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This study evaluated the use of endemic enteric coronaviruses polymerase chain reaction (PCR)-negative testing results as an alternative approach to detect the emergence of animal health threats with similar clinical diseases presentation. This retrospective study, conducted in the United States, used PCR-negative testing results from porcine samples tested at six veterinary diagnostic laboratories. As a proof of concept, the database was first searched for transmissible gastroenteritis virus (TGEV) negative submissions between January 1st, 2010, through April 29th, 2013, when the first porcine epidemic diarrhea virus (PEDV) case was diagnosed. Secondly, TGEV- and PEDV-negative submissions were used to detect the porcine delta coronavirus (PDCoV) emergence in 2014. Lastly, encountered best detection algorithms were implemented to prospectively monitor the 2023 enteric coronavirus-negative submissions. Time series (weekly TGEV-negative counts) and Seasonal Autoregressive-Integrated Moving-Average (SARIMA) were used to control for outliers, trends, and seasonality. The SARIMA's fitted and residuals were then subjected to anomaly detection algorithms (EARS, EWMA, CUSUM, Farrington) to identify alarms, defined as weeks of higher TGEV-negativity than what was predicted by models preceding the PEDV emergence. The best-performing detection algorithms had the lowest false alarms (number of alarms detected during the baseline) and highest time to detect (number of weeks between the first alarm and PEDV emergence). The best-performing detection algorithms were CUSUM, EWMA, and Farrington flexible using SARIMA fitted values, having a lower false alarm rate and identified alarms 4 to 17 weeks before PEDV and PDCoV emergences. No alarms were identified in the 2023 enteric negative testing results. The negative-based monitoring system functioned in the case of PEDV propagating epidemic and in the presence of a concurrent propagating epidemic with the PDCoV emergence. It demonstrated its applicability as an additional tool for diagnostic data monitoring of emergent pathogens having similar clinical disease as the monitored endemic pathogens. [ABSTRACT FROM AUTHOR]

Valley Fever (VF), caused by fungi in the genus Coccidioides, is a prevalent disease in southwestern and western parts of the United States that affects both humans and animals, such as dogs. Although the immune responses to infection with Coccidioides spp. are not fully characterized, antibody-detection assays are used in conjunction with clinical presentation and radiologic findings to aid in the diagnosis of VF. These assays often use Complement Fixation (CF) and Tube Precipitin (TP) antigens as the main targets of IgG and IgM reactivity, respectively. Our group previously reported evidence of over 800 genes expressed at the protein level in C. posadasii. However, antibody reactivity to the majority of these proteins has never been explored. Using a new, high-throughput screening technology, the Nucleic Acid Programmable Protein Array (NAPPA), we screened serum specimens from dogs against 708 of these previously identified proteins for IgG reactivity. Serum from three separate groups of dogs was analyzed and revealed a small panel of proteins to be further characterized for immuno-reactivity. In addition to CF/CTS1 antigen, sera from most infected dogs showed antibody reactivity to endo-1,3-betaglucanase, peroxisomal matrix protein, and another novel reactive protein, CPSG_05795. These antigens may provide additional targets to aid in antibody-based diagnostics. [ABSTRACT FROM AUTHOR]

Objective The aim of this study was to compare the performance of direct amplification of viral nucleic acid from transport medium to extracted nucleic acid for polymerase chain reaction (PCR), sequencing, and genotyping applications. Methods XpressAmp lysate and extracted total nucleic acid from viral transport medium containing nasopharyngeal specimens were evaluated across different molecular applications to determine performance characteristics. Results SARS-CoV-2 quantitative PCR and angiotensin-converting enzyme (ACE) genotyping assays worked well with XpressAmp lysate, almost equal with or better than extracted nucleic acid in some specimens. However, XpressAmp completely failed to perform in next-generation sequencing for strain typing. Both protocols failed to detect ACE2 expression in viral transport medium. Conclusion Direct amplification of viral nucleic acid from viral transport medium containing nasopharyngeal specimen works well for molecular assays with low thresholds of quality; however, it does have limitations with assays that require high quality nucleic acid for input. Use of the XpressAmp protocol significantly improves turnaround time and allows for easy ramp-up of PCR and genotyping assays. [ABSTRACT FROM AUTHOR]

We devised a model to interpret discordant SARS-CoV-2 test results. We estimate that, during March 2020-May 2022, a patient in the United States who received a positive rapid antigen test result followed by a negative nucleic acid test result had only a 15.4% (95% CI 0.6%-56.7%) chance of being infected. [ABSTRACT FROM AUTHOR]

In mid-2022, the COVID-19 cases have reached close to 562 million, but its overall infection rate is hard to confirm. Even with effective vaccines, break-through infections with new variants occur, and safe and reliable testing still plays a critical role in isolation of infected individuals and in control of an outbreak of a COVID-19 pandemic. In response to this urgent need, the diagnostic tests for COVID-19 are rapidly evolving and improving these days. The health authorities of many countries issued requirements for detecting SARS-CoV-2 diagnosis tests during the pandemic and have timely access to these tests to ensure safety and effectiveness. In this study, we compared the requirements of EUA in Taiwan, Singapore, and the United States. For the performance evaluations of nucleic acid extraction, inclusivity, limit of detection (LoD), cross-reactivity, interference, cutoff, and stability, the requirements are similar in the three countries. The use of natural clinical specimens is needed for clinical evaluation in Taiwan and the United States. However, carry-over and cross-contamination studies can be exempted in Taiwan and the United States but are required in Singapore. This review outlines requirements and insight to guide the test developers on the development of IVDs. Considering the rapidly evolving viruses and severe pandemic of COVID-19, timely and accurate diagnostic testing is imperative to the management of diseases. As noted above, the performance requirements for SARS-CoV-2 nucleic acid tests are similar between Taiwan, Singapore and the United States. The differences are mainly in two points: the recommended microorganisms for cross-reactivity study, and the specimen requirement for clinical evaluation. This study provides an overview of current requirements of SARS-CoV-2 nucleic acid tests in Taiwan, Singapore, and the United States. [ABSTRACT FROM AUTHOR]

Cancer remains the second leading cause of death in the United States despite decades of treatment advances. While death rates have fallen for breast, cervical, and colorectal cancers, death rates remain high for the majority of malignancies, primarily given the late stage at which they are diagnosed. The US Preventive Services Task Force currently recommends routine screening for just 4 cancers: breast, cervical, colorectal, and lung (for high-risk individuals); for prostate cancer, recommendations support individual decision making. However, cancers without recommended screening tests account for 71% of cancer deaths in the United States. In addition, screening rates remain below national goals, with numerous barriers to population-based screening. Recently, initial results of studies on blood-based multicancer early detection tests, which rely on measurement of a range of analytes, demonstrate the potential to identify multiple cancers in a single blood test and detect many cancers for which no screening tests are currently recommended. Blood-based tests have the potential to be more accessible and easier to disseminate than organspecific tests. However, it remains unclear if their use can reduce deaths from these cancers. Other issues include cost-effectiveness, the impact of false-positive and false-negative results on patients and costs, and uptake among individuals and clinicians. Research and development of blood-based multicancer early detection tests continue. [ABSTRACT FROM AUTHOR]

