Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo).

BACKGROUND: Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. RESULTS: In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. CONCLUSIONS: The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

Gastroenteritis outbreak at a health function caused by an emerging recombinant strain of Norovirus GII.P16/GII.4 Sydney 2012, Australia.

An emerging recombinant norovirus GII.P16/GII.4 Sydney 2012 strain caused a gastroenteritis outbreak amongst attendees at a large health function in regional New South Wales, Australia. This was the third outbreak caused by the recombinant GII.P16/GII.4 Sydney 2012 strain in this region in 2017, which appears to be emerging as a common strain in the Hunter New England region.

Shaggy Lame Fox Syndrome in Pribilof Island Arctic Foxes ( Alopex lagopus pribilofensis), Alaska.

A previously unrecognized condition is described in wild free-ranging Pribilof arctic foxes ( Alopex lagopus pribilofensis) from the Pribilof Islands, Alaska, USA. This condition is called shaggy lame fox syndrome (SLFS) denoting the primary clinical signs first observed. Criteria used to suspect SLFS on gross examination included emaciation, failure to shed winter pelage and moderate to severe polyarthritis. Criteria used to confirm SLFS histologically included polyarthritis (characterized by lymphoplasmacytic synovitis, tenosynovitis, bursitis, periosteal bony proliferation, and periarticular lymphoplasmacytic vasculitis) and systemic leukocytoclastic vasculitis. Other histological lesions often found included renal cortical infarcts, myocarditis with myocardial infarcts, lymphoplasmacytic meningitis, lymphoplasmacytic cuffing of meningeal and a few cerebral vessels, and cavitating infarcts of the brainstem and thalamus. The cause of SLFS is not known at this time; however, the gross and histological lesions suggest that the cause of SLFS may be a bacterial polyarthritis with a secondary immune-mediated vasculitis. These lesions are consistent with changes described with Erysipelothrix rhusiopathiae in domestic dogs; E. rhusiopathiae was identified from the synovial membrane of a swollen stifle joint and the kidney from one fox using real-time polymerase chain reaction and with culture from a fox that had gross and histological lesions of SLFS. Therefore, E. rhusiopathiae is a possible etiological agent for SLFS.

Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo).

Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.

Aqueous extract of Chrysobalanus icaco leaves, in lower doses, prevent fat gain in obese high-fat fed mice.

ETHNOPHARMACOLOGICAL RELEVANCE: Due to the rise in obesity, the necessity for resources and treatments that could reduce the morbidity and mortality associated to this pandemia has emerged. The development of new anti-obesity drugs through herbal sources has been increasing in the past decades which are being used not only as medicine but also as food supplements. Previous studies with the aqueous extract of Chrysobalanus icaco L (AECI) have demonstrated activity on lowering blood glucose levels and body weight. AIM OF THE STUDY: Investigate C. icaco effects in overall adiposity and glycemic homeostasis. MATERIAL AND METHODS: C57BL/6J mice were randomly assigned to standard chow (SC) or high-fat diet (HFD) and treated with AECI in 0.35mg/mL or 0.7mg/mL concentrations ad libitum. Food intake, feed efficiency, metabolic efficiency, body, fat pads and gastrocnemius weight, adiposity index, serum lipids, fecal lipid excretion, locomotor activity in the open field test and insulin and glucose tolerance tests were analyzed and compared. The major components of the extract were demonstrated through HPLC and its antioxidant activity analyzed through DPPH and lipid peroxidation. RESULTS: The AECI in the 0.35mg/mL concentration did not affect food intake or body weight. However, it promoted lower adipose tissue gain, TG levels, and fecal lipid excretion, increased locomotor activity and lean mass weight, and normalized insulin sensitivity and glucose tolerance. Moreover, AECI showed the presence of myricetin 3-O-glucuronide, rutin, quercitrin and myricitrin and demonstrated high-antioxidant activity. CONCLUSIONS: AECI in lower concentrations can prevent fat storage or enhance fat utilization through the increase of locomotor activity. Also, this reinforces its ability to maintain glucose homeostasis through the normalization of insulin sensitivity and glucose tolerance despite the high-fat diet intake. These activities could be associated to the extract's polyphenol content.

