visualize the state-level data of CKD prevalence generated from 2013 to 2018. We used univariate local indicators of spatial association (LISA) to evaluate geographic differences in prevalence, differential LISA for changes in CKD prevalence over time, and the χ2 test to identify patient characteristics in the top-20th percentile states for the prevalence of CKD.ResultsIn univariate LISA, low-low clusters, in which a state has a low CKD prevalence and the surrounding states have a below-average CKD prevalence, were observed in the northwest region throughout the study period, regardless of the T2DM status, indicating a consistently low prevalence of CKD clustered in these areas. High-high clusters were observed, regardless of the T2DM status, in the southeast region in more recent years, suggesting an increased CKD prevalence in this region.LimitationsHealth care insurance enrollment might not have been representative of the United States; the estimates were based on claims data that likely underestimated the true prevalence.ConclusionsGeographic disparities in CKD prevalence appear increasingly magnified, with an increase in the southeastern region of the United States. This increase is especially problematic because patients with CKD in high-prevalence states experience a greater likelihood of chronic conditions than those in the rest of the United States.

Host and geographic differences in prevalence and diversity of gastrointestinal helminths of foxes (Vulpes vulpes), coyotes (Canis latrans) and wolves (Canis lupus) in Québec, Canada.

Wild canids are hosts to a wide range of parasites and can play a role in transmission of zoonoses. As many parasites are transmitted through food webs, and wild canids are at high trophic levels, parasite prevalence and diversity in wild canids can serve as excellent indicators of ecosystem health. Our main objectives were to update knowledge on the composition of gastrointestinal helminths in wild canids from Québec, Canada, and to describe differences in parasite prevalence and diversity among canid species and regions. Hunters and trappers provided whole carcasses of red foxes (Vulpes vulpes) (N = 176), and intestinal tracts of coyotes (Canis latrans) (N = 77) and gray wolves (Canis lupus) (N = 23) harvested for non-research purposes over the winter of 2016–2017. A modified Stoll's centrifugation sucrose flotation on feces of 250 wild canids was used, and eggs of one family and eight genera of parasitic helminths were recovered: diphyllobothriids, Taenia/Echinococcus spp., Capillaria spp., Toxascaris sp., Toxocara sp., Trichuris sp., Uncinaria sp., and Metorchis sp. Adult Taenia spp. cestodes were recovered from 61 of 276 (22%) canids. Six different species (T. hydatigena, T. twitchelli, T. crassiceps, T. polyacantha, T. krabbei, and T. pisiformis-“like”) were differentiated based on DNA sequenced from 65 individual adult cestodes using primers for the nicotinamide adenosine dinucleotide dehydrogenase subunit 1 (ND1) and cytochrome c oxidase subunit 1 (CO1) mitochondrial DNA loci. Alaria sp. trematodes infected 89 of 276 canids (32%). A subset were identified as A. americana at the CO1 locus. The marine trematode Cryptocotyle lingua was reported for the first time in foxes in the province of Québec. These results help us understand more fully the predator-prey relationships within this group of canids. This baseline data in regional parasite prevalence and intensity is critical in order to detect future changes following ecological disturbances due to climate and landscape alterations.

Molecular detection of influenza A viruses and H5 subtype among migratory Amur falcons (Falco amurensis) and captive birds of prey.

Influenza A viruses (IAVs) and Newcastle disease viruses (NDVs) are major human and animal health threats with geographic differences in prevalence, characteristics and host populations. Currently, there is sparse information on IAVs and NDVs in avian species in South Africa. Because raptors feed on live wild birds which are the reservoir hosts of IAVs and NDVs, we considered them a good sentinel for surveillance. Therefore, in addition to other resident birds of prey, migratory Amur falcons (Falco amurensis) were screened for IAVs and NDVs. Oropharyngeal and cloacal samples were collected from raptor species at three sampling sites in KwaZulu-Natal Province and samples were screened for IAVs and NDVs using molecular and virus isolation methods. IAV-positive samples were further screened for the presence of H5, H7 and H9 viruses. A total of 14 samples from 11 birds (45.8% of all sampled birds) were IAV positive with Ct lower than 36 in duplicate tests. Five out of 24 birds (20.8%) were positive for IAV RNA in duplicate testing, albeit at low concentrations. Among raptor samples, three out of 24 birds (12.5%) were positive for IAVs with viral RNA detected in both cloacal and oropharyngeal swabs. One IAV-positive sample was also positive for H5 subtype (4.1%); all other samples were H5, H7 and H9 negative. Besides, all samples were NDV negative. Overall, our results support the development of more intensive and expanded influenza and other emerging virus studies in raptor species.