Objective: To compile current usage of serum-based prenatal screening for Down syndrome in the United States and compare it with results from a similar 2011/2012 survey. Setting: The College of American Pathologists maternal screening proficiency testing survey includes a supplemental question on the first of three yearly distributions. Methods: Information regarding tests offered and the monthly number of pregnancies tested for US-based laboratories were reviewed. Results were stratified by size of laboratory, tests offered, and pregnancies tested. Findings were compared to an earlier survey. Results: Fifty-six laboratories reported they will have screened 1,131,336 pregnancies in 2020. Of these, 36% are screened by stand-alone first trimester testing, 48% by stand-alone second trimester testing, and 16% using tests that integrate results from both trimesters. Eighty percent of all serum screens were provided by the five laboratories that performed the most screens (at least 50,000). These five performed similar proportions of first or second trimester screens (42.2% and 41.8%, respectively). Compared to eight years earlier, there are now 54% fewer laboratories. Pregnancies screened using the first trimester, second trimester, and integrated protocols were lower by 27%, 69%, and 72%, respectively. The serum screening activity in the US showed a 62% decrease from 2012 levels. During 2012–2020, the number of cell-free DNA tests increased from negligible to 1,492,332. Conclusions: Maternal serum screening for common aneuploidies has changed significantly in eight years with fewer laboratories, a shift toward larger laboratories and a 2.5-fold reduction in pregnancies tested, likely due to the introduction of cell-free DNA screening. [ABSTRACT FROM AUTHOR]

Background: Tumor molecular profiling from patients experiencing exceptional responses to systemic therapy may provide insights into cancer biology and improve treatment tailoring. This pilot study evaluates the feasibility of identifying exceptional responders retrospectively, obtaining pre-exceptional response treatment tumor tissues, and analyzing them with state-of-the-art molecular analysis tools to identify potential molecular explanations for responses.Methods: Exceptional response was defined as partial (PR) or complete (CR) response to a systemic treatment with population PR or CR rate less than 10% or an unusually long response (eg, duration >3 times published median). Cases proposed by patients' clinicians were reviewed by clinical and translational experts. Tumor and normal tissue (if possible) were profiled with whole exome sequencing and, if possible, targeted deep sequencing, RNA sequencing, methylation arrays, and immunohistochemistry. Potential germline mutations were tracked for relevance to disease.Results: Cases reflected a variety of tumors and standard and investigational treatments. Of 520 cases, 476 (91.5%) were accepted for further review, and 222 of 476 (46.6%) proposed cases met requirements as exceptional responders. Clinical data were obtained from 168 of 222 cases (75.7%). Tumor was provided from 130 of 168 cases (77.4%). Of 117 of the 130 (90.0%) cases with sufficient nucleic acids, 109 (93.2%) were successfully analyzed; 6 patients had potentially actionable germline mutations.Conclusion: Exceptional responses occur with standard and investigational treatment. Retrospective identification of exceptional responders, accessioning, and sequencing of pretreatment archived tissue is feasible. Data from molecular analyses of tumors, particularly when combining results from patients who received similar treatments, may elucidate molecular bases for exceptional responses. [ABSTRACT FROM AUTHOR]

Background: The gap between demand and supply for solid organ transplants requires strategies to expand the donor pool. Successful use of hepatitis B virus (HBV)-positive grafts has been reported in liver transplantation., Methods: In this United Network for Organ Sharing database (January 1999 to June 2021) retrospective cohort study, outcomes of kidney transplant (KT) or heart transplant (HT) recipients with HBV donor grafts (hepatitis B surface antigen and/or for HBV nucleic acid test-positive) were examined. Propensity score matching was performed for HBV-positive to negative graft recipients (1:5 for renal transplantation and 1:10 for HT)., Results: Of 448 HBV-positive donors with 896 kidneys, 352 kidneys (39.3%) and 56 hearts (12.5%) were transplanted. Of these, 312 kidneys (88.6%) and 45 hearts (80.3%) were transplanted in hepatitis B surface antigen-negative recipients. Ten-year graft survival was 47.1% and 49% (log-rank P = 0.353), and patient survival was 58% and 59% ( P = 0.999) for KT recipients. Similar figures among HT recipients were 41.9% and 38.9% for graft survival ( P = 0.471), and 54.3% and 61.2% for patient survival ( P = 0.277). Subgroup analyses in recipients with HBV nucleic acid test-positive grafts irrespective of antibodies to HBV core antigen-positive status, and recipients negative for anti-HBs (548 renal transplantation and 209 HT) were similar., Conclusions: Although we are limited by lack of available data on posttransplant anti-HBV treatment, the study observations suggest that using HBV-positive grafts is a reasonable strategy to expand the donor pool among candidates waiting for KT or HT., Competing Interests: The authors declare no funding or conflicts of interest., (Copyright © 2023 Wolters Kluwer Health, Inc. All rights reserved.)

Background: Rare transfusion-transmitted West Nile virus (WNV) cases usually occur due to gaps in testing involving converting to more sensitive nucleic acid testing (NAT) formats (referred to as triggering). Using data from 2014 to 2018, we investigated a strategy used to increase detection early in the triggering period and reviewed its yield as the individual donation (ID)-NAT geographic area was decreased.Methods: Mini-pool-NAT transitioned to ID-NAT following triggering based on one WNV NAT-reactive donation (having an elevated signal, repeat reactive, or in an area with WNV ongoing activity). ID-NAT-triggered geographic areas included an entire state (2014-2017) or collections within a 50-mile radius of the triggering donor's residential zip code (2018). During the MP- to ID-NAT transition, donation samples were retrieved and tested by ID-NAT for those with results not yet released (referred to as in-process testing). Reactive sample confirmation was performed by repeat NAT of an independent sample or antibody testing.Results: ID-NAT included 3.2 million donations of more than 25 million tested year-round, resulting in 684 confirmed positives; all confirmed-positive donations occurred from June to December (0.64/10,000). Overall, 52% (358/684) required ID-NAT for detection, including 68 (19%) antibody negatives. Ten of 19 (53%) identified in-process were ID-NAT-only detectable, including four antibody negatives, or approximately 1 per year (2.8% of ID-NAT-only detectable). With reduced triggering geography, 12 of 19 (63%) were not identified (including 6/10 ID-NAT-only detectable, and 2/4 ID-NAT-only detectable/antibody negative).Conclusion: WNV NAT's utility is between June-December; however, abandoning testing outside of this time may increase risk. While in-process testing identified approximately one ID-NAT-only detectable (antibody-negative) donation per year, reducing the geographic triggered area decreased its effectiveness. [ABSTRACT FROM AUTHOR]

Background The HIV Prevention Trials Network (HPTN) Study 073 (HPTN 073) assessed the feasibility, acceptability, and safety of preexposure prophylaxis (PrEP) for black men who have sex with men (BMSM). The purpose of this analysis was to characterize the relationship between PrEP uptake and use and incident sexually transmitted infections (STIs) among participants enrolled in HPTN 073. Methods A total of 226 human immunodeficiency virus (HIV)–uninfected BMSM were enrolled in 3 US cities; all participants received client-centered care coordination (C4) and were offered daily oral PrEP. Participants were followed for 12 months with STI testing (rectal and urine nucleic acid amplification test for gonorrhea and chlamydia, rapid plasma reagin for syphilis) conducted at baseline, week 26, and week 52. Logistic regression was used to examine associations between STI incidence and PrEP uptake. Generalized estimating equations were used to evaluate associations between age, PrEP acceptance, sexual behaviors, and incident STIs. Results Baseline STI prevalence was 14.2%. Men aged <25 years were more likely to have a baseline STI (25.3% vs 6.7%; odds ratio [OR], 4.39; 95% confidence interval [CI:, 1.91, 10.11). Sixty participants (26.5%) acquired ≥1 STI during follow-up; the incidence rate was 34.2 cases per 100 person-years (95% CI, 27.4, 42.9). In adjusted analyses, baseline STI diagnosis (OR, 4.23; 95% CI, 1.82, 9.87; P <.001) and additional C4 time (OR, 1.03; 95% CI, 1.00, 1.06; P =.027) were associated with having an incident STI. STI incidence was not associated with PrEP acceptance or adherence. Conclusions While we found higher rates of STIs in younger BMSM, overall rates of STI were lower than in prior PrEP trials, with no increase over time. BMSM with STIs at PrEP initiation may require additional interventions that target STI acquisition risk. Clinical Trials Registration NCT01808352. [ABSTRACT FROM AUTHOR]

