First Dark Matter Search Results from the LUX-ZEPLIN (LZ) Experiment.

The LUX-ZEPLIN experiment is a dark matter detector centered on a dual-phase xenon time projection chamber operating at the Sanford Underground Research Facility in Lead, South Dakota, USA. This Letter reports results from LUX-ZEPLIN's first search for weakly interacting massive particles (WIMPs) with an exposure of 60 live days using a fiducial mass of 5.5 t. A profile-likelihood ratio analysis shows the data to be consistent with a background-only hypothesis, setting new limits on spin-independent WIMP-nucleon, spin-dependent WIMP-neutron, and spin-dependent WIMP-proton cross sections for WIMP masses above 9 GeV/c^{2}. The most stringent limit is set for spin-independent scattering at 36 GeV/c^{2}, rejecting cross sections above 9.2×10^{-48} cm at the 90% confidence level.

Evaluation of an infrared thermography camera for measuring body temperature in dairy calves.

The objective of this diagnostic accuracy study was to validate an infrared thermography (IRT) camera and its software (FLIR One, FLIR, Global) for accuracy and precision for ocular temperature readings to serve as a proxy for rectal temperature in commercially housed calves. A total of 318 male Holstein calves were enrolled into this study from the day of arrival to a calf rearing facility until 14 d later. Researchers took an ocular temperature reading using an IRT camera, and a rectal temperature on each calf each day in the morning. The reference standard method for body temperature in the calves was rectal temperature. We assessed the data for agreement between the IRT and the reference standard using Pearson correlations by calf (accuracy), coefficients of determination (precision), and Bland-Altman plots for bias. In addition, a logistic regression model was built using the reference method as the outcome, with IRT as an explanatory variable to assess the diagnostic accuracy of IRT as an indicator of fever (rectal temperature ≥39.5°C). There was a negligible correlation between the IRT readings and rectal temperature (r = 0.22) and the coefficient of determination for IRT to predict rectal temperature was negligible (R2 = 0.05), suggesting poor precision. The average mean difference between the IRT data and rectal temperature was 0.55°C, and the differences between IRT and rectal formed a linear line around the mean difference, suggesting the Bland-Altman analyses showed proportional error and bias. The optimal probability cut-off for IRT readings for fever was at 39.5°C, and had a receiver operating characteristic area under the curve of 0.67, a sensitivity of 61%, a specificity of 71%, and 78% (3,134/4,427) of the samples were correctly labeled as either having a fever or not using IRT readings. In summary, the IRT camera and software were not validated for serving as a proxy for rectal temperature in commercially housed calves due to poor precision, and proportional error partially explained by ambient environmental conditions. We suggest that this infrared thermography system should not replace rectal temperature readings for use in commercially housed calves.

Descriptive analysis of the changes in Johne's disease management practices on Ontario dairy farms through repeat risk assessment.

Johne's disease (JD) control is often based on the culling of positive animals and the adoption of management practices that minimize exposure of calves to the pathogen Mycobacterium avium ssp. paratuberculosis (MAP). From 2010 to 2013, Ontario, Canada, instituted a voluntary Johne's control program consisting of whole-herd testing and a Risk Assessment and Management Plan (RAMP). The RAMP consisted of 38 questions that evaluated 5 different management areas to characterize herd risk for MAP introduction and within-herd spread. The RAMP produced a numerical score for each area, with higher scores associated with higher risk. The RAMP focused on animal purchases, calving management, calf management, and heifer and cow cleanliness and management. In the summer of 2019, the RAMP was repeated on 180 farms that had participated in the JD program of 2010 to 2013 and had bulk tank milk ELISA results from 2013 and 2017. This cross-sectional study demonstrated that many producers changed management practices over the 4- to 7-year period. Producers changed their cattle buying practices, with a reduction in purchasing from multiple sources and more herds refraining from buying in animals. However, overall scores were higher in 2019 than in 2013. The 2019 RAMP indicated that fewer farms were utilizing individual calving pens in 2019 than in 2013 (13% vs. 26%), yet more farms had policies in place to deal with sick or suspect JD cows entering the maternity area (92% vs. 74%). Management changes occurred over time, some of which represent increased risk (crowded maternity pens) and others decreased risk (closed herd, protocols in place for JD-positive cows) for MAP introduction and transmission. These results highlight the importance of frequent risk assessments and the documentation of changes to management practices on-farm as a means to assess herd disease risk more accurately.