Association of Geographic Differences in Prevalence of Uncontrolled Chronic Conditions With Changes in Individuals’ Likelihood of Uncontrolled Chronic Conditions

The prevalence of leading risk factors for morbidity and mortality in the US significantly varies across regions, states, and neighborhoods, but the extent these differences are associated with a person's place of residence vs the characteristics of the people who live in different places remains unclear. To estimate the degree to which geographic differences in leading risk factors are associated with a person's place of residence by comparing trends in health outcomes among individuals who moved to different areas or did not move. This retrospective cohort study estimated the association between the differences in the prevalence of uncontrolled chronic conditions across movers' destination and origin zip codes and changes in individuals' likelihood of uncontrolled chronic conditions after moving, adjusting for person-specific fixed effects, the duration of time since the move, and secular trends among movers and those who did not move. Electronic health records from the Veterans Health Administration were analyzed. The primary analysis included 5 342 207 individuals with at least 1 Veterans Health Administration outpatient encounter between 2008 and 2018 who moved zip codes exactly once or never moved. The difference in the prevalence of uncontrolled chronic conditions between a person's origin zip code and destination zip code (excluding the individual mover's outcomes). Prevalence of uncontrolled blood pressure (systolic blood pressure level >140 mm Hg or diastolic blood pressure level >90 mm Hg), uncontrolled diabetes (hemoglobin A1c level >8%), obesity (body mass index >30), and depressive symptoms (2-item Patient Health Questionnaire score ≥2) per quarter-year during the 3 years before and the 3 years after individuals moved. The study population included 5 342 207 individuals (mean age, 57.6 [SD, 17.4] years, 93.9% men, 72.5% White individuals, and 12.7% Black individuals), of whom 1 095 608 moved exactly once and 4 246 599 never moved during the study period. Among the movers, the change after moving in the prevalence of uncontrolled blood pressure was 27.5% (95% CI, 23.8%-31.3%) of the between-area difference in the prevalence of uncontrolled blood pressure. Similarly, the change after moving in the prevalence of uncontrolled diabetes was 5.0% (95% CI, 2.7%-7.2%) of the between-area difference in the prevalence of uncontrolled diabetes; the change after moving in the prevalence of obesity was 3.1% (95% CI, 2.0%-4.2%) of the between-area difference in the prevalence of obesity; and the change after moving in the prevalence of depressive symptoms was 15.2% (95% CI, 13.1%-17.2%) of the between-area difference in the prevalence of depressive symptoms. In this retrospective cohort study of individuals receiving care at Veterans Health Administration facilities, geographic differences in prevalence were associated with a substantial percentage of the change in individuals' likelihood of poor blood pressure control or depressive symptoms, and a smaller percentage of the change in individuals' likelihood of poor diabetes control and obesity. Further research is needed to understand the source of these associations with a person's place of residence.

Seasonal dynamics of haemosporidian (Apicomplexa, Haemosporida) parasites in house sparrows Passer domesticus at four European sites: comparison between lineages and the importance of screening methods

Infectious diseases often vary seasonally in a predictable manner, and seasonality may be responsible for geographical differences in prevalence. In temperate regions, vector-borne parasites such as malaria are expected to evolve lower virulence and a time-varying strategy to invest more in transmission when vectors are available. A previous model of seasonal variation of avian malaria described a double peak in prevalence of Plasmodium parasites in multiple hosts resulting from spring relapses and transmission to susceptible individuals in summer. However, this model was rejected by a study describing different patterns of seasonal variation of two Plasmodium spp. at the same site, with the double peak only apparent when these species were combined. Here, we assessed the seasonal variation in prevalence of haemosporidian parasites (Plasmodium, Haemoproteus and Leucocytozoon) in house sparrows (Passer domesticus) sampled across 1 year at four temperate European sites spanning a latitudinal range of 17°. We showed that parasite prevalence and diversity decreased with increasing latitude, but the parasite communities differed between sites, with only one Plasmodium lineage (P_SGS1) occurring at all sites. Moreover, the nested PCR method commonly used to detect and identify haemosporidian parasites strongly underestimated co-infections of Haemoproteus and Plasmodium, significantly biasing the pattern of seasonal variation, so additional molecular methods were used. Finally, we showed that: (i) seasonal variation in prevalence of haemosporidian parasites varied between study sites and parasite lineages/species/genera, describing further cases where the double peak model is not met; (ii) the seasonal dynamics of single lineages (P_SGS1) varied between sites; and (iii) unexpectedly, seasonality was greatest at the southernmost site, a pattern that was mostly driven by lineage H_PADOM05. Limitations of the genotyping methods and consequences of pooling (parasite lineages, sites and years) in studies of haemosporidian parasites are discussed and recommendations proposed, since these actions may obscure the patterns of prevalence and limit ecological inferences.