The impacts of invertebrate RNA virus population dynamics on virulence and infection outcomes are poorly understood. Deformed wing virus (DWV), the main viral pathogen of honey bees, negatively impacts bee health, which can lead to colony death. Despite previous reports on the reduction of DWV diversity following the arrival of the parasitic mite Varroa destructor, the key DWV vector, we found high genetic diversity of DWV in infested United States honey bee colonies. Phylogenetic analysis showed that divergent US DWV genotypes are of monophyletic origin and were likely generated as a result of diversification after a genetic bottleneck. To investigate the population dynamics of this divergent DWV, we designed a series of novel infectious cDNA clones corresponding to coexisting DWV genotypes, thereby devising a reverse-genetics system for an invertebrate RNA virus quasispecies. Equal replication rates were observed for all clone-derived DWV variants in single infections. Surprisingly, individual clones replicated to the same high levels as their mixtures and even the parental highly diverse natural DWV population, suggesting that complementation between genotypes was not required to replicate to high levels. Mixed clone–derived infections showed a lack of strong competitive exclusion, suggesting that the DWV genotypes were adapted to coexist. Mutational and recombination events were observed across clone progeny, providing new insights into the forces that drive and constrain virus diversification. Accordingly, our results suggest that Varroa influences DWV dynamics by causing an initial selective sweep, which is followed by virus diversification fueled by negative frequency-dependent selection for new genotypes. We suggest that this selection might reflect the ability of rare lineages to evade host defenses, specifically antiviral RNA interference (RNAi). In support of this hypothesis, we show that RNAi induced against one DWV strain is less effective against an alternate strain from the same population. [ABSTRACT FROM AUTHOR]

Recently, United States Food and Drug Administration (FDA) and European Commission (EC) approved Alnylam Pharmaceuticals' RNA interference (RNAi) therapeutic, ONPATTRO™ (Patisiran), for the treatment of the polyneuropathy of hereditary transthyretin-mediated (hATTR) amyloidosis in adults. This is the first RNAi therapeutic all over the world, as well as the first FDA-approved treatment for this indication. As a milestone event in RNAi pharmaceutical industry, it means, for the first time, people have broken through all development processes for RNAi drugs from research to clinic. With this achievement, RNAi approval may soar in the coming years. In this paper, we introduce the basic information of ONPATTRO and the properties of RNAi and nucleic acid therapeutics, update the clinical and preclinical development activities, review its complicated development history, summarize the key technologies of RNAi at early stage, and discuss the latest advances in delivery and modification technologies. It provides a comprehensive view and biotechnological insights of RNAi therapy for the broader audiences. [ABSTRACT FROM AUTHOR]

A small PCR-generated DNA fragment was introduced into a pharmaceutical grade ink as a molecular taggant, and the DNA tagged ink was delivered onto the surface of capsules by standard high-speed offset printing. The amount of DNA in the ink on each capsule is roughly 10−12 fold lower than that allowed as safe by the United States Food and Drug Administration (FDA) and the WHO with regards to acceptable limits of residual DNA. The printed ink on the capsule surface was sampled by swabbing, followed by direct analysis of the DNA-swab complex, without subsequent DNA purification. It was shown that DNA recovered from the ink by swabbing was suitable for PCR-CE analysis—a widely used method in forensic science and was also suitable for qPCR and isothermal DNA amplification, when coupled with portable devices similar to those used for environmental sampling and food safety testing. The data set a precedent: A small DNA fragment could be introduced as an excipient into a pharmaceutical application, and thereafter tracked through the pharmaceutical supply chain via forensic DNA authentication. [ABSTRACT FROM AUTHOR]

Highlights • NxTAG chemistry offers an easy workflow, low hands-on-time and scalable throughput. • All post-extraction assay steps take place in a single, closed tube. • Clinical performance of NxTAG RPP is comparable to that of the xTAG RVP assay. • Analytical performance is also similar or better than xTAG and xTAG FAST assays. Abstract The Luminex® NxTAG® Respiratory Pathogen Panel (NxTAG RPP) is an IVD-cleared assay for the simultaneous detection and identification of nucleic acids from 18 respiratory viruses and 2 (or 3 outside of the U.S.) atypical bacterial pathogens in nasopharyngeal swabs. Its scalability allows concurrent testing of up to 96 samples in a single batch. Nucleic acid extracted from 200 µL of raw specimen using the easyMAG® extractor is added directly to pre-plated, lyophilized bead reagents (LBRs), where multiplexed RT-PCR and hybridization to MagPlex-TAG™ microspheres occurs within a sealed reaction well using a single cycling program. Data acquisition is done on the MAGPIX® instrument which reads and sorts the reaction products directly from the sealed well following transfer of the assay plate from the thermal cycler. NxTAG is the newest innovation in bead-based nucleic acid chemistry developed by Luminex. Here we provide the detailed assay protocol and present data which describe the clinical and analytical performance characteristics of NxTAG RPP. [ABSTRACT FROM AUTHOR]

Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recently divided into two species based on gene sequence data from three loci and heuristic morphological assessment. Here, we re-evaluate the two-species hypothesis for D. couperi by evaluating both population genetic and gene sequence data. Our analyses of 14 microsatellite markers revealed 6–8 genetic population clusters with significant admixture, particularly across the contact zone between the two hypothesized species. Phylogenetic analyses of gene sequence data with maximum-likelihood methods suggested discordance between mitochondrial and nuclear markers and provided phylogenetic support for one species rather than two. For these reasons, we place Drymarchon kolpobasileus into synonymy with D. couperi. We suggest inconsistent patterns between mitochondrial and nuclear DNA are driven by high dispersal of males relative to females. We advocate for species delimitation exercises that evaluate admixture and gene flow in addition to phylogenetic analyses, particularly when the latter reveal monophyletic lineages. This is particularly important for taxa, such as squamates, that exhibit strong sex-biased dispersal. Problems associated with over-delimitation of species richness can become particularly acute for threatened and endangered species, because of high costs to conservation when taxonomy demands protection of more individual species than are supported by accumulating data. [ABSTRACT FROM AUTHOR]

Background: In 2016, universal individual donation nucleic acid testing (ID-NAT) of donated blood for Zika virus began in U.S. states and territories.Objective: To assess the cost-effectiveness of universal ID-NAT in the first year of screening compared with alternatives for the 50 states and separately for Puerto Rico.Design: Microsimulation that captured Zika-related harms to transfusion recipients, sexual partners, and their infants.Data Sources: National testing results compiled by AABB and costs, utilities, and outcome probabilities estimated from the literature.Target Population: Transfusion recipients.Time Horizon: Lifetime.Perspective: Societal.Intervention: Universal ID-NAT, universal mini-pool NAT (MP-NAT), and ID-NAT exclusively for components transfused to women of childbearing age. Seasonally targeted strategies in Puerto Rico and geographically targeted strategies in the 50 states were also considered.Outcome Measures: Costs, quality-adjusted life-years (QALYs), and outcomes.Results of Base-case Analysis: In Puerto Rico, MP-NAT exclusively during high mosquito season was cost-effective at $81 123 per QALY (95% CI, -$49 138 to $978 242 per QALY). No screening policy was cost-effective in the 50 states. Universal ID-NAT cost $341 million per QALY (CI, $125 million to $2.90 billion per QALY) compared with no screening in the 50 states.Results of Sensitivity Analysis: In Puerto Rico, MP-NAT only during the season of high mosquito activity was most cost-effective in 64% of probabilistic sensitivity analysis iterations. In the 50 states, no intervention was cost-effective in 99.99% of iterations. Cost-effectiveness was highly dependent on the rate of assumed infectious donations.Limitation: Data were limited on the component-specific transmissibility of Zika and long-term sequelae of infection.Conclusion: Screening was cost-effective only in the high mosquito season in Puerto Rico, and no evaluated screening policy was cost-effective in the 50 states. During periods with lower rates of Zika-infectious donations, the cost-effectiveness of screening will be even less favorable.Primary Funding Source: None. [ABSTRACT FROM AUTHOR]

