NK cells in self-limited HCV infection exhibit a more extensively differentiated, but not memory-like, repertoire

Natural killer (NK) cells have long been thought of as a purely innate immune cell population, but increasing reports have described developmental and functional qualities of NK cells that are commonly associated with cells of the adaptive immune system. Of these features, the ability of NK cells to acquire functional qualities associated with immunological memory and continuous differentiation resulting in the formation of specific NK cell repertoires has recently been highlighted in viral infection settings. By making use of a unique cohort of monitored, at-risk intravenous drug users in this study, we were able to dissect the phenotypic and functional parameters associated with NK cell differentiation and NK cell memory in patients 3 years after acute HCV infection and either the subsequent self-clearance or progression to chronicity. We observed increased expression of cytolytic mediators and markers CD56bright and NKp46+ of NK cells in patients with chronic, but not self-limited HCV infection. Patients with a self-limited infection expressed higher levels of differentiation-associated markers CD57 and KIRs, and lower levels of NKG2A. A more extensively differentiated NK cell phenotype is associated with self-clearance in HCV patients, while the NK cells of chronic patients exhibited more naïve and effector NK cell phenotypic and functional characteristics. The identification of these distinct NK cell repertoires may shed light on the role NK cells play in determining the outcome of acute HCV infections, and the underlying immunological defects that lead to chronicity

Cross-genotype AR3-specific neutralizing antibodies confer long-term protection in injecting drug users after HCV clearance

Background & AimsUnderstanding immune protection against hepatitis C virus (HCV) infection is necessary for designing an effective vaccine. A number of broadly-reactive, neutralizing antibodies have been isolated from B cells of HCV-infected subjects. However, it remains unclear whether B cells producing such antibodies contribute to the clearance and long-term immune protection against HCV.MethodsWe analysed the B-cell repertoire of thirteen participants from the Amsterdam Cohort Study among injecting drug users with a median follow-up of 17.5 years. Five subjects ultimately became chronically infected either after primary infection or after reinfection. Eight subjects, at the end of study follow-up, were HCV RNA negative following spontaneous clearance of one or multiple infections. From each subject, 10,000 CD27+IgG+ B cells, collected 0.75 year after HCV infection, were cultured to characterize the antibody repertoire.ResultsUsing a multiplex flow cytometry-based assay to study the antibody binding to E1E2 from genotype 1 to 6, we found that a high frequency of cross-genotype antibodies was associated with spontaneous clearance of one or multiple infections (p-value=0.03). Epitope specificity of these cross-genotype antibodies was determined by alanine mutant scanning in four subjects, who were HCV RNA negative following spontaneous clearance of one or multiple infections. Interestingly, the cross-genotype antibodies were mainly AR3-specific and showed cross-neutralizing activity against HCV. In addition to AR3 antibodies, three subjects developed antibodies recognizing AR4 of which one monoclonal antibody showed cross-neutralizing capacity.ConclusionsTogether, these data suggest that a strong B-cell response producing cross-genotype and neutralizing antibodies, especially targeting AR3, contribute to HCV clearance and long-term immune protection against HCV

Direct-Acting Antiviral Treatment for Hepatitis C Genotypes Uncommon in High-Income Countries:A Dutch Nationwide Cohort Study

Background. The majority of hepatitis C virus (HCV) infections are found in low- and middle-income countries, which harbor many region-specific HCV subtypes. Nevertheless, direct-acting antiviral (DAA) trials have almost exclusively been conducted in high-income countries, where mainly epidemically spread HCV subtypes are present. Recently, several studies have demonstrated suboptimal DAA efficacy for certain nonepidemic subtypes, which could hamper global HCV elimination. Therefore, we aimed to evaluate DAA efficacy in patients treated for a nonepidemic HCV genotype infection in the Netherlands. Methods. We performed a nationwide retrospective study including patients treated with interferon-free DAAs for an HCV genotype other than 1a/1b/2a/2b/3a/4a/4d. The genotype was determined by NS5B region phylogenetic analysis. The primary end point was SVR-12. If stored samples were available, NS5A and NS5B sequences were obtained for resistance-associated substitutions (RAS) evaluation. Results. We included 160 patients, mainly infected with nonepidemic genotype 2 (41%) and 4 (31%) subtypes. Most patients were from Africa (45%) or South America (24%); 51 (32%) were cirrhotic. SVR-12 was achieved in 92% (140/152) of patients with available SVR-12 data. Only 73% (8/11) genotype 3-infected patients achieved SVR-12, the majority being genotype 3b patients with 63% (5/8) SVR. Regardless of SVR, all genotype 3b patients had 30K and 31M RAS. Conclusions. (T)he DAA efficacy we observed in most nonepidemic genotypes in the Netherlands seems reassuring. However, the low SVR-12 rate in subtype 3b infections is alarming, especially as it is common in several HCV-endemic countries. Alongside earlier results, our results indicate that a remaining challenge for global HCV elimination is confirming and monitoring DAA efficacy in nonepidemic genotypes