Navel healing in male and female Holstein calves over the first 14 days of life: A longitudinal cohort study.

The objectives of this study were (1) to describe navel healing in male and female neonatal Holstein calves over a 14-d observation period, and (2) to determine the associations of dam parity, calving factors, and calf factors with navel measurements and time to healing. A total of 68 Holstein calves (43 female and 25 male) were enrolled. Navel healing outcomes (cessation of navel discharge, navel cord remnant drying, navel cord remnant drop-off) and navel stump measurement outcomes (proximal diameter, distal diameter, length) were recorded every 24 ± 1 h for a 14-d observation period. Data were also collected for dam parity, calving factors (time of birth, calving ease), and calf factors (calf sex, calf vitality at birth, birth weight, average daily gain, serum total protein, and medical treatment or treatments). The mean time to navel cord remnant drying was 2 d, and all calves had dry navels by d 5. A total of 56% of calves retained their navel cord remnant beyond the end of the observation period, and calves began to shed their navel cord remnants as early as d 2. In addition, at least once during the observation period, 85% of calves had a proximal navel diameter measurement over a 13-mm threshold recently proposed to identify navel infections. For distal navel diameter measurements, 72% of calves had a diameter over the 13-mm threshold at least once during the observation period. No associations were identified between navel healing outcomes and dam, calving, and calf factors. Navel measurement outcomes were associated with calving and calf factors. Specifically, proximal navel stump diameter was associated with the day of observation (decreased from d 5 to 14), calf sex (smaller in female calves), time of birth (larger in calves born overnight or unobserved, compared with the morning), and birth weight (larger in birth weights >44.1 kg compared with <38.5 kg). Distal navel stump diameter was associated with calf sex, medical treatment, and day of observation; however, we observed an interaction between sex and day of observation (larger in male calves on d 3 to 7, d 9, and d 12, compared with female calves), and sex and medical treatment (larger in untreated male calves, no difference between treated male and female calves). Navel stump length was associated with time of birth (longer in calves born overnight or unobserved compared with any other time) and the interaction of birth weight and day of observation (longer in birth weights >44.1 kg compared with 38.6-41.5 kg on d 3, 8-10, and 13, and 41.6-44.0 kg on d 3, 5, 7-8, and 13). The wide range in time to navel cord remnant drying and drop-off suggest that these measures may not be adequate indicators of calf age on their own. More research on navel healing is required to improve our understanding of factors that influence navel measurements and time to healing, as well as how this information could be used in an objective assessment of navel health.

Global distribution of white spot syndrome virus genotypes determined using a novel genotyping assay.

White spot disease, caused by infection with white spot syndrome virus (WSSV), is a serious panzootic affecting prawn aquaculture. The disease has spread rapidly around the prawn-culturing regions of the world through a number of previously identified mechanisms. The ability to distinguish and trace strains of WSSV is of great benefit to identify, and then limit, the translocation routes of the disease. Here, we describe a novel genotyping method using 34 short tandem repeat regions of the viral genome concurrently. This technique is highly sensitive to strain differences when compared to previous methods. The efficacy of the described method is demonstrated by testing WSSV isolates from around the globe, showing regional genotypic differences. The differences in the genotypes were used to create a global minimum spanning network, and in most cases the observed relationships were substantiated with verification of transboundary movement. This novel panel of STR markers will provide a valuable epidemiological tool for white spot disease. We have applied this to an outbreak of the disease in Queensland, Australia, that occurred in 2016. While the results indicate that the source of this outbreak currently remains cryptic, the analyses have provided valuable insights with which to further study the origins of the strains involved.

Peripheral quantitative computed tomography-derived muscle density and peripheral magnetic resonance imaging-derived muscle adiposity: precision and associations with fragility fractures in women.

PURPOSE: To determine the degree to which muscle density and fractures are explained by inter and intramuscular fat (IMF). METHODS: Women ⋝50 years of age (Hamilton, ON, Canada) had peripheral magnetic resonance imaging and peripheral quantitative computed tomography scans at 66% of the tibial length. Muscle on computed tomography images was segmented from subcutaneous fat and bone using fixed thresholds, computing muscle density. IMF was segmented from muscle within magnetic resonance images using a region-growing algorithm, computing IMF volume. Fracture history over the last 14 years was obtained. Odds ratios for fractures were determined for muscle density, adjusting for IMF volume, total hip BMD, age and body mass index. RESULTS: Women with a history of fractures were older (N=32, age:75.6±8.3 years) than those without (N=39, age: 67.0±5.2 years) (<0.01). IMF volume explained 49.3% of variance in muscle density (p<0.001). Odds for fractures were associated with lower muscle density even after adjusting for IMF volume but were attenuated after adjusting for age. CONCLUSIONS: Muscle adiposity represents only 50% of the muscle density measurement. Properties of muscle beyond its adiposity may be related to fractures, but larger and prospective studies are needed to confirm these associations.