Comparative transcriptomic analyses to scrutinize the assumption that genotoxic PAHs exert effects via a common mode of action.

In this study, the accuracy of the assumption that genotoxic, carcinogenic polycyclic aromatic hydrocarbons (PAHs) act via similar mechanisms of action as benzo(a)pyrene (BaP), the reference PAH used in the human health risk assessment of PAH-containing complex mixtures, was investigated. Adult male Muta™Mouse were gavaged for 28 days with seven individual, genotoxic PAHs. Global gene expression profiles in forestomach, liver, and lung (target tissues of exposure) were determined at 3 days post-exposure. The results are compared with our previously published results from mice exposed to BaP via the same exposure regimen. Although all PAHs showed enhanced ethoxyresorufin-O-deethylase activity, DNA adduct formation, and lacZ mutant frequency in the lungs, the unsupervised cluster analysis of differentially expressed genes revealed that the transcriptional changes are both PAH- and tissue-specific, with lung showing the most response. Further bioinformatics-/pathway-based analysis revealed that all PAHs induce expression of genes associated with carcinogenic processes, including DNA damage response, immune/inflammatory response, or cell signaling processes; however, the type of pathways and the magnitude of change varied for each PAH and were not the same as those observed for BaP. Benchmark dose modeling showed transcriptomic data closely reflected the known tumor incidence for the individual PAHs in each tissue. Collectively, the results suggest that the underlying mechanisms of PAH-induced toxicity leading to tumorigenesis are tissue-specific and not the same for all PAHs; based on the tissue type considered, use of BaP as a reference chemical may overestimate or underestimate the carcinogenic potential of PAHs.

Emergence of a novel GII.17 norovirus ­ End of the GII.4 era?

In the winter of 2014/15 a novel GII.P17-GII.17 norovirus strain (GII.17 Kawasaki 2014) emerged, as a major cause of gastroenteritis outbreaks in China and Japan. Since their emergence these novel GII.P17-GII.17 viruses have replaced the previously dominant GII.4 genotype Sydney 2012 variant in some areas in Asia but were only detected in a limited number of cases on other continents. This perspective provides an overview of the available information on GII.17 viruses in order to gain insight in the viral and host characteristics of this norovirus genotype. We further discuss the emergence of this novel GII.P17-GII.17 norovirus in context of current knowledge on the epidemiology of noroviruses. It remains to be seen if the currently dominant norovirus strain GII.4 Sydney 2012 will be replaced in other parts of the world. Nevertheless, the public health community and surveillance systems need to be prepared in case of a potential increase of norovirus activity in the next seasons caused by this novel GII.P17-GII.17 norovirus.

Evolution of norovirus.

Norovirus (NoV) is now the dominant aetiological agent of acute gastroenteritis, and, with the recent introduction of rotavirus vaccines in many countries, this is likely to remain the case. NoV has a significant impact on human wellbeing in terms of morbidity, economic costs and mortality in developing countries. NoVs are divided into six genogroups (GI-GVI), but only GI, GII and GIV are known to infect humans, with GII being the most prevalent, causing >95% of human infections. The immune system is thought to drive selection of emerging pandemic NoVs through both antigenic drift and shift. This phenomenon results in the replacement of dominant circulating viruses approximately every 3 years, with new variants able to re-infect hosts previously infected with earlier viruses. This review explores the evolutionary aspects of contemporary NoVs.

Derivation of point of departure (PoD) estimates in genetic toxicology studies and their potential applications in risk assessment.

