Viral whole genome sequencing reveals high variations in APOBEC3 editing between HPV risk categories.

High-risk human papillomavirus (HPV) infections are responsible for cervical cancer. However, little is known about the differences between HPV types and risk categories regarding their genetic diversity and particularly APOBEC3-induced mutations - which contribute to the innate immune response to HPV. Using a capture-based next-generation sequencing, 156 HPV whole genome sequences covering 43 HPV types were generated from paired cervical and anal swabs of 30 Togolese female sex workers (FSWs) sampled in 2017. Genetic diversity and APOBEC3-induced mutations were assessed at the viral whole genome and gene levels. Thirty-four pairwise sequence comparisons covering 24 HPV types in cervical and anal swabs revealed identical infections in the two anatomical sites. Differences in genetic diversity among HPV types was observed between patients. The E6 gene was significantly less conserved in low-risk HPVs (lrHPVs) compared to high-risk HPVs (hrHPVs) (p = 0.009). APOBEC3-induced mutations were found to be more common in lrHPVs than in hrHPVs (p = 0.005), supported by our data and by using large HPV sequence collections from the GenBank database. Focusing on the most common lrHPVs 6 and 11 and hrHPVs 16 and 18, APOBEC3-induced mutations were predominantly found in the E4 and E6 genes in lrHPVs, but were almost absent in these genes in hrHPVs. The variable APOBEC3 mutational signatures could contribute to the different oncogenic potentials between HPVs. Further studies are needed to conclusively determine whether APOBEC3 editing levels are associated to the carcinogenic potential of HPVs at the type and sublineage scales.

Real-world data on long-acting intramuscular maintenance therapy with cabotegravir and rilpivirine mirror Phase 3 results.

INTRODUCTION: Cabotegravir, an integrase strand transfer inhibitor, and rilpivirine, an NNRTI, constitute the first long-acting (LA), injectable, two-drug ART regimen approved for the maintenance of virological suppression in persons living with HIV-1 (PLHIV). The aim of this study was to assess clinical effectiveness and tolerability of LA cabotegravir/rilpivirine in a real-world setting. PATIENTS AND METHODS: We conducted a retrospective, single centre study, including all PLHIV receiving LA cabotegravir/rilpivirine as standard-of-care in our tertiary centre even if initiated in clinical trials. RESULTS: Between 2014 and 2022, 126 PLHIV initiated LA cabotegravir/rilpivirine. All were ART-experienced, and 98.4% had a viral load (VL) of <50 copies/mL before LA cabotegravir/rilpivirine initiation. Median BMI at cabotegravir/rilpivirine initiation was 24 IQR (23-28). During a median follow-up of 9 months IQR (7-24), 27 patients discontinued cabotegravir/rilpivirine because of virological failure, 6 for adverse events, 11 for personal reasons unrelated to treatment tolerance and 5 for other reasons. Virological failure was not associated with a higher BMI, nor with weight gain during LA intramuscular (IM) cabotegravir/rilpivirine treatment, inadequate cabotegravir and rilpivirine concentrations, VL blips or the use of oral lead-in (OLI) or not. No drug resistance-associated mutation emerged. Adverse events leading to treatment interruption were injection-site pain (n = 3) and neuropsychological side effects (n = 3). A correlation between BMI and both cabotegravir and rilpivirine concentrations at 1 month post-initiation of LA-IM cabotegravir/rilpivirine was observed, with no impact of OLI. CONCLUSIONS: Data from this real-world cohort of PLHIV who received cabotegravir/rilpivirine LA injections suggest that this regimen is effective and well tolerated. Virological failures were not associated with the acquisition of resistance mutations.

Criteria and non-criteria antiphospholipid autoantibodies screening in patients with late pregnancy morbidity: A cross-sectional study.