Search for dark matter annihilations in the sun with the 79-string IceCube detector.

We have performed a search for muon neutrinos from dark matter annihilation in the center of the Sun with the 79-string configuration of the IceCube neutrino telescope. For the first time, the DeepCore subarray is included in the analysis, lowering the energy threshold and extending the search to the austral summer. The 317 days of data collected between June 2010 and May 2011 are consistent with the expected background from atmospheric muons and neutrinos. Upper limits are set on the dark matter annihilation rate, with conversions to limits on spin-dependent and spin-independent scattering cross sections of weakly interacting massive particles (WIMPs) on protons, for WIMP masses in the range 20-5000 GeV/c2. These are the most stringent spin-dependent WIMP-proton cross section limits to date above 35 GeV/c2 for most WIMP models.

Bone mineralization is elevated and less heterogeneous in adults with type 2 diabetes and osteoarthritis compared to controls with osteoarthritis alone.

PURPOSE: The purpose of this study was to determine whether trabecular bone mineralization differed in adults with type 2 diabetes compared to adults without type 2 diabetes. METHODS: Proximal femur specimens were obtained following a total hip replacement procedure from men and women ≥65 years of age with and without type 2 diabetes. A scanning electron microscope was used for quantitative backscattered electron imaging (qBEI) analysis of trabecular bone samples from the femoral neck. Gray scale images (pixel size=5.6 µm(2)) were uploaded to ImageJ software and gray level (GL) values were converted to calcium concentrations (weight [wt] % calcium [Ca]) using data obtained with energy dispersive X-ray spectrometry. The following bone mineralization density distribution (BMDD) outcomes were collected: the weighted mean bone calcium concentration (CaMEAN), the most frequently occurring bone calcium concentration (CaPEAK) and mineralization heterogeneity (CaWIDTH). Differences between groups were assessed using the Student's t-test for normally distributed data and Mann-Whitney U-test for non-normally distributed data. An alpha value of <0.05 was considered significant. RESULTS: Thirty-five Caucasian participants were recruited (mean [standard deviation, SD] age, 75.5 [6.5]years): 14 adults with type 2 diabetes (years since type 2 diabetes diagnosis, 13.5 [7.4]years) and 21 adults without type 2 diabetes. In the adults with type 2 diabetes, bone CaMEAN was 4.9% greater (20.36 [0.98]wt.% Ca versus 19.40 [1.07]wt.% Ca, p=0.015) and CaWIDTH was 9.4% lower (median [interquartile range] 3.55 [2.99-4.12]wt.% Ca versus 3.95 [0.71]wt.% Ca, p<0.001) compared to controls. There was no between-group difference in CaPEAK (21.12 [0.97]wt.% Ca for type 2 diabetes versus 20.44 [1.30]wt.% Ca for controls, p=0.121). CONCLUSION: The combination of elevated mean calcium concentration in bone and lower mineralization heterogeneity in adults with type 2 diabetes may have deleterious effects on the biomechanical properties of bone. These microscopic alterations in bone mineralization, which may be mediated by suppressed bone remodeling, further elucidate higher fracture risk in adults with type 2 diabetes.

Measurement of the atmospheric νe flux in IceCube.

We report the first measurement of the atmospheric electron neutrino flux in the energy range between approximately 80 GeV and 6 TeV, using data recorded during the first year of operation of IceCube's DeepCore low-energy extension. Techniques to identify neutrinos interacting within the DeepCore volume and veto muons originating outside the detector are demonstrated. A sample of 1029 events is observed in 281 days of data, of which 496±66(stat)±88(syst) are estimated to be cascade events, including both electron neutrino and neutral current events. The rest of the sample includes residual backgrounds due to atmospheric muons and charged current interactions of atmospheric muon neutrinos. The flux of the atmospheric electron neutrinos is consistent with models of atmospheric neutrinos in this energy range. This constitutes the first observation of electron neutrinos and neutral current interactions in a very large volume neutrino telescope optimized for the TeV energy range.

A novel method of bladder neck imbrication to improve early urinary continence following robotic-assisted radical prostatectomy.