AR-quiver approach to affine canonical basis elements

AbstractThis is the continuation of [Y. Li, Affine quivers of type A˜n and canonical bases, math.QA/0501175]. We describe the affine canonical basis elements in the case when the affine quiver has arbitrary orientation. This generalizes the description in [G. Lusztig, Affine quivers and canonical bases, Publ. Math. Inst. Hautes Études Sci. 76 (1992) 111–163]

Hepatitis C virus transmission between eight high-income countries among men who have sex with men: a whole-genome analysis.

BACKGROUND Microelimination of the hepatitis C virus (HCV) among men who have sex with men (MSM) could be complicated by continuous external introductions and the emergence of phylogenetic clusters harbouring clinically significant resistance-associated substitutions (RAS). To investigate international clustering and the prevalence and transmission of RAS, we aimed to analyse whole-genome HCV sequences from MSM with a recently acquired infection who participated in a large, international HCV treatment trial. METHODS For this whole-genome analysis, we obtained HCV sequences from 128 MSM who had acquired HCV within the past 12 months and were participating in the REACT trial. The participants from whom sequences were obtained were recruited at 24 sites in eight countries. We inferred maximum-likelihood phylogenies and identified transmission clusters for HCV genotypes separately. We constructed time-scaled phylogenies to estimate cluster introduction dates and used a Bayesian Skygrid approach to estimate the effective population size over the past 50 years. We calculated the prevalence of RAS and the extent of RAS transmission in the study population. FINDINGS The majority of recent HCV infections were part of international networks that arose in the late 1990s and early 2000s. Sequences obtained in the same country clustered frequently, and in 36% of subclusters since 2015 we found evidence of international transmission. European MSM were more likely than non-European MSM to be in a cluster (odds ratio 11·9 [95% CI 3·6-43·4], p<0·0001). The effective population size decreased rapidly since around 2015 in Europe. RAS associated with substantially diminished cure rates were infrequently detected and transmission of highly resistant viruses was not observed. INTERPRETATION Despite antiviral treatment becoming widely available, international transmission of HCV among MSM has still occurred over the past 8 years, which could complicate microelimination of the virus in this population. RAS-enriched clusters and widespread RAS transmission are currently not a threat to elimination goals. These findings support an international approach for HCV microelimination among MSM. FUNDING National Institutes of Health and Dr. C.J. Vaillant Fonds

Reasons for not commencing direct-acting antiviral treatment despite unrestricted access for individuals with HIV and hepatitis C virus: a multinational, prospective cohort study.

BACKGROUND Individuals with HIV and hepatitis C virus (HCV) who remain untreated with direct-acting antivirals can contribute to HCV transmission and HCV-related mortality. We aimed to compare rates of uptake of direct-acting antivirals following unrestricted access to this treatment in high-income countries and examine factors associated with remaining untreated. METHODS This multinational, prospective cohort study used data from the International Collaboration on Hepatitis C Elimination in HIV Cohorts (InCHEHC). We analysed data from nine observational cohorts participating in the InCHEHC, including data from six high-income countries (Australia, Canada, France, the Netherlands, Spain, and Switzerland). We included individuals aged 18 years and older, with HIV and HCV (ie, HCV-RNA positive without evidence of spontaneous clearance) during unrestricted access to interferon-free direct-acting antiviral treatment in each country. We calculated the cumulative proportion of participants who remained untreated with direct-acting antivirals, with follow-up starting after the date of unrestricted access or cohort inclusion, whichever occurred most recently. Factors associated with the commencement rate of direct-acting antiviral treatment were assessed using competing-risks regression with the Fine-Gray method. FINDINGS The date of unrestricted access to direct-acting antiviral treatment for people with HIV ranged from Nov 1, 2014, in France to Nov 1, 2017, in Switzerland. We included 4552 individuals with HIV-HCV, mainly men who have sex with men (MSM; n=2156 [47%]) and people who inject or have injected drugs (n=1453 [32%]). 1365 (30%) of 4552 participants remained untreated with direct-acting antivirals. For individuals treated with direct-acting antivirals, median time from start of follow-up to treatment was 5 months (IQR 2-12). For individuals who were not treated with direct-acting antivirals, median follow-up was 22 months (8-30). Being linked to care in Australia, France, or the Netherlands, on antiretroviral therapy, having undetectable HIV RNA, and shorter duration since first positive HCV test were independently associated with higher commencement rate of direct-acting antiviral treatment. Compared with MSM, male heterosexuals and females with unknown or other routes of HIV transmission (ie, neither injection drug use nor heterosexual transmission) had lower rates of commencement. INTERPRETATION Despite unrestricted access, almost a third of individuals with HIV-HCV remained untreated with direct-acting antivirals during follow-up, with variation in commencement rate of HCV treatment between countries and key populations. Increased efforts are required to reach the remaining individuals with HIV who are HCV-viraemic to achieve HIV-HCV micro-elimination. FUNDING None