Background: Characteristics of US blood donors with recent (RBI) or occult (OBI) hepatitis B virus (HBV) infection are not well defined.Methods: Donors with RBI and OBI were identified by nucleic acid and serologic testing among 34.4 million donations during 2009-2015. Consenting donors were interviewed and their HBV S-gene sequenced.Results: The overall rate of HBV-infected donors was 7.95 per 100,000; of these, 0.35 per 100,000 and 1.70 per 100,000 were RBI and OBI, respectively. RBI (n = 120) and OBI (n = 583) donors constituted 26% of all HBV-infected (n = 2735) donors. Detection of HBV DNA in 92% of OBI donors required individual donation nucleic acid testing. Donors with OBI compared to RBI were older (mean age, 48 vs 39 years; p < 0.0001) with lower median viral loads (9 vs. 529 IU/mL; p < 0.0001). A higher proportion of OBI than RBI donors were born or resided in an endemic country (39% vs. 5%; p = 0.0078). Seventy-seven percent of all RBI and OBI donors had multiple sex partners, an HBV-risk factor. Of 40 RBI and 10 OBI donors whose S gene was sequenced, 33 (83%) and 6 (60%), respectively, carried HBV subgenotype A2; 18 (55%) and 2 (33%), respectively, shared an identical sequence. Infection with 1 or more putative HBV-immune-escape mutants was identified in 5 (50%) of OBI but no RBI donors.Conclusion: RBI and OBI continue to be identified at low rates, confirming the importance of comprehensive HBV DNA screening of US blood donations. HBV-infected donors require referral for care and evaluation and contact tracing; their HBV strains may provide important information on emergent genotypes. [ABSTRACT FROM AUTHOR]

Tenofovir (TFV), a nucleotide reverse transcriptase inhibitor, requires two phosphorylation steps to form a competitive inhibitor of HIV reverse transcriptase. Adenylate kinase 2 (AK2) has been previously demonstrated to phosphorylate tenofovir to tenofovir-monophosphate, while creatine kinase, muscle (CKM), pyruvate kinase, muscle (PKM) and pyruvate kinase, liver and red blood cell (PKLR) each have been found to phosphorylate tenofovir-monophosphate to the pharmacologically active tenofovir-diphosphate. In the present study, genomic DNA isolated from dried blood spots collected from 505 participants from Bangkok, Thailand; Cape Town, South Africa; and New York City, USA were examined for variants in AK2, CKM, PKM, and PKLR using next-generation sequencing. The bioinformatics tools SIFT and PolyPhen predicted that 19 of the 505 individuals (3.7% frequency) carried variants in at least one kinase that would result in a decrease or loss of enzymatic activity. To functionally test these predictions, AK2 and AK2 variants were expressed in and purified from E. coli, followed by investigation of their activities towards tenofovir. Interestingly, we found that purified AK2 had the ability to phosphorylate tenofovir-monophosphate to tenofovir-diphosphate in addition to phosphorylating tenofovir to tenofovir-monophosphate. Further, four of the six AK2 variants predicted to result in a loss or decrease of enzyme function exhibited a ≥30% decrease in activity towards tenofovir in our in vitro assays. Of note, an AK2 K28R variant resulted in a 72% and 81% decrease in the formation of tenofovir-monophosphate and tenofovir-diphosphate, respectively. These data suggest that there are naturally occurring genetic variants that could potentially impact TFV activation. [ABSTRACT FROM AUTHOR]

The 13th century Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13th century CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13th century CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations. [ABSTRACT FROM AUTHOR]

Obesity has been on the rise in the US and worldwide for the last several decades. Obesity has been associated with chronic disease development, such as certain types of cancer, type 2 diabetes, cardiovascular disease, and liver diseases. Previously, we reported that obesity promotes DMBA-induced mammary tumor development using the obese Zucker rat model. The intestinal microbiota is composed of a diverse population of obligate and facultative anaerobic microorganisms, and these organisms carry out a broad range of metabolic activities. Obesity has been linked to changes in the intestinal microbiota, but the composition of the bacterial populations in lean and obese Zucker rats has not been carefully studied. Therefore, the objective of this study was to determine the effects of obesity on the gut microbiota in this model. Lean and obese female Zucker rats (n = 16) were fed an AIN-93G-like diet for 8 weeks. Rats were weighed twice weekly, and fecal samples were collected at the beginning and end of the experiment. 16S rRNA gene sequencing was used to evaluate the composition of the fecal bacterial populations. At the outset of the study, the lean rats exhibited much lower ratios of the Firmicutes to Bacteroidetes phyla than the obese rats, but after 60 days, this ratio in the lean rats exceeded that of the obese. This shift was associated with reductions in the Bacteroidaceae, S24-7 and Paraprevotellaceae families in the lean rats. Obese rats also showed increased levels of the genus Akkermansia at day 60. PCoA plots of beta diversity showed clustering of the different test groups, indicating clear differences in intestinal microbiota populations associated with both the time point of the study and the lean or obese status in the Zucker rat model for obesity. [ABSTRACT FROM AUTHOR]

Background: In the United States, annual screening for rectal gonorrhea and chlamydia is only recommended for men who report receptive anal sex (RAS), but other behaviors (e.g., rimming) may lead to rectal Chlamydia trachomatis and Neisseria gonorrhoeae acquisition., Methods: We enrolled individuals assigned male sex at birth who reported sex with men and denied RAS in the past 2 years or reported RAS 1 to 2 years ago but were tested and treated since last RAS. Participants enrolled in-person at the Sexual Health Clinic in Seattle, Washington (December 2019-July 2022), or online (July 2021-March 2022). Participants completed a survey that asked about 13 non-RAS behaviors and self-collected a rectal swab for gonorrhea/chlamydia nucleic acid amplification testing. We used log binomial regression to estimate the prevalence of rectal gonorrhea/chlamydia (adjusted prevalence ratio [aPR]) by behavior, adjusting for all other behaviors., Results: We enrolled 292 participants (247 in-person and 45 online); 277 (95%) had nucleic acid amplification testing results. Rectal gonorrhea/chlamydia test positivity was 14.1% overall: 10.5% for rectal chlamydia and 4.3% for rectal gonorrhea. Most participants (70%) reported ≥1 behavior that involved direct contact with their anus. We observed a higher risk of rectal chlamydia for those who did versus did not report perianal play at 12 months (aPR, 2.39; 95% confidence interval, 1.10-5.22) and 2 months (aPR, 2.21; 95% confidence interval, 1.02-4.79). This was the only behavior significantly associated with testing positive., Conclusions: Rectal C. trachomatis and N. gonorrhoeae prevalence was high among men who deny RAS, suggesting other possible routes of acquisition. Rectal screening for those who deny RAS should be made with careful consideration of individual- and population-level effects., Competing Interests: Conflict of Interest and Sources of Funding: C.M.K. and L.A.B. report research support from Hologic, Inc, for this study. L.A.B. has received research support from SpeeDx outside of the submitted work and has received research support and consulting fees from Nabriva, unrelated to the submitted work. O.O.S. has received research support from Hologic, Inc, and SpeeDx outside of the submitted work. All other authors declare no conflicts of interest., (Copyright © 2023 American Sexually Transmitted Diseases Association. All rights reserved.)