Early return of continence forms an important component of quality of life for patients after robotic-assisted radical prostatectomy (RALP). Here we describe the steps of bladder neck imbrication and vesico-urethral anastomosis improving early continence after RALP. Between April 2008 and July 2009, 202 consecutive patients underwent RALP for clinically localised prostate cancer in a tertiary referral centre by a single surgeon. One hundred and thirty-two (65 %) of these patients agreed to participate in the study. Prior to November 2008, 51 patients underwent standard RALP as described by Patel et al. From November 2008, 81 patients underwent a novel method of bladder neck imbrication. The robotic urethro-vesical anastomosis commences on the posterior wall of the urethra and proceeds anteriorly. In our technique the anastomosis is halted with the suture arms fixed to the anterior abdominal wall. A new suture is used to perform a two-layer repair, anchoring proximally then continuing anteriorly to the level of the urethral stump, where it returns upon itself. The aim is to narrow the urethra to 16 Fr and tighten the second layer to create an imbrication effect. Posterior reconstruction was performed in all patients. Outcome measures were recorded prospectively using the Expanded Prostate Cancer Index Composite tool. Our technique shows significant improvement at all stages of follow-up in urinary summary and incontinence scores. Absolute continence rates increased from 8.2 to 20.5 %, 26.7 to 44.3 %, and 47.7 to 62.3 % at 1.5, 3 and 6 months, respectively. These results support the use of our technique in patients undergoing RALP.

Limits on neutrino emission from gamma-ray bursts with the 40 string IceCube detector.

IceCube has become the first neutrino telescope with a sensitivity below the TeV neutrino flux predicted from gamma-ray bursts if gamma-ray bursts are responsible for the observed cosmic-ray flux above 10(18) eV. Two separate analyses using the half-complete IceCube detector, one a dedicated search for neutrinos from pγ interactions in the prompt phase of the gamma-ray burst fireball and the other a generic search for any neutrino emission from these sources over a wide range of energies and emission times, produced no evidence for neutrino emission, excluding prevailing models at 90% confidence.

Single oligoarray-based detection of specific M918T mutation in RET oncogene in multiple endocrine neoplasia type 2B.

The most important mutation associated with Multiple Endocrine Neoplasia type 2B (MEN 2B) is the change of thymine to cytosine in codon 918 of exon 16 in the RET oncogene (ATG â†’ ACG). The aim of this work was to develop a single oligoarray by using tandem hybridization to detect the T918C/RET mutation for MEN 2B patients. Two genetically non-related families were studied; each family had a member affected by MEN2B. Both patients presented the T918C/RET mutation in a heterozygous fashion. None of the relatives was positive for this mutation; thus, these cases arose de novo. The proper mutation was confirmed by with different tools, PCR-Fok I endonuclease, direct sequencing, and also using our oligoarray. In this case, it is suitable to use a DNA target smaller than 150 bases with single- or double-stranded DNA and short probes of 7-mer. It was also possible to detect the mutation by employing different sources of DNA, fresh or paraffin-embedded tissues. Therefore, the present oligoarray can identify the most common M918T mutation of RET oncogene from a variety of DNA sources with good specificity and be a good alternative in the molecular diagnosis for MEN 2B cases.

Limits on a muon flux from neutralino annihilations in the sun with the IceCube 22-string detector.

A search for muon neutrinos from neutralino annihilations in the Sun has been performed with the IceCube 22-string neutrino detector using data collected in 104.3 days of live time in 2007. No excess over the expected atmospheric background has been observed. Upper limits have been obtained on the annihilation rate of captured neutralinos in the Sun and converted to limits on the weakly interacting massive particle (WIMP) proton cross sections for WIMP masses in the range 250-5000 GeV. These results are the most stringent limits to date on neutralino annihilation in the Sun.

Quantitative analysis of subchondral sclerosis of the tibia by bone texture parameters in knee radiographs: site-specific relationships with joint space width.