INTRODUCTION: Antiphospholipid syndrome (APS) is a cause of pregnancy morbidity. We aim to determine the frequency of criteria and non-criteria anti-phospholipid (aPL) autoantibodies in patients admitted for unexplained fetal death (UFD), pre-eclampsia (PE) and/or fetal growth restriction (FGR). METHODS: All consecutive patients with UFD, PE and/or FGR followed in the department of Obstetrics, Bichat Hospital, University of Paris, Paris, between January 2019 and December 2021 were screened. Patients with available serum stored from the index pregnancy were included. Patients with previously known APS or twin pregnancy were excluded. Testing for aPL autoantibodies included anti-cardiolipin (aCL), anti-ß2GPI (aß2GPI), anti-phosphatidylethanolamine (aPE), anti-phosphatidylserine/prothrombin (aPS/PT) IgG/IgM and anti-annexin V IgG. When available, placenta specimens were analyzed by a pathologist blinded to the aPL status. All clinical characteristics, pregnancy features, and comorbidities were extracted from electronic medical records. RESULTS: Overall 167 (32 (28.8-35.7) years) patients with UFD (n = 28; 16.8 %), PE (n = 60; 35.9 %) and/or FGR (n = 105; 62.9 %) were screened for aPL autoantibodies. Moderate titers of aPL autoantibodies were detected in 33 (n = 33/167, 19.8 %) patients. aPL autoantibodies were non-criteria aPE IgG/IgM in most cases (n = 28/33, 84.8 %). aPS/PT IgG/IgM were found in 11 (n = 11/33, 33.3 %) cases and aCL or aß2GP1 IgG/IgM in 4 (n = 4/33, 12.1 %). Multivariable logistic regression showed that aPL autoantibodies were mostly associated with UFD (OR 4.37 [1.72-11.20], p = 0.002), PE ≤ 34th week of gestation (3.22 [0.86-11.90], p = 0.070) and chronic deciduitis (8.03 [0.89-67.2], p = 0.060) DISCUSSION: The frequency of aPL autoantibodies, mostly aPE, is high in patients with late pregnancy morbidity and may qualify obstetrical APS.

Street adolescents in low income setting exposed to hepatitis B and C, and disadvantaged by lifestyle: a Togolese cross-sectional study.

BACKGROUND: In Togo, few data are available on viral hepatitis in street adolescents, a vulnerable population due to their lifestyle. The aim of this study was to describe the lifestyle of street adolescents (sexual practices and drug use), to estimate the prevalence of hepatitis B and C viruses, and to describe their HBV immunization profile in Togo. METHODS: A cross-sectional study was conducted in Lomé (Togo) in July 2021. Street adolescents aged between 13 and 19 years were included. A questionnaire was used to document lifestyle. ELISA tests were performed for Hepatitis B surface antigen (HBsAg), Hepatitis B core and surface antibodies (anti-HBc, anti-HBs), and antibodies against hepatitis C virus (anti-HCV). RESULTS: A total of 299 adolescents (5.4% female) with a median age of 15 years (IQR: 14-17) were included. Of these, 70.6% (211/299) were sexually active and 70.6% (149/211) had not used a condom during their last sexual intercourse. Drug use was reported by 42.1% of the adolescents. The most used substances were cannabis (39.0%), cocaine (36.6%), glue solvents (19.5%), and tramadol (11.4%). However, cocaine use may have been overestimated due to information bias. Current HBV infection (HBsAg+) was detected in 3.7% (95%CI: 1.9-6.5) of the adolescents. Isolated anti-HBc + was present in 5.3%. All three HBV markers (HBsAg, anti-HBs, and anti-HBc) were negative in 71.6% of adolescents. Anti-HCV was detected in 4.7% of adolescents. CONCLUSION: Nearly one in 10 street adolescents has markers for HBV contact/current infection, and approximately 72% of street adolescents may still be infected with HBV, as they have no HBV markers. HCV is also circulating in this population. Given the reported high-risk sexual practices and high levels of drug use, there is an urgent need to develop integrated strategies to prevent infections, including HBV, and drug dependence in this population.

Salvage Therapy Including Foscarnet and Ibalizumab for Multidrug-Resistant Human Immunodeficiency Virus Type 2 Infection.

We evaluated Ibalizumab (IBA)-containing standardized optimized salvage regimen (with or without a 4-week foscarnet induction) in individuals harboring multidrug-resistant human immunodeficiency virus type 2 (HIV-2). Nine were included; 2 achieved virological suppression after foscarnet induction with a sustained suppression at Week 24 after IBA initiation, and an additional individual at Week 24 after Ibalizumab initiation.

RSV-GenoScan: An automated pipeline for whole-genome human respiratory syncytial virus (RSV) sequence analysis.

BACKGROUND: Advances in high-throughput sequencing (HTS) technologies and reductions in sequencing costs have revolutionised the study of genomics and molecular biology by making whole-genome sequencing (WGS) accessible to many laboratories. However, the analysis of WGS data requires significant computational effort, which is the major drawback in implementing WGS as a routine laboratory technique. OBJECTIVE: Automated pipelines have been developed to overcome this issue, but they do not exist for all organisms. This is the case for human respiratory syncytial virus (RSV), which is a leading cause of lower respiratory tract infections in infants, the elderly, and immunocompromised adults. RESULTS: We present RSV-GenoScan, a fast and easy-to-use pipeline for WGS analysis of RSV generated by HTS on Illumina or Nanopore platforms. RSV-GenoScan automates the WGS analysis steps directly from the raw sequence data. The pipeline filters the sequence data, maps the reads to the RSV reference genomes, generates a consensus sequence, identifies the RSV subgroup, and lists amino acid mutations, insertions and deletions in the F and G viral genes. This enables the rapid identification of mutations in these coding genes that are known to confer resistance to monoclonal antibodies. AVAILABILITY: RSV-GenoScan is freely available at https://github.com/AlexandreD-bio/RSV-GenoScan.