Elevated risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variants compared with Alpha variant in vaccinated individuals

The extent to which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) break through infection- or vaccine-induced immunity is not well understood. We analyzed 28,578 sequenced SARS-CoV-2 samples from individuals with known immune status obtained through national community testing in the Netherlands from March to August 2021. We found evidence of an increased risk of infection by the Beta (B.1.351), Gamma (P.1), or Delta (B.1.617.2) variants compared with the Alpha (B.1.1.7) variant after vaccination. No clear differences were found between vaccines. However, the effect was larger in the first 14 to 59 days after complete vaccination compared with ≥60 days. In contrast to vaccine-induced immunity, there was no increased risk for reinfection with Beta, Gamma, or Delta variants relative to the Alpha variant in individuals with infection-induced immunity.</p

No chikungunya virus infections among Dutch long-term travellers to (sub)tropical countries: A prospective study 2008-2011

Background: Chikungunya is an arthropod-borne viral disease now identified in over 60 countries in Asia, Africa, Europe, and the Americas. Chikungunya virus (CHIKV) has spread in the last 15 years to many countries, causing large local outbreaks. CHIKV infection can be clinically misdiagnosed in areas where dengue and/or Zika infections occur. Prospective studies are necessary to calculate the true incidence rate of CHIKV infection in travellers. The aim of this study was to obtain the attack and incidence rates of CHIKV infection among long-term travellers and identify associated risk factors. Methods: A previously collected prospective cohort of Dutch long-term travellers (12-52 weeks) to subtropical and tropical countries was tested. From December 2008 to September 2011, participants were recruited at the travel clinic of the Public Health Service Amsterdam. A weekly diary was kept during travel in which participants recorded their itinerary, symptoms, and physician visits. On return, their pre- and post-travel blood samples were tested for the presence of IgG antibodies to CHIKV antigen. Seroconversions were confirmed by an in-house CHIKV neutralisation test. Results: The median age of 603 participants was 25 years (interquartile range [IQR]: 23-29); 35.7% were male; median travel duration was 20 weeks (IQR: 15-25), and purpose of travel was predominantly tourism (62%). The presence of anti-CHIKV IgG in the pre-travel sample, suggestive of previous CHIKV infection, was found for 3/603 participants (0.5%); all three had been previously travelling in either Africa or Asia. In one traveler who visited Latin America, a seroconversion was found (0.2%) but the CHIKV neutralisation test was negative, making the incidence rate 0. Conclusion: No chikungunya virus infections were found in this 2008-2011 prospective cohort of long-term travellers. We recommend the research be repeated, particularly as the sample size of our cohort might have been too small. Also, extensive spread of chikungunya virus has likely increased incidence rates among travellers since 2013

Hepatitis E in long-term travelers from the Netherlands to subtropical and tropical countries, 2008–2011

Hepatitis E virus (HEV) is a common cause of acute viral hepatitis. Virus genotypes 1 and 2 infect humans in developing countries by the fecal–oral route. To assess attack rates and disease incidence for travelers, we prospectively studied 604 long-term travelers to subtropical and tropical countries. Participants donated blood samples pretravel and posttravel and kept a diary. A total of 89/604 (15%) pretravel samples were positive for HEV IgG by ELISA, suggesting previous HEV infection. Seroconversion for HEV was found for 19/515 travelers (attack rate 3.7%, incidence 1.8 cases/1,000 person-weeks). We believe there is a substantial risk for acquiring HEV infection among long-term travelers. Although HEV infection does not seem to be a major problem in this healthy cohort, hygienic measures should be stressed in all pretravel health advice, particularly for pregnant women and immunocompromised travelers who are at risk for severe disease

Real-time PCR for the detection of Giardia lamblia

Microscopy is considered to be the gold standard for diagnosis of Giardia lamblia infection. However, this method is time-consuming and not very sensitive. We developed a real-time PCR assay based on the small subunit ribosomal RNA gene of G. lamblia for the specific detection of G. lamblia DNA in stool samples and thereafter compared the results with microscopy and antigen detection. The G. lamblia real-time PCR was positive in 102 of 104 fecal samples known to contain G. lamblia cysts and was positive in 10 fecal samples in which G. lamblia antigen was detected but in which no cysts were found with microscopic examination of concentrated fecal samples. The real-time PCR is as specific and sensitive as antigen detection and is more sensitive than microscopy. Moreover, in two patients we were able to detect G. lamblia earlier in the course of infection than with any of the other method