Genetic toxicology data have traditionally been employed for qualitative, rather than quantitative evaluations of hazard. As a continuation of our earlier report that analyzed ethyl methanesulfonate (EMS) and methyl methanesulfonate (MMS) dose-response data (Gollapudi et al., 2013), here we present analyses of 1-ethyl-1-nitrosourea (ENU) and 1-methyl-1-nitrosourea (MNU) dose-response data and additional approaches for the determination of genetic toxicity point-of-departure (PoD) metrics. We previously described methods to determine the no-observed-genotoxic-effect-level (NOGEL), the breakpoint-dose (BPD; previously named Td), and the benchmark dose (BMD10 ) for genetic toxicity endpoints. In this study we employed those methods, along with a new approach, to determine the non-linear slope-transition-dose (STD), and alternative methods to determine the BPD and BMD, for the analyses of nine ENU and 22 MNU datasets across a range of in vitro and in vivo endpoints. The NOGEL, BMDL10 and BMDL1SD PoD metrics could be readily calculated for most gene mutation and chromosomal damage studies; however, BPDs and STDs could not always be derived due to data limitations and constraints of the underlying statistical methods. The BMDL10 values were often lower than the other PoDs, and the distribution of BMDL10 values produced the lowest median PoD. Our observations indicate that, among the methods investigated in this study, the BMD approach is the preferred PoD for quantitatively describing genetic toxicology data. Once genetic toxicology PoDs are calculated via this approach, they can be used to derive reference doses and margin of exposure values that may be useful for evaluating human risk and regulatory decision making.

Accuracy of nuchal translucency measurement depends on equipment used and its calibration.

OBJECTIVES: To determine the effect of different ultrasound machine-probe combinations on nuchal translucency (NT) measurements and to assess how this impacts on the accuracy of the NT-derived component of first-trimester screening for trisomy 21. METHODS: Sixteen different ultrasound machine-probe combinations were used for axial measurement of 2.0-, 3.0- and 4.0-mm spaced targets in an ultrasound phantom. Differences between the measured and known values were determined. The mean of the axial measurements was used to calculate adjusted risks for trisomy 21, given specific clinical scenarios. RESULTS: Differences observed using different machine-probe combinations for the 2.0-mm target ranged from 1.8-2.2 mm; for the 3.0-mm target, 2.7-3.2 mm; and for the 4-mm target, 3.7-4.3 mm, and exceeded those due to intraobserver variability. For a fetal crown-rump length of 50.0 mm and NT measurement of 2.0 mm, the maximum/minimum measurements in the fetus of a 40-year-old woman led to derived risks ranging from 1 in 32 (NT, 2.2 mm) to 1 in 189 (NT, 1.8 mm) and in the fetus of a 20-year-old with an NT of 3.0 mm these ranged from 1 in 102 (NT, 3.2 mm) to 1 in 160 (NT, 2.7 mm). CONCLUSIONS: We have described the effect of machine-probe combinations on small but very precise ultrasound measurements. Such machine-probe combinations led to greater variability than those ascribed to intraobserver differences, and significantly affected the screening risk for the same fixed measurement. This finding has implications for Down syndrome screening algorithms and audit of ultrasound operators. Furthermore, most ultrasound machines are neither calibrated nor specified for measurements of tenths of a mm.

Soil ingestion rate determination in a rural population of Alberta, Canada practicing a wilderness lifestyle.

The inadvertent ingestion of contaminated soil can be a major pathway for chemical exposure to humans. Few studies to date have quantified soil ingestion rates to develop exposure estimates for human health risk assessments (HHRA), and almost all of those were for children in suburban/urban environments. Here we employed a quantitative mass balance tracer approach on a rural population practicing outdoor activities to estimate inadvertent soil ingestion. This study followed 9 subjects over a 13 day period in Cold Lake, Alberta, near the largest in situ thermal heavy oil (bitumen) extraction operation in the world. The mean soil ingestion rate in this study using Al Ce, La, and Si tracers was 32 mg d(-1), with a 90th percentile of 152 mg d(-1) and median soil ingestion rate of 18 mg d(-1). These soil ingestion values are greater than the standard recommended soil ingestion rates for HHRA from Health Canada, and are similar to soil ingestion estimates found in the only other study on a rural population.