Background: Hepatitis E virus (HEV) is a nonenveloped emerging virus of increasing worldwide interest. Antibody prevalence, RNA frequencies, and transfusion transmissions have been reported. We investigated the HEV RNA and antibody frequencies in US blood donors.Study Design and Methods: Individual-donation HEV RNA testing was performed on 18,829 donations from six US geographic regions using a CE-marked nucleic acid test (95% limit of detection, 7.9 IU/mL). Repeat-reactive donations were confirmed by in-house, real-time polymerase chain reaction (PCR; 10.3 IU/mL). Total HEV seroprevalence in a randomly selected subset of donations (n = 4499) was assessed by a direct, double-antigen sandwich assay; reactives were further tested for immunoglobulin (Ig)G and IgM. As part of the total antibody confirmatory algorithm, the cutoff was adjusted.Results: Two donations tested confirmed-positive for RNA (PCR not quantifiable, IgM/IgG positive; and 14 IU/mL, antibody negative) for a frequency of 1 in 9500 (95% confidence interval [CI], 1:2850-1:56,180) and 99.96% specificity (95% CI, 99.92%-99.98%); both donors were from the Midwest United States. Antibody prevalence was 9.5% (95% CI, 8.7-10.5) before the cutoff adjustment and 7.7% (95% CI, 7.0%-8.5%) after adjustment; 0.58% (95% CI, 0.39%-0.85%) were IgM positive.Conclusions: We confirmed comparatively low rates and low viral loads of HEV RNA in US blood donors indicating the need for individual-donation testing if screening is implemented. Antibody prevalence rates were comparable to those reported by one US study using a different assay, but lower than those reported in another study using yet a third assay. We did not answer the question of whether US blood donation screening is warranted. Selective strategies involving providing HEV-negative blood to severely immunosuppressed patients at risk of developing hepatitis may be considered. [ABSTRACT FROM AUTHOR]

Significant advances have been made in the molecular analyses of the human physiological state. In general, these techniques have been termed "omics" because of their requirements for sophisticated analyses of large datasets. Application of these new omics technologies has led to advances in medical practice related to public health as well as a new field termed personalized medicine. The Department of Defense (DoD) consistently needs the ability to identify people who have been exposed to environmental hazards during deployments and in their day-to-day jobs. The department currently has a biorepository of sera collected from military service members and has used that repository to study potential environmental exposures (toxins and infectious diseases) since 1987. The DoD Serum Repository is also linked to service member health records, making it a very powerful tool for studies related to force health protection and public health practice. However, this repository does not contain a reliable source of nucleic acid. Accordingly, to take advantage of modern molecular omics technologies, the DoD should establish an enhanced biospecimen repository that can support future questions related to force health protection. This article briefly discusses the various omics techniques, and how they can be used for analyses to support medical practice and public health. [ABSTRACT FROM AUTHOR]

The role of Pleistocene climate changes in promoting evolutionary diversification in global biota is well documented, but the great majority of data regarding this subject come from North America and Europe, which were greatly affected by glaciation. The effects of Pleistocene changes on cold- and/or dry-adapted species in tropical areas where glaciers were not present remain sparsely investigated. Many such species are restricted to small areas surrounded by unfavourable habitats, which may represent potential interglacial microrefugia. Here, we analysed the phylogeographic structure and diversification history of seven cactus species in the Pilosocereus aurisetus complex that are restricted to rocky areas with high diversity and endemism within the Neotropical savannas of eastern South America. We combined palaeodistributional estimates with standard phylogeographic approaches based on two chloroplast DNA regions ( trnT-trnL and trnS-trnG), exon 1 of the nuclear gene PhyC and 10 nuclear microsatellite loci. Our analyses revealed a phylogeographic history marked by multiple levels of distributional fragmentation, isolation leading to allopatric differentiation and secondary contact among divergent lineages within the complex. Diversification and demographic events appear to have been affected by the Quaternary climatic cycles as a result of isolation in multiple patches of xerophytic vegetation. These small patches presently harbouring P. aurisetus populations seem to operate as microrefugia, both at present and during Pleistocene interglacial periods; the role of such microrefugia should be explored and analysed in greater detail. [ABSTRACT FROM AUTHOR]

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species. [ABSTRACT FROM AUTHOR]

Pyrenophora semeniperda (anamorph Drechslera campulata) is a necrotrophic fungal seed pathogen that has a wide host range within the Poaceae. One of its hosts is cheatgrass (Bromus tectorum), a species exotic to the United States that has invaded natural ecosystems of the Intermountain West. As a natural pathogen of cheatgrass, P. semeniperda has potential as a biocontrol agent due to its effectiveness at killing seeds within the seed bank; however, few genetic resources exist for the fungus. Here, the genome of P. semeniperda isolate assembled from sequence reads of 454 pyrosequencing is presented. The total assembly is 32.5 Mb and includes 11,453 gene models encoding putative proteins larger than 24 amino acids. The models represent a variety of putative genes that are involved in pathogenic pathways typically found in necrotrophic fungi. In addition, extensive rearrangements, including inter- and intrachromosomal rearrangements, were found when the P. semeniperda genome was compared to P. tritici-repentis, a related fungal species. [ABSTRACT FROM AUTHOR]

In mid-2022, the COVID-19 cases have reached close to 562 million, but its overall infection rate is hard to confirm. Even with effective vaccines, break-through infections with new variants occur, and safe and reliable testing still plays a critical role in isolation of infected individuals and in control of an outbreak of a COVID-19 pandemic. In response to this urgent need, the diagnostic tests for COVID-19 are rapidly evolving and improving these days. The health authorities of many countries issued requirements for detecting SARS-CoV-2 diagnosis tests during the pandemic and have timely access to these tests to ensure safety and effectiveness. In this study, we compared the requirements of EUA in Taiwan, Singapore, and the United States. For the performance evaluations of nucleic acid extraction, inclusivity, limit of detection (LoD), cross-reactivity, interference, cutoff, and stability, the requirements are similar in the three countries. The use of natural clinical specimens is needed for clinical evaluation in Taiwan and the United States. However, carry-over and cross-contamination studies can be exempted in Taiwan and the United States but are required in Singapore. This review outlines requirements and insight to guide the test developers on the development of IVDs. Considering the rapidly evolving viruses and severe pandemic of COVID-19, timely and accurate diagnostic testing is imperative to the management of diseases. As noted above, the performance requirements for SARS-CoV-2 nucleic acid tests are similar between Taiwan, Singapore and the United States. The differences are mainly in two points: the recommended microorganisms for cross-reactivity study, and the specimen requirement for clinical evaluation. This study provides an overview of current requirements of SARS-CoV-2 nucleic acid tests in Taiwan, Singapore, and the United States., Competing Interests: Conflicts of interest: The authors declare that they have no conflicts of interest related to the subject matter or materials discussed in this article., (Copyright © 2022, the Chinese Medical Association.)

