Distinct viral reservoirs in individuals with spontaneous control of HIV-1.

Sustained, drug-free control of HIV-1 replication is naturally achieved in less than 0.5% of infected individuals (here termed 'elite controllers'), despite the presence of a replication-competent viral reservoir1. Inducing such an ability to spontaneously maintain undetectable plasma viraemia is a major objective of HIV-1 cure research, but the characteristics of proviral reservoirs in elite controllers remain to be determined. Here, using next-generation sequencing of near-full-length single HIV-1 genomes and corresponding chromosomal integration sites, we show that the proviral reservoirs of elite controllers frequently consist of oligoclonal to near-monoclonal clusters of intact proviral sequences. In contrast to individuals treated with long-term antiretroviral therapy, intact proviral sequences from elite controllers were integrated at highly distinct sites in the human genome and were preferentially located in centromeric satellite DNA or in Krüppel-associated box domain-containing zinc finger genes on chromosome 19, both of which are associated with heterochromatin features. Moreover, the integration sites of intact proviral sequences from elite controllers showed an increased distance to transcriptional start sites and accessible chromatin of the host genome and were enriched in repressive chromatin marks. These data suggest that a distinct configuration of the proviral reservoir represents a structural correlate of natural viral control, and that the quality, rather than the quantity, of viral reservoirs can be an important distinguishing feature for a functional cure of HIV-1 infection. Moreover, in one elite controller, we were unable to detect intact proviral sequences despite analysing more than 1.5 billion peripheral blood mononuclear cells, which raises the possibility that a sterilizing cure of HIV-1 infection, which has previously been observed only following allogeneic haematopoietic stem cell transplantation2,3, may be feasible in rare instances.

Autologous IgG antibodies block outgrowth of a substantial but variable fraction of viruses in the latent reservoir for HIV-1.

In untreated HIV-1 infection, rapid viral evolution allows escape from immune responses. Viral replication can be blocked by antiretroviral therapy. However, HIV-1 persists in a latent reservoir in resting CD4+ T cells, and rebound viremia occurs following treatment interruption. The reservoir, which is maintained in part by clonal expansion, can be measured using quantitative viral outgrowth assays (QVOAs) in which latency is reversed with T cell activation to allow viral outgrowth. Recent studies have shown that viruses detected in QVOAs prior to treatment interruption often differ from rebound viruses. We hypothesized that autologous neutralizing antibodies directed at the HIV-1 envelope (Env) protein might block outgrowth of some reservoir viruses. We modified the QVOA to reflect pressure from low concentrations of autologous antibodies and showed that outgrowth of a substantial but variable fraction of reservoir viruses is blocked by autologous contemporaneous immunoglobulin G (IgG). A reduction in outgrowth of >80% was seen in 6 of 15 individuals. This effect was due to direct neutralization. We established a phylogenetic relationship between rebound viruses and viruses growing out in vitro in the presence of autologous antibodies. Some large infected cell clones detected by QVOA carried neutralization-sensitive viruses, providing a cogent explanation for differences between rebound virus and viruses detected in standard QVOAs. Measurement of the frequency of reservoir viruses capable of outgrowth in the presence of autologous IgG might allow more accurate prediction of time to viral rebound. Ultimately, therapeutic immunization targeting the subset of variants resistant to autologous IgG might contribute to a functional cure.

Canine nematode and Giardia spp. infections in dogs in Edmonton, Alberta, the "CANIDA" study.

BACKGROUND: Canine intestinal parasite prevalence may be influenced by geographical region, age, and health status of the dog. Behaviors such as predation, scavenging, or roaming as well as routine administration of anthelmintics also play a role. The purpose of this study was to evaluate fecal test results using zinc sulfate flotation by centrifugation combined with coproantigen testing directed at protein antigens excreted or secreted by hookworms (Ancylostoma spp. Uncinaria stenocephala), ascarids (Toxocara canis, Toxascaris spp. Baylisascaris spp.), whipworms (Trichuris vulpis), and Giardia spp. during active infection in owned dogs visiting dog parks in Western Canada. METHODS: A total of 774 participants were recruited from Edmonton, Alberta, Canada. Canine fecal samples were collected from seven dedicated off-leash dog parks. Participating dog owners responded to a questionnaire regarding their dogs' signalment, previous veterinary history, and use of parasite-preventive products. Fecal samples were tested using zinc sulfate centrifugation combined with coproantigen testing. RESULTS: The overall prevalence of canine intestinal parasites in client-owned dogs was similar to previous studies conducted in the US. Mean age of dogs tested was 4 years, with puppies and older dogs having higher rates of infection than the mean. Fecal flotation centrifugation found 3.2% hookworm, ascarid, whipworm, and Giardia spp.-positive infections. Coproantigen testing identified 5.8% positive infections, including all of the above that were detected using fecal flotation centrifugation. CONCLUSIONS: Coproantigen testing detected more hookworm, ascarid, whipworm, and Giardia spp.-positive samples in addition to detecting all positive results found using fecal flotation centrifugation. Fecal flotation centrifugation combined with coproantigen testing improves sensitivity over flotation alone and may detect pre-patent or sub-clinical infections in dogs visiting public dog parks.