Rare occurrence of occult hepatitis C virus in apparently uninfected injecting drug users: a two-centre, masked, case-control study.

Occult hepatitis C virus (HCV) is a phenomenon where serum HCV RNA is not detected by sensitive commercial assays, but viral RNA is detected by ultrasensitive techniques. Occult HCV infection has not previously been studied in highly exposed, but apparently uninfected (EU) individuals. Two studies examining occult infection in EU subjects were undertaken - an initial two-centre, masked, case-control study based on cross-sectional samples (n = 35 subjects) and a single-centre confirmatory study based on longitudinal samples (n = 32 subjects). Plasma and peripheral blood mononuclear cells were tested for HCV RNA using an ultrasensitive nested polymerase chain reaction assays. Two EU subjects in the first study (10%) and one in the second study (3%) were found to have consistently detectable HCV RNA. Occult HCV infection occurs in high-risk, apparently uninfected subjects.

Indications for worldwide increased norovirus activity associated with emergence of a new variant of genotype II.4, late 2012.

Globally, surveillance systems showed an increasein norovirus activity in late 2012. Molecular datashared through the NoroNet network suggest thatthis increase is related to the emergence of a newnorovirus genotype II.4 variant, termed Sydney 2012.Healthcare institutions are advised to be prepared fora severe norovirus season.

Quantitative approaches for assessing dose-response relationships in genetic toxicology studies.

Genetic toxicology studies are required for the safety assessment of chemicals. Data from these studies have historically been interpreted in a qualitative, dichotomous "yes" or "no" manner without analysis of dose-response relationships. This article is based upon the work of an international multi-sector group that examined how quantitative dose-response relationships for in vitro and in vivo genetic toxicology data might be used to improve human risk assessment. The group examined three quantitative approaches for analyzing dose-response curves and deriving point-of-departure (POD) metrics (i.e., the no-observed-genotoxic-effect-level (NOGEL), the threshold effect level (Td), and the benchmark dose (BMD)), using data for the induction of micronuclei and gene mutations by methyl methanesulfonate or ethyl methanesulfonate in vitro and in vivo. These results suggest that the POD descriptors obtained using the different approaches are within the same order of magnitude, with more variability observed for the in vivo assays. The different approaches were found to be complementary as each has advantages and limitations. The results further indicate that the lower confidence limit of a benchmark response rate of 10% (BMDL(10) ) could be considered a satisfactory POD when analyzing genotoxicity data using the BMD approach. The models described permit the identification of POD values that could be combined with mode of action analysis to determine whether exposure(s) below a particular level constitutes a significant human risk. Subsequent analyses will expand the number of substances and endpoints investigated, and continue to evaluate the utility of quantitative approaches for analysis of genetic toxicity dose-response data.

A pilot study to assess the feasibility of using naturally-occurring radionuclides as mass balance tracers to estimate soil ingestion.

The relatively few soil ingestion studies that have been conducted to date to support soil ingestion rate values used for contaminated site human health risk assessments (HHRAs) typically have measured mass balance elemental tracers (e.g., Al, Si, Ba, Ce, Mn, Ti, V, Zr), found in soil to estimate soil ingestion. This pilot study, involving a canine subject fed a known amount of tracer on a daily basis, assessed the use of alternative mass balance tracers, specifically naturally occurring radionuclides of the (238)U and (232)Th decay series, to estimate soil ingestion. A novel method of estimating soil ingestion via difference in isotopic ratios between the two decay series in food and soil was also assessed. The results of the study showed that the mean (214)Pb and (212)Pb activities measured in fecal samples were greater than what was contained in the soil inoculant, suggesting that the tracers were not being significantly absorbed in the GI tract. The mean daily soil ingestion rates, calculated after subtracting the contribution of tracers in the soil inoculant, were 3.9 g d(-1) (standard deviation 3.6 g d(-1)) for the isotope tracers, and 1.9 g(-1) (standard deviation 2.1 g d(-1)) for the 3 most reliable elemental tracers. The differences were not statistically significant and further evaluation of isotopic tracers for soil ingestion studies is warranted. Similarly, soil ingestion estimates calculated using the Isotope Ratio Method were not significantly different than when calculated using (212)Pb; however, the Isotope Ratio Method was observed to positively bias the soil ingestion estimates by approximately 50%.