Epidemiology of congenital cerebral anomalies in Europe: a multicentre, population-based EUROCAT study

ObjectivesTo describe the epidemiology and geographical differences in prevalence of congenital cerebral anomalies in Europe.Design and settingCongenital cerebral anomalies (International Classification of Diseases, 10th Revision code Q04) recorded in 29...

Temporal and Geographical Variability of Prevalence and Incidence of Autism Spectrum Disorder Diagnoses in Children in Catalonia, Spain.

This study aims to estimate the prevalence of autism spectrum disorders (ASD) in 2017 and the ASD diagnosis incidence between 2009 and 2017 in children living in Catalonia region in Spain, and their temporal and geographical variability. We used administrative data for all children aged 2–17 years who were insured in the public Catalan Health System between 2009 and 2017. We identified all ASD cases diagnosed between 2009 and 2017 (ICD‐9 codes 299.0, 299.1, 299.8, and 299.9). We estimated the ASD prevalence in 2017 and the overall annual incidence between 2009 and 2017, then stratified by sex, age group, and healthcare area. We used Poisson regression models to assess temporal trends in the incidence and mixed‐effects Poisson regression models to assess geographical variability. We observed an ASD prevalence of 1.23% (95% confidence interval [CI] 1.21–1.25) in 2017, with 1.95% (95% CI 1.92–1.99) for boys and 0.46% (95% CI 0.44–0.48) for girls, the highest prevalence being in 11‐ to 17‐year‐olds (1.80%, 95% CI 1.76–1.83). The ASD diagnosis incidence increased from 0.07% (95% CI 0.06–0.09) in 2009 to 0.23% (95% CI 0.21–0.24) in 2017, with a higher increase in girls, and in children aged 2–5 years at the time of diagnosis. We only observed geographical differences in prevalence in the 2017 data. We also detected a threefold increase in the diagnosis incidence overall, which was even more pronounced in girls and at early ages. In conclusion, the ASD prevalence observed in this study was 1.23% in 2017, with a sex ratio of 4.5 in favor of boys, which is consistent with previous studies. Autism Res 2019. © 2019 International Society for Autism Research, Wiley Periodicals, Inc.Lay SummaryAutism spectrum disorders (ASD) are currently well known in our society as one of the most common neurodevelopmental disorders during childhood. The results of our study showed that, in 2017 in Catalonia, slightly more than one in a 100 children had an ASD diagnosis, it was more common in boys than in girls, and also in older children. In addition, between 2009 and 2017, we observed an increase in the number of new cases diagnosed each year. The data presented in this study will assist in planning and evaluating the needs of health services in this geographical region.

Possible Clinical Implications of Geographic Differences in Prevalence of Double Transverse Foramen

The double transverse foramen (DBLTF) is a cervical spine anatomic variant. Current literature has presented prevalence values of DBLTF in Caucasian Mediterranean subjects that seem to be higher than those observed in other samples of subjects. Therefore we aimed to test if Caucasian Mediterranean subjects present a higher prevalence of the DBLTF than sub-Saharan African subjects. We analyzed the presence of DBLTF in cervical spines of 100 skeletons from Caucasian Mediterranean subjects and 91 skeletons from sub-Saharan African subjects, resulting in a total of 1337 cervical vertebrae having been studied. No DBLTF was found in vertebrae C1, C2, and C3. The pattern of prevalence observed in all samples analyzed indicated the prevalence ranged from exhibiting the most to the least prevalence as C6 > C5 > C7 > C4. The sub-Saharan African subjects presented a significant reduced DBLTF prevalence of 2.2%, 14.3%, 19.8%, and 3.3% in C4 (P= 0.043), C5 (P= 0.004), C6 (P < 0.001), and C7 (P= 0.041), respectively, than that presented by Caucasian Mediterranean subjects (9.0%, 32.0%, 45.0%, 11.0% in C4, C5, C6, and C7, respectively). Our study has revealed that this anatomic variation is more frequently found in Caucasian Mediterranean subjects than in sub-Saharan African subjects.