Detection of Giardia and helminths in Western Europe at local K9 (canine) sites (DOGWALKS Study).

BACKGROUND: Intestinal parasite contamination from infected dogs can place other dogs and humans at risk. A study was initiated to estimate the prevalence of canine intestinal parasitism by collecting fecal samples in cities across Western Europe. METHODS: Fresh fecal samples were collected from 2469 dogs visiting 164 parks in 33 cities across 12 countries. Each owner responded to a questionnaire focusing on their dog's signalment and recent anthelmintic treatment history. The collected samples were examined for hookworms, whipworms, ascarids and Giardia using a coproantigen diagnostic immunoassay and microscopy following centrifugal flotation. RESULTS: Nematodes or Giardia were detected in at least one sample from 100% of cities and in 93.3% of parks. Nematodes were detected in 57% of parks. Overall, 22.8% of dogs tested positive for an intestinal parasite, with Giardia being the most commonly identified parasites (17.3% of dogs, 83.5% of parks). For nematode infection, 7.6% of all dogs tested positive, with 9.9% of dogs aged < 1 year infected, 7.7% of those aged 1-3 years, 7.3% of those aged 4-6 years and 6.6% of those aged ≥ 7 years. Among the nematodes detected, ascarids were the most prevalent (3.6% of dogs, parks, 28.7% of parks), being most common in dogs aged < 1 year but also present in older dogs, including those aged ≥ 7 years. Hookworms and whipworms were detected in 3.2% and 2.3% of dogs of all ages, respectively, and in 37.2% and 17.7% of parks, respectively. A larger proportion of fecal samples tested positive with the coproantigen immunoassay than with centrifugal flotation. Positive test results for Giardia were sevenfold higher when both diagnostic tests were used than when centrifugal flotation alone was used, and there were 60% more positive test results for nematodes when both tests were used than when flotation alone was used. Overall, 77.2% of owners reported previous anthelmintic treatment, among whom at least 62.7% failed to follow recommended treatment frequency. Dogs receiving anthelmintic within the previous month had a lower percentage of nematode infection than those in which > 1 month had passed since the previous dose. CONCLUSIONS: The prevalence estimates of intestinal parasite infections in dogs reported here highlight the need for owner education concerning guidelines for regular testing and treatment, even in older dogs. Failure to adhere to guidelines can result in ongoing transmission of these infections, including those with zoonotic potential. Combining coproantigen immunoassay with centrifugal flotation for diagnostic testing and regular anthelmintic treatment are important measures for ensuring optimal intestinal parasite control.

A 3-year retrospective analysis of canine intestinal parasites: fecal testing positivity by age, U.S. geographical region and reason for veterinary visit.

BACKGROUND: Canine life stage is a key factor in parasite prevalence as clinical signs associated with parasitism are more common in pups. In adult dogs, health status and geographical region may also play a role in parasite prevalence. The purpose of this study was to evaluate fecal test results using zinc sulfate flotation by centrifugation combined with fecal antigen testing for hookworms (Ancylostoma spp. Uncinaria stenocephala), ascarids (Toxocara canis, Toxascaris spp., Baylisascaris spp.) and whipworms (Trichuris vulpis) sorted by age, geographical region and veterinary visit type. METHODS: A retrospective sample of intestinal parasite panels submitted to IDEXX Laboratories from 1,626,104 individual dogs were selected from the continental USA from 1 January 2017 to 31 December 2019. These data contain results from fecal exams performed using zinc sulfate flotation by centrifugation paired with coproantigen immunoassay results for hookworms, ascarids, whipworms and Giardia (Fecal Dx® with Giardia coproantigen immunoassay plate). For paired testing, if either the coproantigen assay or flotation test was positive, the sample was considered to be positive. Data were summarized by age category, U.S. Census Bureau geographical region (Northeast, South, Midwest, West) and veterinary visit type. Visit types were subdivided into Wellness Visits and Other Clinical Visits in which a fecal sample was submitted. RESULTS: In dogs presenting for either Wellness Visits or Other Clinical Visits in which Giardia testing was included, Giardia had the highest positivity (combined results for microscopy and coproantigen: 12.2 and 10.8%, respectively), followed by hookworms (combined microscopy and coproantigen: 4.1 and 4.2%, respectively), ascarids (combined microscopy and coproantigen: 2.5 and 1.7%, respectively) and whipworms (combined microscopy and coproantigen: 1.1 and 1.4%, respectively). When all test results were pooled together, pups aged 2-6 months were observed to have the highest proportion of positive results by either microscopy or coproantigen immunoassay regardless of clinical visit type. Parasite positivity varied by geographical region. Regardless of visit type, age or geographical region, the coproantigen method was observed to find a higher proportion of positive test results than microscopy in Giardia, ascarids, hookworms and whipworms. CONCLUSIONS: The Fecal Dx® coproantigen immunoassay combined with the zinc sulfate flotation by centrifugation method uncovers a higher number of positive hookworm, ascarid and whipworm infections than zinc sulfate flotation alone in both pups and adult dogs across all geographical regions of the USA regardless of visit type.