Higher Levels of SARS-CoV-2 Genetic Variation in Immunocompromised Patients: A Retrospective Case-Control Study.

BACKGROUND: A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection lasts longer in immunocompromised hosts than in immunocompetent patients. Prolonged infection is associated with a higher probability of selection for novel SARS-CoV-2 mutations, particularly in the spike protein, a critical target for vaccines and therapeutics. METHODS: From December 2020 to September 2022, respiratory samples from 444 immunocompromised patients and 234 health care workers positive for SARS-CoV-2, diagnosed at 2 hospitals in Paris, France, were analyzed using whole-genome sequencing using Nanopore technology. Custom scripts were developed to assess the SARS-CoV-2 genetic diversity between the 2 groups and within the host. RESULTS: Most infections were SARS-CoV-2 Delta or Omicron lineages. Viral genetic diversity was significantly higher in infections of immunocompromised patients than those of controls. Minor mutations were identified in viruses sequenced from immunocompromised individuals, which became signature mutations for newer SARS-CoV-2 variants as the epidemic progressed. Two patients were coinfected with Delta and Omicron variants. The follow-up of immunocompromised patients revealed that the SARS-CoV-2 genome evolution differed in the upper and lower respiratory tracts. CONCLUSIONS: This study found that SARS-CoV-2 infection in immunocompromised patients is associated with higher genetic diversity, which could lead to the emergence of new SARS-CoV-2 variants with possible immune evasion or different virulence characteristics.

Respiratory syncytial virus in adults with comorbidities: an update on epidemiology, vaccines, and treatments.

BACKGROUND: Respiratory syncytial virus (RSV) is widely known as a frequent cause of respiratory distress among adults, particularly in older people. Recent years have witnessed several improvements in respiratory virus detection, leading to more questions about therapeutic management strategies. OBJECTIVES: This narrative review focuses on the RSV burden in older people and adults with risk factors and provides an update on the main recent developments regarding managing this infection. SOURCES: A comprehensive PubMed search was conducted till August 2023 to identify studies on RSV among the adult population. We included observational studies, RCTs on vaccines, and different therapies. CONTENT: This review should give clinicians an overview of RSV epidemiology and burden among older people and adults with pre-existing risk factors, the most recent randomized clinical trials on RSV vaccines, and the existing data on the different therapeutics existing and under development. IMPLICATIONS: There is a growing body of evidence on RSV burden in adults. The landscape of preventive and curative treatments is quickly evolving.

Genomic diversity of mpox virus in Paris area (France) during the 2022 outbreak.

In May 2022, several countries reported mpox cases from patients without history of traveling to endemic areas. France was one of the most affected European countries by this outbreak. In this study, the clinical characteristics of mpox cases in France were described, and the genetic diversity of the virus was studied. Patients diagnosed with mpox infection (quantitative polymerase chain reaction ct < 28) between May 21, and July 4, 2022 and between 16th August and 10th September 2022 were included to this study. Twelve amplicons corresponding to the most polymorphic regions of the mpox genome and covering ~30 000 nucleotides were generated and sequenced using the S5 XL Ion Torrent technology to evaluate the genetic diversity of mpox sequences. One hundred and forty-eight patients were diagnosed with mpox-infection. 95% were men, 5% transgender (M-to-F), 50% were taking human immunodeficiency virus (HIV) pre-exposure prophylaxis, and 25% were HIV seropositive. One hundred and sixty-two samples (some patients had two samples) were sequenced and compared to GenBank sequences. Overall, low genetic diversity of mpox sequences was found compared with pre-epidemic Western-African sequences, with 32 distinct mutational patterns. This study provides a first glance at the mutational landscape of early mpox 2022 circulating strains in Paris (France).

Improving Human Papillomavirus-Related Cervical Cancer Screening in Patients With Systemic Lupus Erythematosus.

Women with systemic lupus erythematosus (SLE), especially when exposed to immunosuppressive drugs, are at higher risk of human papillomavirus (HPV)-related cervical cancer.1 A recent study has shown that cervical cancer screening (CCS) coverage is worryingly low in this population.2.