Prevalence of Borrelia burgdorferi, Anaplasma spp., Ehrlichia spp. and Dirofilaria immitis in Canadian dogs, 2008 to 2015: a repeat cross-sectional study

BackgroundVector-borne pathogens are emerging concerns in multiple regions of Canada. Determining regional prevalence of canine vector-borne pathogens and documenting change will improve clinician awareness, enable targeted prevention, enhance diagnosis and ideally reduce the risk of disease. Study objectives were to: (i) estimate the prevalence of positive canine vector-borne test results from samples submitted in Canada; (ii) assess change in prevalence over time, from baseline (2008) to 2015; and (iii) estimate the prevalence of pathogen co-infections.MethodsThis repeat cross-sectional study evaluated 753,468 test results for D. immitis antigen and B. burgdorferi, Ehrlichia canis/ewingii/muris serology, and 753,208 test results for Anaplasma phagocytophilum/platys serology using the SNAP® 4Dx®Test and SNAP 4Dx® Plus Test.ResultsBased on all submitted samples from Canada (2008–2015), the period seroprevalence of B. burgdorferi, Ehrlichia spp., Anaplasma spp. and D. immitis antigen were 2.0%, 0.5%, 0.4% and 0.2%, respectively. Over the 7 years (2008 compared to 2015) we observed a significant increase in seroprevalence for B. burgdorferi (144.4%) and Ehrlichia spp. (150%). Co-infections (positive for two or more pathogens on a single 4 pathogen test kit) were estimated at 5.4% (1162/21,612) of total positive tests.ConclusionsThe temporal rise and geographical differences in prevalence detected for these pathogens (notably B. burgdorferi) are consistent with anecdotal information on canine illness related to tick-borne pathogen exposure in multiple regions of Canada, particularly canine Lyme disease.

Global Distribution of Human Protoparvoviruses.

Development of next-generation sequencing and metagenomics has revolutionized detection of novel viruses. Among these viruses are 3 human protoparvoviruses: bufavirus, tusavirus, and cutavirus. These viruses have been detected in feces of children with diarrhea. In addition, cutavirus has been detected in skin biopsy specimens of cutaneous T-cell lymphoma patients in France and in 1 melanoma patient in Denmark. We studied seroprevalences of IgG against bufavirus, tusavirus, and cutavirus in various populations (n = 840), and found a striking geographic difference in prevalence of bufavirus IgG. Although prevalence was low in adult populations in Finland (1.9%) and the United States (3.6%), bufavirus IgG was highly prevalent in populations in Iraq (84.8%), Iran (56.1%), and Kenya (72.3%). Conversely, cutavirus IgG showed evenly low prevalences (0%–5.6%) in all cohorts, and tusavirus IgG was not detected. These results provide new insights on the global distribution and endemic areas of protoparvoviruses.

Geographic Differences in Baseline Prostate Inflammation and Relationship with Subsequent Prostate Cancer Risk: Results from the Multinational REDUCE Trial.

Background: Prostate cancer incidence rates vary 25-fold worldwide. Differences in PSA screening are largely, but not entirely, responsible. We examined geographic differences in prevalence of histologic prostate inflammation and subsequent prostate cancer risk.Methods: Seven thousand nonHispanic white men were enrolled in the REduction by DUtasteride of prostate Cancer Events (REDUCE) trial from Europe (n = 4,644), North America (n = 1,746), South America (n = 466), and Australia/New Zealand (n = 144). Histologic inflammation in baseline negative prostate biopsies was classified as chronic (lymphocytes/macrophages) or acute (neutrophils). Multivariable logistic regression was used to examine associations between region and prostate inflammation, and between region and prostate cancer risk at 2-year biopsy.Results: Prevalence of prostate inflammation varied across region, with broadly similar patterns for acute and chronic inflammation. Relative to Europe, prevalence of acute inflammation was higher in North America [odds ratio (OR), 1.77; 95% confidence interval (CI), 1.51-2.08] and Australia/New Zealand (OR, 2.07; 95% CI, 1.40-3.06). Men from these regions had lower prostate cancer risk than Europeans at biopsy. Among North Americans, prevalence of acute inflammation was higher in Canada versus the United States (OR, 1.40; 95% CI, 1.07-1.83), but prostate cancer risk did not differ between these regions. Among Europeans, prevalence of acute inflammation was lower in Northern and Eastern (OR, 0.79; 95% CI, 0.65-0.97 and OR 0.62; 95% CI, 0.45-0.87, respectively), relative to Western Europe, and these men had higher prostate cancer risk at biopsy.Conclusions: Prevalence of histologic prostate inflammation varied by region. Geographic differences in prostate inflammation tracked inversely with geographic differences in prostate cancer risk.Impact: Characterization of premalignant prostate biology and the relationship with subsequent prostate cancer risk could inform prostate cancer prevention efforts. Cancer Epidemiol Biomarkers Prev; 27(7); 783-9. ©2018 AACR.