The Death of Freddie Gray and Its Impact on Homicides in Baltimore and Maryland.

This study evaluated the impact that Freddie Gray's death on April, 19, 2015, had on homicides within Baltimore, Prince George's County, and the rest of Maryland. The numbers of these deaths were compared in the 2 years prior and after his death. The average number of homicide per month in Baltimore and Prince George's County, but not the rest of Maryland, showed a statistically significant increase in the 2 years after his death, with a sudden spike in homicides in Baltimore immediately following his death. Spatial density ("heat") maps of homicides showed an increase in clustering of deaths after Freddie Gray's demise in portions of Baltimore, particularly near his arrest site. Hot spot maps showed a massive expansion of statistically significant clusters of homicides in areas of West and East Baltimore after his death. An emerging hot spot analysis revealed consecutive hot spots in large areas of West Baltimore with new hot spots prominent along the southern edge of this area. A review of the history of Baltimore, as well as discussions with Baltimore homicide detectives, revealed that prior socioeconomic and political trends likely primed Baltimore for the protests and violence that occurred after Freddie Gray's death. It is probable that a perceived "overcharging" of officers involved in his death by the State's Attorney resulted in a "pullback" from policing that directly led to increased homicides in Baltimore.

Retrospective analysis of feline intestinal parasites: trends in testing positivity by age, USA geographical region and reason for veterinary visit.

BACKGROUND: The goals of this retrospective study were to estimate parasite positivity in samples from cats using zinc sulfate fecal flotation by centrifugation ("centrifugation") and coproantigen and examine trends with age, geographical region and reason for visit to veterinarian. Common methods of parasite detection, such as centrifugal flotation, passive flotation, or direct smear, may underrepresent the true prevalence of intestinal parasites in cats. Coproantigen testing detects more positive samples than traditional methods alone. METHODS: Feline fecal test results from the continental USA containing results for fecal exams performed using centrifugation paired with coproantigen results for ascarid, hookworm, whipworm and Giardia were obtained from the database of a national commercial reference laboratory comprised of multiple regional sites. RESULTS: Parasite positivity was highest in samples from young cats and decreased with cat age. The western region of the USA had lower total parasite positivity than other regions for all parasites except Giardia. Cats receiving fecal tests during veterinary wellness visits had only slightly lower parasite positivity than samples from cats during sick clinical visits. CONCLUSIONS: This study showed a larger population of cats are at increased risk of parasitism than commonly believed and coproantigen testing produces more positive test results for the four parasites that antigen can detect than centrifugation of feline fecal samples.

Detection of gastrointestinal parasitism at recreational canine sites in the USA: the DOGPARCS study.

BACKGROUND: The rapid growth in off-leash dog parks provides opportunity for canine socialization activities but carries risk of exposure to intestinal parasites. This study assessed the prevalence of these infections in dogs visiting off-leash dog parks. METHODS: Fresh defecations were collected from dogs visiting parks in 30 metropolitan areas across the USA. Samples were analyzed by coproantigen immunoassay (CAI) (Fecal Dx® and Giardia Test, IDEXX Laboratories, Inc.) and zinc sulfate centrifugal flotation (CF). Owners responded to a questionnaire on their dog's signalment and use of heartworm/intestinal parasite control medications (HWCM). RESULTS: Samples were examined from 3006 dogs, 87.9% aged at least 12 months, visiting 288 parks. At least one intestinal parasite was detected in 622 (20.7%) samples, nematodes in 263 (8.8%), with hookworms, whipworms and ascarids in 7.1, 1.9 and 0.6% of samples, respectively. A sample positive for one or more intestinal parasites was found in 245 (85.1%) parks, with nematodes found in 143 (49.7%). Combined, CAI and CF detected 78.4% more intestinal nematode infections than CF alone. Hookworm and whipworm infections were detected in all age groups, but ascarids were only detected in dogs less than 4 years-old. Approximately 42% of dogs aged less than 1 year were positive for nematodes or Giardia. Based on owner reports, HWCM was current for 68.8% of dogs, dogs previously diagnosed with intestinal parasitism were more likely to be receiving a HWCM than those without such history, and a significantly lower (P = 0.0003) proportion of dogs receiving a HWCM were positive for intestinal nematodes compared with those not on such medication. CONCLUSIONS: Intestinal parasites, the most common of which were Giardia, Ancylostoma caninum and Trichuris vulpis, were found in 20% of dogs and 85% of dog parks across the USA. Enhanced detection of canine intestinal parasitism was achieved by combining CF and CAI. Canine intestinal parasites are common across the USA and dog health can be improved by regular testing of fecal samples and routine administration of medications effective against the most common infections.

Correction to: Detection of gastrointestinal parasitism at recreational canine sites in the USA: the DOGPARCS study.

An amendment to this paper has been published and can be accessed via the original article.