OBJECTIVES: To determine the ability of radiographic bone texture (BTX) parameters to quantify subchondral tibia sclerosis and to examine clinical relevance for assessing osteoarthritis (OA) progression. We examined the relationship between BTX parameters and each of (1) location-specific joint space width (JSW) [JSW(x)] and minimum JSW (mJSW) of the affected compartment, and (2) knee alignment (KA) angle in knee radiographs of participants undergoing total knee arthroplasty (TKA). DESIGN: Digitized fixed-flexion knee radiographs were analyzed for run-length and topological BTX parameters in a subchondral region using an algorithm. Medial JSW(x) was computed at x=0.200, 0.225, 0.250 and 0.275 according to a coordinate system defined by anatomic landmarks. mJSW was determined for medial and lateral compartment lesions. KA angles were determined from radiographs using an anatomic landmark-guided algorithm. JSW measures and the magnitude of knee malalignment were each correlated with BTX parameters. Reproducibility of BTX parameters was measured by root-mean square coefficients of variation (RMSCV%). RESULTS: Run-length BTX parameters were highly reproducible (RMSCV%<1%) while topological parameters showed poorer reproducibility (>5%). In TKA participants (17 women, 13 men; age: 66+/-9 years; body mass index (BMI): 31+/-6 kg m(-2); WOMAC: 41.5+/-16.1; Kellgren-Lawrence score mode: 4), reduced trabecular spacing (Tb.Sp) and increased free ends (FE) were correlated with decreased JSW after accounting for BMI, gender and knee malalignment. These relationships were dependent on site of JSW measurement. CONCLUSION: High reproducibility in quantifying bone sclerosis using Tb.Sp and its significant relationship with JSW demonstrated potential for assessing OA progression. Increased trabecular FE and reduced porosity observed with smaller JSW suggest collapsing subchondral bone or trabecular plate perforation in advanced knee OA.

Extending the search for neutrino point sources with IceCube above the horizon.

Point source searches with the IceCube neutrino telescope have been restricted to one hemisphere, due to the exclusive selection of upward going events as a way of rejecting the atmospheric muon background. We show that the region above the horizon can be included by suppressing the background through energy-sensitive cuts. This improves the sensitivity above PeV energies, previously not accessible for declinations of more than a few degrees below the horizon due to the absorption of neutrinos in Earth. We present results based on data collected with 22 strings of IceCube, extending its field of view and energy reach for point source searches. No significant excess above the atmospheric background is observed in a sky scan and in tests of source candidates. Upper limits are reported, which for the first time cover point sources in the southern sky up to EeV energies.

Reproducibility of computer-assisted joint alignment measurement in OA knee radiographs.

OBJECTIVES: (1) To investigate the reproducibility of computer-assisted measurements of knee alignment angle (KA) from digitized radiographs of osteoarthritis (OA) participants requiring total knee arthroplasty (TKA) and (2) to determine whether landmark choice affects the precision of KA measurements on radiographs. METHODS: Using a custom algorithm, femoral, central, and tibial measurement-guiding rules were interactively placed on digitized posteroanterior fixed-flexion knee radiographs by mouse control and positioned according to different anatomic landmarks. The angle subtended by lines connecting these guiding rules was measured by three readers to assess interobserver, intraobserver and experience-inexperience reproducibility. Test-retest reproducibility was evaluated with duplicate radiographs from a healthy cohort. Reproducibility was assessed using root-mean square coefficients of variation (RMSCV%). The Bland-Altman method was performed on data obtained from varying anatomic landmarks (confidence interval, CI= 95%). RESULTS: From 16 healthy and 30 TKA participants, reproducibility analyses revealed a high degree of intraobserver (n=38, RMSCV=0.56%), interobserver (n=38, RMSCV=0.72%), test-retest (n=16, RMSCV=0.87%) and experience-inexperience (n=38, RMSCV=0.73%) reproducibility with variances below 1%. Varying the orientation of tibial and femoral rules according to anatomic landmarks produced a difference that exceeded an a priori limit of agreement of -1.11 degrees to +1.67 degrees. CONCLUSION: Our custom-designed software provides a robust method for measuring KAs within digitized knee radiographs. Although test-retest analyses were only performed in a healthy cohort, we anticipate a similar degree of reproducibility in an OA sample. A standardized set of anatomic landmarks employed for KA measurement is recommended since arbitrary selection of landmarks resulted in imprecise KA measurement even with a computer-assisted technique.

Could a policy of provision of hip protectors to elderly nursing home residents result in cost savings in acute hip fracture care? The case of Ontario, Canada.