Sorghum genotypes currently used for grain production in the United States were developed from African landraces that were imported starting in the mid-to-late 19th century. Farmers and plant breeders selected genotypes for grain production with reduced plant height, early flowering, increased grain yield, adaptation to drought, and improved resistance to lodging, diseases and pests. DNA polymorphisms that distinguish three historically important grain sorghum genotypes, BTx623, BTx642 and Tx7000, were characterized by genome sequencing, genotyping by sequencing, genetic mapping, and pedigree-based haplotype analysis. The distribution and density of DNA polymorphisms in the sequenced genomes varied widely, in part because the lines were derived through breeding and selection from diverse Kafir, Durra, and Caudatum race accessions. Genomic DNA spanning dw1 (SBI-09) and dw3 (SBI-07) had identical haplotypes due to selection for reduced height. Lower SNP density in genes located in pericentromeric regions compared with genes located in euchromatic regions is consistent with background selection in these regions of low recombination. SNP density was higher in euchromatic DNA and varied >100-fold in contiguous intervals that spanned up to 300 Kbp. The localized variation in DNA polymorphism density occurred throughout euchromatic regions where recombination is elevated, however, polymorphism density was not correlated with gene density or DNA methylation. Overall, sorghum chromosomes contain distal euchromatic regions characterized by extensive, localized variation in DNA polymorphism density, and large pericentromeric regions of low gene density, diversity, and recombination. [ABSTRACT FROM AUTHOR]

Background This study assessed the clinical sensitivity of three fully automated, human immunodeficiency virus ( HIV), hepatitis C virus ( HCV), and hepatitis B virus ( HBV) triplex nucleic acid test ( NAT) assays by individual donation ( ID- NAT) and at operational minipool ( MP- NAT) sizes used worldwide. Study Design and Methods MPX, Ultrio, and Ultrio Plus were used to test 2222 pedigreed, marker-positive samples with varying viral loads, each from a unique US blood donor. NAT-positive, seronegative yield samples (16 HBV, 156 HCV, and 23 HIV) were tested in replicates of three; undiluted; and in 1:6, 1:8, and 1:16 dilutions ( MP6, MP8, and MP16), simulating various MP sizes. Seropositive samples (1276 HBV, 488 HCV, and 263 HIV) were tested by ID- NAT in singlet. Results MPX- MP6 and Ultrio Plus- MP16 had equivalent HCV sensitivity. Although Ultrio Plus- MP16 for HIV trended toward lesser sensitivity, this was not corroborated in a large substudy of low-viral-load samples in which Ultrio Plus- MP8/ MP16 showed 100% reactivity. MPX- ID and Ultrio Plus- ID HBV clinical sensitivity were identical, but MPX- MP6 was significantly more sensitive than Ultrio Plus- MP16; the differential yield projected to one HBV NAT yield per 4.72 million US donations. Ultrio Plus HBV sensitivity did not increase at MP8 versus MP16. Ultrio Plus versus Ultrio sensitivity was significantly increased in HBV-infected donors with early acute, late acute or chronic, and occult infections. No difference in sensitivity was noted for any virus for MPX- MP6 versus Ultrio Plus- ID. Conclusions Our data support US donation screening with MPX- MP6 or Ultrio Plus- MP16 since the HBV DNA detection of Ultrio Plus was significantly enhanced (vs. Ultrio) without compromising HIV or HCV RNA detection. [ABSTRACT FROM AUTHOR]

Lung cancer is the leading cause of cancer deaths worldwide. In the United States, only one in six lung cancer patients survives five years after diagnosis. These statistics may improve if new therapeutic targets are identified. We previously reported that an enzyme of fatty acid metabolism, very long-chain acyl-CoA synthetase 3 (ACSVL3), is overexpressed in malignant glioma, and that depleting glioblastoma cells of ACSVL3 diminishes their malignant properties. To determine whether ACSVL3 expression was also increased in lung cancer, we studied tumor histologic sections and lung cancer cell lines. Immunohistochemical analysis of normal human lung showed moderate ACSVL3 expression only in bronchial epithelial cells. In contrast, all of 69 different lung tumors tested, including adeno-, squamous cell, large cell, and small cell carcinomas, had robustly elevated ACSVL3 levels. Western blot analysis of lung cancer cell lines derived from these tumor types also had significantly increased ACSVL3 protein compared to normal bronchial epithelial cells. Decreasing the growth rate of lung cancer cell lines did not change ACSVL3 expression. However, knocking down ACSVL3 expression by RNA interference reduced cell growth rates in culture by 65–76%, and the ability of tumor cells to form colonies in soft agar suspension by 65–80%. We also conducted studies to gain a better understanding of the biochemical properties of human ACSVL3. ACSVL3 mRNA was detected in many human tissues, but the expression pattern differed somewhat from that of the mouse. The enzyme activated long- and very long-chain saturated fatty acid substrates, as well as long-chain mono- and polyunsaturated fatty acids to their respective coenzyme A derivatives. Endogenous human ACSVL3 protein was found in a punctate subcellular compartment that partially colocalized with mitochondria as determined by immunofluorescence microscopy and subcellular fractionation. From these studies, we conclude that ACSVL3 is a promising new therapeutic target in lung cancer. [ABSTRACT FROM AUTHOR]

Objective: This study aimed to describe trends in the utilization of nucleic acid amplification (NAAT) testing for gonorrhea and chlamydia in US pediatric emergency departments. Nucleic acid amplification has been recommended over genital culture by the American Academy of Pediatrics and Centers for Disease Control and Prevention for children evaluated for sexual abuse., Methods: We conducted a multicenter study of children aged 12 months to 11 years tested for gonorrhea and chlamydia between 2004 and 2018 at 22 hospitals in the Pediatric Health Information System. We included patients diagnosed with maltreatment concerns and/or genitourinary (GU) symptoms. The primary outcome was prevalence of testing with NAAT, culture, or both. We analyzed groups based on patient sex, as well as diagnoses of maltreatment versus GU symptoms., Results: A total of 36,312 visits were analyzed. Visits were 73.4% girls and 26.6% boys. During the study period, there was an increase in use of NAAT-only testing for girls (49.3% to 94.3%; P < 0.001) and boys (54.5% to 96.1%; P < 0.001). There was a decrease in use of culture alone for girls (40% to 1.6%; P < 0.001) and boys (38.7% to 0.8%; P < 0.001). Use of both tests in the same encounter was higher among children diagnosed with maltreatment than GU symptoms, regardless of sex (P < 0.001)., Conclusions: Over a 14-year period, downtrend of culture use with increase in NAAT was observed, suggesting general adherence to evidence-based guidelines. Almost 10% of children diagnosed with maltreatment continued to be tested with culture. This could indicate provider concerns regarding test accuracy, legal admissibility, or lack of test availability., Competing Interests: Disclosure: The authors declare no conflict of interest., (Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.)

Potato common scab, caused by Streptomyces spp., is an annual production problem for potato growers, and not effectively controlled by current methods. A field with naturally occurring common scab suppression has been identified in Michigan, and confirmed to have a biological basis for this disease suppression. This field and an adjacent scab nursery conducive to disease were studied using pyrosequencing to compare the two microbial communities. Total DNA was extracted from both the disease-conducive and -suppressive soils. A phylogeneti-cally taxon-informative region of the J6S rRNA gene was used to establish operational taxonomic units (OTUs) to characterize bacterial community richness and diversity. In total, 1,124 OTUs were detected and 565 OTUs (10% dissimilarity) were identified in disease-conducive soil and 859 in disease-suppressive soil, including 300 shared both between sites. Common phyla based on relative sequence abundance were Acidobacteria, Proteobacteria, and Firmicutes. Sequences of Lysobaaer were found in significantly higher numbers in the disease-suppressive soil, as were sequences of group 4 and group 6 Acidobacteria. The relative abundance of sequences identified as the genus Bacillus was significantly higher by an order of magnitude in the disease-conducive soil. [ABSTRACT FROM AUTHOR]