Usability of the international HAVNet hepatitis A virus database for geographical annotation, backtracing and outbreak detection.

BackgroundHAVNet is an international laboratory network sharing sequences and corresponding metadata on hepatitis A virus in an online database. Aim: We give an overview of the epidemiological and genetic data and assess the usability of the present dataset for geographical annotation, backtracing and outbreak detection. Methods: A descriptive analysis was performed on the timeliness, completeness, epidemiological data and geographic coverage of the dataset. Length and genomic region of the sequences were reviewed as well as the numerical and geographical distribution of the genotypes. The geographical signal in the sequences was assessed based on a short common nt stretch using a 100% identity analysis. Results: The 9,211 reports were heterogeneous for completeness and timeliness, and for length and genomic region of the sequences. Some parts of the world were not represented by the sequences. Geographical differences in prevalence of HAV genotypes described previously could be confirmed with this dataset and for a third (1,075/3,124) of the included sequences, 100% identity of the short common sequence coincided with an identical country of origin. Conclusion: Analysis of a subset of short, shared sequences indicates that a geographical annotation on the level of individual countries is possible with the HAVNet data. If the current incompleteness and heterogeneity of the data can be improved on, HAVNet could become very useful as a worldwide reference set for geographical annotation and for backtracing and outbreak detection.

Origins and Spread of Machado-Joseph Disease Ancestral Mutations Events.

Machado-Joseph disease (MJD) is the most common autosomal dominant spinocerebellar ataxia reported worldwide, but it shows marked geographic differences in prevalence. The study of ancestral origins and spreading routes of MJD mutational events has contributed to explain such differences. During human evolution, at least two independent de novo MJD expansions occurred in distinct haplotype backgrounds: TTACAC and GTGGCA (named Joseph and Machado lineages). The most ancient Joseph lineage, probably of Asian origin, has been introduced recently in Europe, where founder effects are responsible for the high MJD prevalence, as occurs in the Portuguese/Azorean island of Flores and Northeastern mainland. The Machado lineage is geographically more restricted, with most known families in Portugal (island of São Miguel and along the Tagus valley). The hypothesis of other mutational origins has been raised, namely to explain the disease among Australian aborigines; however, a comprehensive haplotype study suggested the introduction of the Joseph lineage in that community via Asia. Also, additional SNP-based haplotypes (TTAGAC, TTGGAC and GTGCCA) were observed in other MJD families, but phylogenetic analysis with more polymorphic flanking markers did not point to independent mutational events, reinforcing the hypothesis of a very low mutation rate underlying this repeat expansion locus.

Genetic factors affecting EBV copy number in lymphoblastoid cell lines derived from the 1000 Genome Project samples.

Epstein-Barr virus (EBV), human herpes virus 4, has been classically associated with infectious mononucleosis, multiple sclerosis and several types of cancers. Many of these diseases show marked geographical differences in prevalence, which points to underlying genetic and/or environmental factors. Those factors may include a different susceptibility to EBV infection and viral copy number among human populations. Since EBV is commonly used to transform B-cells into lymphoblastoid cell lines (LCLs) we hypothesize that differences in EBV copy number among individual LCLs may reflect differential susceptibility to EBV infection. To test this hypothesis, we retrieved whole-genome sequenced EBV-mapping reads from 1,753 LCL samples derived from 19 populations worldwide that were sequenced within the context of the 1000 Genomes Project. An in silico methodology was developed to estimate the number of EBV copy number in LCLs and validated these estimations by real-time PCR. After experimentally confirming that EBV relative copy number remains stable over cell passages, we performed a genome wide association analysis (GWAS) to try detecting genetic variants of the host that may be associated with EBV copy number. Our GWAS has yielded several genomic regions suggestively associated with the number of EBV genomes per cell in LCLs, unraveling promising candidate genes such as CAND1, a known inhibitor of EBV replication. While this GWAS does not unequivocally establish the degree to which genetic makeup of individuals determine viral levels within their derived LCLs, for which a larger sample size will be needed, it potentially highlighted human genes affecting EBV-related processes, which constitute interesting candidates to follow up in the context of EBV related pathologies.