A survey of the traditional food consumption that may contribute to enhanced soil ingestion in a Canadian First Nation community.

Soil ingestion rates in the order of 400 mg d(-1) have been proposed and considered plausible for use in human health risk assessments (HHRA) of Aboriginal populations and justified by qualitative assessments of the traditional subsistence activities that could enhance soil ingestion. The purpose of this study was to assess and document the subsistence activities and food consumption practiced by a First Nation Community living in a wilderness community in Canada to allow for a comparison with the previous qualitative assessments of Aboriginal populations and a quantitative mass balance tracer element study of the community conducted concurrently. An ethno-cultural survey was conducted of the Xeni Gwet'in First Nations community living in the Nemiah Valley, approximately 230 km west of Williams Lake, British Columbia. The community diet was observed to consist mainly of fish and big game, and was supplemented by berries and roots. Outdoor cultural gatherings, hunting and food gathering trips and sporting events, with their attendant potential for enhanced soil exposure, were observed to be an important facet of community life. The survey concluded that a significant portion of the Xeni Gwet'in practise a lifestyle similar to the subsistence lifestyles of other indigenous communities, where soil exposure scenarios in the order of hundreds of mg d(-1) have been proposed.

A soil ingestion pilot study of a population following a traditional lifestyle typical of rural or wilderness areas.

The relatively few soil ingestion studies underpinning the recommended soil ingestion rates for contaminated site human health risk assessments (HHRAs) that have been conducted to date assessed soil ingestion in children living in urban or suburban areas of the United States, and to a lesser extent, Europe. However, the lifestyle of populations living in North American urban and suburban environments is expected to involve limited direct contact with soil. Conversely, many populations, such as indigenous and Aboriginal peoples residing in rural and wilderness areas of North America and worldwide, participate in activities that increase the frequency of direct contact with soil. Qualitative exposure of Aboriginal populations inhabiting wilderness areas suggest that high levels of soil ingestion may occur that are many times greater than those recommended by regulatory agencies for use in HHRAs. Accordingly, a study of subjects selected from a wilderness community in Canada was conducted using mass balance tracer methods to estimate soil ingestion and the results compared with previous soil ingestion studies and regulatory guidelines for the soil ingestion rates used in HHRA of contaminated sites. A pilot study of 7 subjects living in the Nemiah Valley of British Columbia was conducted over a 3-week period. The mean soil ingestion rate estimated in this study using the 4 elemental tracers with the lowest food-to-soil ratios (i.e., Al, Ce, La, Si), was observed to be approximately 75 mg d(-1) (standard deviation 120 mg d(-1)), the median soil ingestion rate was 50 mg d(-1), and the 90th percentile was 211 mg d(-1). These soil ingestion rate estimates are higher than the soil ingestion estimates currently recommended for HHRAs of adults, and higher than those obtained in most previous studies of adults. However, the estimates are lower than the earlier qualitative assessments of subsistence lifestyles.

Transmission of hepatitis C virus to recipients of parenteral vitamin therapy in a primary care facility.

BACKGROUND AND OBJECTIVES: The Australian prevalence of hepatitis C virus (HCV) is approximately 1%, with the majority of cases acquired through injecting drug use. However, occasionally HCV infection occurs in healthcare settings. Three new HCV infections were identified amongst patients attending a general practice in Sydney, Australia, specialising in parenteral vitamin therapy. STUDY DESIGN: An investigation was conducted to identify the source of infection and mechanism of transmission. Molecular analysis was conducted by sequencing the HCV NS5A, Core and NS5B regions. RESULTS: Two sources were identified using molecular epidemiology - a genotype 3a case was the source for a case acquired in late 2004 and a genotype 1b case the source for one case acquired in late 2006 and another in early 2007. The common risk factor was parenteral vitamin C therapy. CONCLUSIONS: Inadequate infection control was apparent and likely to have resulted in blood contamination of the healthcare workers, their equipment, the clinic environment and parenteral medications. Molecular and clinical epidemiology clearly identified parenteral transmission of HCV, highlighting the risks of blood contamination of parenteral equipment and use of multi-dose flasks on more than one patient.