UNLABELLED: Hip fractures are an important problem in nursing homes. Hip protectors are external devices that decrease the risk of hip fracture in elderly nursing home residents. We estimated the overall healthcare cost savings from a hypothetical strategy of provision of hip protectors to elderly nursing home residents in Ontario, Canada. In a recent meta-analysis, we determined that a strategy of provision of hip protectors decreases the risk of hip fracture in nursing home residents. INTRODUCTION: Our objective was to determine whether the provision of hip protectors to all Ontario nursing home residents aged > or =65 years could result in cost savings, stemming from reductions in initial hospitalizations for hip fracture. METHODS: We conducted a cost analysis from a Ministry of Health perspective (one year cycle length). The efficacy of the intervention was estimated from a meta-analysis of randomized controlled trials. RESULTS: A strategy of provision of hip protectors to all 60,775 elderly Ontario nursing home residents could result in an overall mean cost savings of 6.0 million Canadian dollars in one year (95% credibility interval, -26.4 million, 39.7 million), with a probability of cost savings of 0.63 (assuming no additional labor costs). In sensitivity analyses, decreasing hip protector price increased cost savings, whereas additional labor expenditures for application for hip protectors decreased cost savings. CONCLUSION: In conclusion, if hip protectors can be provided to elderly Ontario nursing home residents without additional labor expenditures, there is a reasonable probability that such a strategy may result in healthcare cost savings.

Accuracy and test-retest precision of quantitative cartilage morphology on a 1.0 T peripheral magnetic resonance imaging system.

OBJECTIVE: Quantitative magnetic resonance imaging (qMRI) of knee cartilage morphology is a powerful research tool but relies on expensive and often inaccessible 1.5 T whole-body equipment. Here we examine the reproducibility and accuracy of qMRI at 1.0 T by direct comparison with previously validated technology. METHODS: Coronal images of the knee were obtained in six healthy and six osteoarthritic participants. Two data sets were acquired with a 1.5T whole-body magnetic resonance imaging (MRI) system and two with a 1.0 T peripheral MRI system, with repositioning between scans. Proprietary software was used to analyze surface area, volume, and thickness of femoral and tibial cartilage. RESULTS: At 1.0 T, precision errors for surface areas (root-mean-square (RMS) coefficient of variation (CV%)=1.7-2.6%) were higher than those at 1.5 T (1.0-2.1%). For volume and thickness, precision errors were 2.9-5.5% at 1.0 T compared to 1.6-3.4% at 1.5 T. High levels of agreement were found between the two scanners over all plates. With the exception of lateral femoral cartilage (volume and thickness), no statistically significant systematic bias was found between 1.0 T and 1.5 T. CONCLUSIONS: This is the first reported study to show that knee cartilage morphology can be determined with a reasonable degree of accuracy and precision using a 1.0 T peripheral scanner. Peripheral MRI is less costly, can be performed in clinical offices, and is associated with higher patient comfort and tolerance than 1.5 T whole-body MRI. Implementation of qMRI with peripheral systems may thus permit its more widespread use in clinical research and patient care.

Limits on the high-energy gamma and neutrino fluxes from the SGR 1806-20 giant flare of 27 December 2004 with the AMANDA-II detector.

On 27 December 2004, a giant gamma flare from the Soft Gamma-Ray Repeater 1806-20 saturated many satellite gamma-ray detectors, being the brightest transient event ever observed in the Galaxy. AMANDA-II was used to search for down-going muons indicative of high-energy gammas and/or neutrinos from this object. The data revealed no significant signal, so upper limits (at 90% C.L.) on the normalization constant were set: 0.05(0.5) TeV-1 m;{-2} s;{-1} for gamma=-1.47 (-2) in the gamma flux and 0.4(6.1) TeV-1 m;{-2} s;{-1} for gamma=-1.47 (-2) in the high-energy neutrino flux.

Molecular variants of human papillomavirus type 16 and risk for cervical neoplasia in South Africa.

Non-European variants of human papillomavirus (HPV) type 16 are generally associated with a greater risk of cervical neoplasia than European prototype variants. We investigated whether this association would persist in a population in which non-European HPV 16 variants were more common. We sequenced HPV 16 isolates in cervical samples collected from 93 Black South African women enrolled in a cervical cancer screening study and examined associations between cervical neoplasia identified though colposcopy with cervical biopsy and the specific HPV 16 variant identified. The European prototype variant (EP) was the most commonly identified variant in this population (47% of all isolates), but African variants (Af-1 and Af-2) were also quite common (41% of all isolates). In contrast to previous studies, we found no evidence that non-European variants were associated with an increased risk of neoplasia. Rather, most of the HPV 16-associated cancers were found in association with EP (71% of 14 cases). In this setting where African HPV 16 variants were common, no increased risk for cervical neoplasia was found among women with these variants compared with other HPV 16 variants.