A survey of 238 golf courses in 10 states of the western United States found root-knot nematodes (Meloidogyne spp.) in 60% of the putting greens sampled. Sequence and phylogenetic analyses of I 8S rRNA, D2-D3 of 285 rRNA, internal transcribed spacer-rRNA, and mitochondrial DNA gene sequences were used to identify specimens from golf courses. The most common species, M.maryland was found in 58 golf courses distributed from Southern California to Wash- ington in the coastal or cooler areas of those states. In the warmer re- gions of the Southwest, M. tnarylondi was recovered fron 38 golf courses and M. grenninis from 11 golf courses. This constitutes the first report of M. ,narvlandi in Arizona, California, Hawaii, Nevada, and Utah, and the first report of M. grarniois in Arizona, Hawaii, and Ne- vada. Two golf courses in Washington were infested with M.minor, the first record of this nematode in the Western Hemisphere. Columbia root-knot nematode, M. chirwoodi, was found in a single golf course in California. Polyrnerase chain reaction restriction fragment length poly- morphism of the intergenic region between the cytochrorne oxidase and 16S rRNA genes in the mitochondrial genome with restriction enzyme Sspl was able to distinguish populations of M. graminis from M. mnarylandi, providing a fast and inexpensive method for future diag- nosis of these nematodes from turf. [ABSTRACT FROM AUTHOR]

Background: Colorectal cancer is the third most incident cancer and cause of cancer-related death in the United States. MicroRNAs, a class of small non-coding RNAs, have been implicated in the pathogenesis and prognosis of colorectal cancer, although few studies have examined the relationship between germline mutation in the microRNAs with risk and prognosis. We therefore investigated the association between a SNP in hsa-mir-608, which lies within the 10q24 locus, and colorectal cancer. Methods and Results: A cohort consisting of 245 cases and 446 controls was genotyped for rs4919510. The frequency of the GG genotype was significantly higher in African Americans (15%) compared to Caucasians (3%) controls. There was no significant association between rs4919510 and colorectal cancer risk (African American: ORGG vs. CC 0.89 [95% CI, 0.41-1.80]) (Caucasian: ORGG vs. CC 1.76, ([95% CI, 0.48-6.39]). However, we did observe an association with survival. The GG genotype was associated with an increased risk of death in Caucasians (HRGG vs. CC 3.54 ([95% CI, 1.38-9.12]) and with a reduced risk of death in African Americans (HRGG vs. CC 0.36 ([95% CI 0.12-1.07). Conclusions: These results suggest that rs4910510 may be associated with colorectal cancer survival in a manner that is dependent on race. [ABSTRACT FROM AUTHOR]

Background At least 10% of the 56,000 annual new HIV infections in the United States are caused by individuals with acute HIV infection (AHI). It unknown whether the health benefits and costs of routine nucleic acid amplification testing (NAAT) are justified, given the availability of newer fourth-generation immunoassay tests. Methods Using a dynamic HIV transmission model instantiated with U.S. epidemiologic, demographic, and behavioral data, I estimated the number of acute infections identified, HIV infections prevented, quality-adjusted life years (QALYs) gained, and the cost-effectiveness of alternative screening strategies. I varied the target population (everyone aged 15-64, injection drug users [IDUs] and men who have sex with men [MSM], or MSM only), screening frequency (annually, or every six months), and test(s) utilized (fourth-generation immunoassay only, or immunoassay followed by pooled NAAT). Results Annual immunoassay testing of MSM reduces incidence by 9.5% and costs <$10,000 per QALY gained. Adding pooled NAAT identifies 410 AHI per year, prevents 9.6% of new cases, costs $92,000 per QALY gained, and remains <$100,000 per QALY gained in settings where undiagnosed HIV prevalence exceeds 4%. Screening IDUs and MSM annually with fourth-generation immunoassay reduces incidence by 13% with cost-effectiveness <$10,000 per QALY gained. Increasing the screening frequency to every six months reduces incidence by 11% (MSM only) or 16% (MSM and IDUs) and costs <$20,000 per QALY gained. Conclusions Pooled NAAT testing every 12 months of MSM and IDUs in the United States prevents a modest number of infections, but may be cost-effective given sufficiently high HIV prevalence levels. However, testing via fourth-generation immunoassay every six months prevents a greater number of infections, is more economically efficient, and may obviate the benefits of acute HIV screening via NAAT. [ABSTRACT FROM AUTHOR]

Ovarian cancer is currently the most lethal gynecologic cancer in the United States. There is an urgent need for the development of innovative therapies against ovarian cancer, such as immunotherapy. The toll-like receptor 3 ligand, polyriboinosinic:polyribocytidylic acid (poly(I:C), has emerged as a promising adjuvant for activating the host immune responses for the control of tumors. We reasoned that a strategy to enhance the intracellular uptake of poly(I:C) will likely improve the poly(I:C) adjuvant effect. Since polyethylenimine (PEI) has been shown to increase the transfection efficiency of nucleic acids, we characterized the antitumor effects in mouse ovarian surface epithelial cells (MOSEC) tumor-bearing mice treated intraperitoneally with poly(I:C) and PEI. We observed that tumor-bearing mice treated with poly(I:C) and PEI generated significantly better therapeutic antitumor effects against MOSEC tumors compared with treatment with poly(I:C) alone. Furthermore, we found that NK cells play a significant role in the antitumor effects generated by treatment with poly(I:C) in combination with PEI. Intraperitoneal administration of poly(I:C) with PEI led to the uptake of poly(I:C) mainly by CD11b+ macrophages, resulting in the high expression of MHC class II and IL-12 (M1 phenotype). In addition, adoptive transfer of CD11b+ macrophages from mice treated with poly(I:C) and PEI was found to lead to increased number of activated NK cells in the recipient mice. Taken together, our data indicate that PEI can potentially be used to improve the uptake of poly(I:C) by CD11b+ macrophages, leading to the activation of NK cells and the control of murine ovarian tumors. [ABSTRACT FROM AUTHOR]

We examined the prevalence, quantity, and diversity of Campylobacter species in the excreta of 159 California gull (Larus californicus) samples using culture-, PCR-, and quantitative PCR (qPCR)-based detection assays. Campylobacter prevalence and abundance were relatively high in the gull excreta examined; however, C. jejuni and C. lari were detected in fewer than 2% of the isolates and DNA extracts from the fecal samples that tested positive. Moreover, molecular and sequencing data indicated that most L. californicus campylobacters were novel (<97% 16S rRNA gene sequence identity to known Campylobacter species) and not closely related to species commonly associated with human illness. Campylobacter estimates were positively related with those of fecal indicators, including a gull fecal marker based on the Catellicoccus marimammalium 16S rRNA gene. [ABSTRACT FROM AUTHOR]

Please cite this paper as: Pabbaraju et al. (2011) Comparison of a singleplex real-time RT-PCR assay and multiplex respiratory viral panel assay for detection of influenza 'A' in respiratory specimens. Influenza and Other Respiratory Viruses 5(2), 99-103. Evaluation of different molecular tests for the detection of pandemic (H1N1) 2009 virus is important before the next wave of the pandemic. To compare a hydrolysis probe-based real-time RT-PCR assay recommended by the CDC to the xTAG respiratory viral panel (RVP) (Luminex Molecular Diagnostics) for the detection of influenza A. Eleven thousand eight hundred and ninety-eight respiratory specimens were tested by the real-time RT-PCR and RVP assays for the detection of influenza A. The distribution of seasonal H1, H3 and pandemic H1N1 subtypes in these specimens was compared. The RVP assay was generally unable to identify influenza A-positive samples with a low viral load, whereas the real-time RT-PCR assay detected most of these samples resulting in a subset of specimens that could not be confirmed as either seasonal or pandemic influenza A subtypes. When the prevalence of influenza A is high, the CDC recommended real-time RT-PCR has significant advantages as a frontline assay, namely higher sensitivity and shorter time to reporting a result. Anticipated scenarios would be during the peaks of the pandemic and episodes of seasonal influenza. Furthermore, the better sensitivity of the RT-PCR makes it the preferred assay to detect influenza in patients with severe respiratory disease tested late in their clinical course. If pandemic (H1N1) 2009 virus is not the dominant virus and there is a high proportion of other respiratory viruses circulating, laboratories will be faced with the decision to use the RVP assay for the detection of pandemic (H1N1) 2009 virus. [ABSTRACT FROM AUTHOR]