The neonatal but not the mature heart adapts to acute tachycardia by beneficial modification of the force-frequency relationship.

The force-frequency relationship (FFR) reflects alterations in intracellular calcium cycling during changing heart rate (HR). Tachycardia-induced heart failure is associated with depletion of intracellular calcium. We hypothesized (1) that the relative resistance to tachycardia-induced heart failure seen in neonatal pigs is related to differences in calcium cycling, resulting in different FFR responses and (2) that pretreatment with digoxin to increase intracellular calcium would modifies these changes. LV +dP/dt was measured during incremental right atrial pacing in 16 neonatal and 14 adult pigs. FFR was measured as the change in +dP/dt as HR was increased. Animals were randomized to control or intravenous bolus digoxin (n = 8 neonate pigs in the 0.05 mg/kg group and n = 7 adult pigs in the 0.025 mg/kg group) and paced for 90 min at 25 bpm greater than the rate of peak +dP/dt. Repeat FFR was then obtained. The postpacing FFR in neonatal control pigs shifted rightward, with peak force occurring 30 bpm greater than baseline (P < 0.03). There was no vertical shift; thus, force at 150 bpm decreased (P < 0.03) and force at 300 beats/min increased (P < 0.08). In adult control pigs, FFR shifted downward (P < 0.01), with decreased force generation at all HRs. In both neonates and adult pigs, digoxin increased +dP/dt at all HRs; however, in neonate pigs digoxin decreased the contractile reserve by abrogation of the rightward shift of FFR. An adaptive response to tachycardia in the neonate pig leads to improved force generation at greater HRs. Conversely, the response of the mature pig heart is maladaptive with decreased force generation. Pretreatment with digoxin modifies these responses.

Patterns and characteristics of hepatitis C transmission clusters among HIV-positive and HIV-negative individuals in the Australian trial in acute hepatitis C.

BACKGROUND: Injecting drug users remain the population at greatest risk of acquiring hepatitis C virus (HCV) infection, although a recent increase in cases of sexually transmitted HCV infection has been observed among human immunodeficiency virus (HIV)-infected individuals. The extent to which these separate epidemics overlap is unknown. METHODS: The Australian Trial in Acute Hepatitis C (ATAHC) enrolled 163 individuals (29% of whom were HIV infected) with recent HCV infection. E1/HVR1 sequences were used to construct phylogenetic trees demonstrating monophyletic clusters or pairs, and viral epidemic history and phylogeography were assessed using molecular clock analysis. Individual clusters were characterized by clinical and demographic characteristics. RESULTS: Transmission through injection drug use occurred for 73% of subjects, with sexual transmission occurring for 18% (92% of whom were HIV infected). Among 112 individuals with available E1/HVR1 sequences, 23 (20%) were infected with a strain of HCV identical to that of another subject, comprising 4 homologous clusters and 3 monophyletic pairs, the majority of which (78%) were HIV infected. Clusters contained individuals with both injection drug use-related and sex-related acquisition, and in all clusters (except for 1 female HIV-uninfected pair), individuals identified as men who have sex with men, irrespective of HIV status. CONCLUSIONS: This large unique study of HIV-infected and HIV-uninfected individuals with recently acquired HCV infection demonstrates that clustering is common in the HIV-infected population and that it occurred almost invariably among men who have sex with men, irrespective of the actual mode of acquisition. These findings suggest the coexistence of both injection drug use and sexual risk behaviors for individuals in the same social networks and have implications for the development of public health messages. Clinical trial registration. NCT00192569.