Abstract MP060: Contributors to the Geographic Disparity in Stroke Incidence in the United States: Results From the Reasons for Geographic and Racial Disparities in Stroke Cohort

Introduction: Geographic disparities in US stroke risk have recently been confirmed by REGARDS, but contributors to this are unknown. Higher prevalence of risk factors (RF) and lower socioeconomic status (SES) may contribute to this geographic disparity. For a RF/SES to contribute to this disparity it must both : 1) have a large geographic difference in prevalence, and 2) be powerfully associated with stroke risk. Methods: The 1,623 counties of residence of 24,863 REGARDS participants were placed in quartiles of Vital Statistics stroke mortality. Logistic regression assessed the geographic difference in prevalence of each RF/SES by quartile of stroke mortality. Proportional hazards was used to calculate HR stroke for each RF/SES. Mediation analysis then estimated the proportion of increased stroke incidence in counties with high stroke mortality explained by each RF/SES. Results: Higher county-level stroke mortality was significantly associated with low neighborhood SES (nSES), and more weakly associated with low education and presence of RFs (left column of table). Over 8-years follow-up there were 1,194 stroke events. Hypertension, diabetes and heart disease were all more strongly associated with higher stroke risk (HR ≥1.59) than nSES (HR = 1.21) (center column of table). The large differences in nSES between regions overcame the somewhat weaker association of nSES with stroke risk, since nSES was the largest single contributor to the geographic disparity in stroke incidence, accounting for 20.5% of the disparity (95% CI: 7.1 - 34.0) (right column in table). In multivariable analysis nSES, hypertension and diabetes collectively mediated27% of the geographic disparity (95% CI: 20.0% - 34.0%), but the association with county-level mortality remained significant (p = 0.006). Conclusion: Lower nSES played the largest role in explaining the county-level geographic disparity in stroke incidence in REGARDS, however, 73% of the excess risk of stroke incidence was not explained by any studied factors.

Distribution and Prevalence of Haemosporidian Parasites in the Northern Cardinal (Cardinalis cardinalis).

Avian haemosporidian parasites provide a model system for understanding ecological and evolutionary host-parasite interactions. The diversity and distribution of these parasites remains incomplete, and, here, we provide the first range-wide assessment of avian haemosporidians in a continentally distributed host, the Northern Cardinal ( Cardinalis cardinalis ). Based on molecular techniques, we show geographical differences in prevalence and lineage diversity between host subspecies and identify several novel lineages. We use phylogenetic reconstruction to show where these lineages fit into the expanding evolutionary tree of avian haemosporidian lineages. All except 1 subspecies of Northern Cardinal are highly parasitized by a wide diversity of Plasmodium and Parahaemoproteus. Compared to published studies that used microscopy to determine prevalence in this host, we find a much higher number of infected individuals (67.4% vs. 45% or less). Consistent with previous studies, Parahaemoproteus from the Northern Cardinal was found to be highly host specific and geographically structured, whereas Plasmodium was less host specific and geographically unstructured.

Siphonostomatoid copepods infecting Squalus acutipinnis Regan, 1908 off South Africa

Squalus acutipinnis (previously included in S. megalops) individuals caught off the east, south and west coasts of South Africa were examined for siphonostomatoid copepod infection. Collected siphonostomatoids were fixed and preserved in 70% ethanol and studied under microscopes using both transmitted and incidental light. The copepods were identified and the host-parasite associations estimated by calculating their prevalence, mean intensity and mean abundance. The siphonostomatoids represented four families and six species, and included new host records for Nemesis sp., Lernaeopoda sp. and Eudactylina acanthii, and a new geographical record for E. acanthii. Squalus acutipinnis individuals were infected by relatively low loads of siphonostomatoids. The most commonly found species was Achtheinus pinguis, the only species found off all three coasts. There was no difference in the prevalence of A. pinguis in sharks sampled off the three coasts but the highest mean intensity was found on the East Coast followed by the West Coast. The overall prevalence of A. pinguis was 33.6%, and was an order of magnitude higher than that of the other siphonostomatoids recorded. At such low levels of infection it will thus be necessary to examine a large number of hosts to determine the biodiversity of siphonostomatoids and geographical differences in prevalence in South African waters.