HIV-1 carrying the ''Q151M complex'' reverse transcriptase (RT) mutations (A62V/V75I/F77L/F116Y/Q151M, or Q151Mc) is resistant to many FDA-approved nucleoside RT inhibitors (NRTIs), but has been considered susceptible to tenofovir disoproxil fumarate (TFV-DF or TDF). We have isolated from a TFV-DF-treated HIV patient a Q151Mc-containing clinical isolate with high phenotypic resistance to TFV-DF. Analysis of the genotypic and phenotypic testing over the course of this patient's therapy lead us to hypothesize that TFV-DF resistance emerged upon appearance of the previously unreported K70Q mutation in the Q151Mc background. Virological analysis showed that HIV with only K70Q was not significantly resistant to TFV-DF. However, addition of K70Q to the Q151Mc background significantly enhanced resistance to several approved NRTIs, and also resulted in high-level (10-fold) resistance to TFV-DF. Biochemical experiments established that the increased resistance to tenofovir is not the result of enhanced excision, as K70Q/Q151Mc RT exhibited diminished, rather than enhanced ATP-based primer unblocking activity. Pre-steady state kinetic analysis of the recombinant enzymes demonstrated that addition of the K70Q mutation selectively decreases the binding of tenofovir-diphosphate (TFV-DP), resulting in reduced incorporation of TFV into the nascent DNA chain. Molecular dynamics simulations suggest that changes in the hydrogen bonding pattern in the polymerase active site of K70Q/Q151Mc RT may contribute to the observed changes in binding and incorporation of TFV-DP. The novel pattern of TFV-resistance may help adjust therapeutic strategies for NRTI-experienced patients with multi-drug resistant (MDR) mutations. [ABSTRACT FROM AUTHOR]

Background: The ancestry of African-descended Americans is known to be drawn from three distinct populations: African, European, and Native American. While many studies consider this continental admixture, few account for the genetically distinct sources of ancestry within Africa - the continent with the highest genetic variation. Here, we dissect the within- Africa genetic ancestry of various populations of the Americas self-identified as having primarily African ancestry using uniparentally inherited mitochondrial DNA. Methods and Principal Findings: We first confirmed that our results obtained using uniparentally-derived group admixture estimates are correlated with the average autosomal-derived individual admixture estimates (hence are relevant to genomic ancestry) by assessing continental admixture using both types of markers (mtDNA and Y-chromosome vs. ancestry informative markers). We then focused on the within-Africa maternal ancestry, mining our comprehensive database of published mtDNA variation (∼5800 individuals from 143 African populations) that helped us thoroughly dissect the African mtDNA pool. Using this well-defined African mtDNA variation, we quantified the relative contributions of maternal genetic ancestry from multiple W/WC/SW/SE (West to South East) African populations to the different pools of today's African-descended Americans of North and South America and the Caribbean. Conclusions: Our analysis revealed that both continental admixture and within-Africa admixture may be critical to achieving an adequate understanding of the ancestry of African-descended Americans. While continental ancestry reflects gender-specific admixture processes influenced by different socio-historical practices in the Americas, the within-Africa maternal ancestry reflects the diverse colonial histories of the slave trade. We have confirmed that there is a genetic thread connecting Africa and the Americas, where each colonial system supplied their colonies in the Americas with slaves from African colonies they controlled or that were available for them at the time. This historical connection is reflected in different relative contributions from populations of W/WC/SW/SE Africa to geographically distinct Africa-derived populations of the Americas, adding to the complexity of genomic ancestry in groups ostensibly united by the same demographic label. [ABSTRACT FROM AUTHOR]

Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability. [ABSTRACT FROM AUTHOR]

Aim: To identify a DNA sequence specific to a bacterium found in poultry litter that was indicative of faecal contamination by poultry sources. Methods and Results: Faecally contaminated poultry litter and soils were used as source material for the development of a quantitative polymerase chain reaction (qPCR) method targeting the 16S rRNA gene of a Brevibacterium sp. The identified sequence had 98% nucleotide identity to the 16S rRNA gene of Brevibacterium avium. The qPCR method was tested on 17 soiled litter samples; 40 chicken faecal samples; and 116 nontarget faecal samples from cattle, swine, ducks, geese, and human sewage collected across the United States. The 571-bp product was detected in 76% of poultry-associated samples, but not in 93% of faecal samples from other sources. Marker concentrations were 107–109 gene copies per gram in soiled litter, up to 105 gene copies per gram in spread-site soils, and 107 gene copies per litre in field run-off water. Results were corroborated by a blinded study conducted by a second laboratory. Conclusion: The poultry-specific PCR product is a useful marker gene for assessing the impact of faecal contamination as a result of land-applied poultry litter. Significance and Impact of the Study: This study describes the first quantitative, sensitive and specific microbial source tracking method for the detection of poultry litter contamination. [ABSTRACT FROM AUTHOR]

Biofllms are colonies of microorganisms that live on wetted surfaces in a matrix consisting of polysaccharides, proteins, and nucleic acids. According to the National Institute of Health (NIH), biofilms play a role in over 80 percent of microbial infections in the body and these infections are remarkably difficult to treat with antimicrobial compounds. The objective here is to understand and predict the physical interaction between a biofilm and the surrounding fluid flow. We have developed a biofilm-fluid interaction model, based on the lmmersed Boundary Method, to simulate the interaction between the biofilm and a moving fluid. The model predictions of biofilm deformation quantitatively agree with experimental measurements for a range of biofilms using a simple immersed elastic solid to model the biofilm matrix. An immersed viscoelastic solid model is also developed and compared with experimental measurements. The results show that the viscoelastic behaviour inherent in the immersed boundary method (even when using a simple immersed elastic solid) is sufficient for some biofilms, but a slightly viscoelastic solid gives more general agreement with experimental measurements. [ABSTRACT FROM AUTHOR]

This study examined metal levels (especially U and Ni) in the tail tissues of water snakes from contaminated (Tim's Branch) and reference areas on the Department of Energy's Savannah River Site (SRS). Home ranges of snakes were quantified to determine the ratio of the habitat that they use in relation to the contaminated areas to better estimate exposure Compared to conventional methods that do not. The exposure assessment indicated that water snakes in the contaminated areas could expect U exposure at 3-4 orders of magnitude greater than the Agency for Toxic Substances and Disease Registry's Minimum Risk Level (MRL) from ingestion of amphibians and fish. Ni and U, in addition to Se, Mn, and Cu, were related to increased DNA double-strand breakage (DDSB) in water snakes. We report burdens for each metal individually, but the results of the DDSB indicated that these metals did not behave independently, but as a suite. If we did not have a secondary endpoint (DDSB), we might have assumed from the exposure predictions and tissue burden analyses that U was the sole metal of concern to water snakes in Tim's Branch. These data also imply that these toxicants do not biomagnify at the spatial and temporal scale of this study. [ABSTRACT FROM AUTHOR]