Phylodynamics of SARS-CoV-2 in France, Europe, and the world in 2020.

Although France was one of the most affected European countries by the COVID-19 pandemic in 2020, the dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) movement within France, but also involving France in Europe and in the world, remain only partially characterized in this timeframe. Here, we analyzed GISAID deposited sequences from January 1 to December 31, 2020 (n = 638,706 sequences at the time of writing). To tackle the challenging number of sequences without the bias of analyzing a single subsample of sequences, we produced 100 subsamples of sequences and related phylogenetic trees from the whole dataset for different geographic scales (worldwide, European countries, and French administrative regions) and time periods (from January 1 to July 25, 2020, and from July 26 to December 31, 2020). We applied a maximum likelihood discrete trait phylogeographic method to date exchange events (i.e., a transition from one location to another one), to estimate the geographic spread of SARS-CoV-2 transmissions and lineages into, from and within France, Europe, and the world. The results unraveled two different patterns of exchange events between the first and second half of 2020. Throughout the year, Europe was systematically associated with most of the intercontinental exchanges. SARS-CoV-2 was mainly introduced into France from North America and Europe (mostly by Italy, Spain, the United Kingdom, Belgium, and Germany) during the first European epidemic wave. During the second wave, exchange events were limited to neighboring countries without strong intercontinental movement, but Russia widely exported the virus into Europe during the summer of 2020. France mostly exported B.1 and B.1.160 lineages, respectively, during the first and second European epidemic waves. At the level of French administrative regions, the Paris area was the main exporter during the first wave. But, for the second epidemic wave, it equally contributed to virus spread with Lyon area, the second most populated urban area after Paris in France. The main circulating lineages were similarly distributed among the French regions. To conclude, by enabling the inclusion of tens of thousands of viral sequences, this original phylodynamic method enabled us to robustly describe SARS-CoV-2 geographic spread through France, Europe, and worldwide in 2020.

High SARS-CoV-2 seroprevalence among street adolescents in Lomé, Togo, 2021.

BACKGROUND: There is almost no data on the circulation of SARS-CoV-2 among street adolescents. We conducted a study to document the immunization status of street adolescents in Togo against different variants of SARS-CoV-2. METHODS: A cross-sectional study was carried out in 2021 in Lomé, the city with the highest number of COVID 19 cases in Togo (60%). Adolescents aged 13- and 19 years old living on the street were eligible for inclusion. A standardized questionnaire was administered face-to-face to adolescents. A sample of blood was taken and aliquots of plasma were transported to the virology laboratory of the Hôpital Bichat-Claude Bernard (Paris, France). SARS-CoV-2 anti-S and anti-N IgG were measured using chemiluminescent microparticle immunoassay. A quantitative miniaturized and parallel-arranged ELISA assay was used to detect IgG antibodies specifically directed against the different SARS-CoV-2 Variants of Concern (VOC). RESULTS: A total of 299 street adolescents (5.2% female), median age 15 years, interquartile range (14-17 years), were included in this study. The prevalence of SARS-CoV-2 infection was 63.5% (95%CI: 57.8-69.0). Specific-IgG against the ancestral Wuhan strain was developed by 92.0% of subjects. The proportion of patients being immunized against each VOC was 86.8%, 51.1%, 56.3%, 60.0, and 30.5% for the Alpha, Beta, Gamma, Delta, and Omicron VOCs, respectively. CONCLUSION: This study showed a very high prevalence with approximately 2/3 of Togolese street adolescents having antibodies to SARS-CoV-2 due to a previous infection. These results confirm an under-reporting of COVID-19 cases in Togo, questioning the hypothesis of low virus circulation in Togo and even in Africa.

Molecular confirmation of HIV-1 and HIV-2 coinfections among initially serologically dually-reactive samples from patients living in West Africa.

OBJECTIVES: This study aimed to confirm the co-infection with HIV-1 and HIV-2, among West African patients using in-house HIV type/group enzyme-immuno assays and molecular diagnosis. DESIGN: A cross-sectional survey was conducted from April 2016 to October 2017 in the biggest HIV clinics of Côte d'Ivoire and Burkina Faso. METHOD: A first serological confirmation was done in the referral laboratory using an in-house, indirect immuno-enzymatic essay allowing the qualitative detection of both HIV-1 and HIV-2 antibodies. In order to separately detect anti-HIV-1 and anti-HIV-2 antibodies, a type/group specific enzyme-immuno assay (HIV-GSEIA) was used. To confirm the co-infections, HIV-1 and HIV-2 DNA-qualitative PCR assays were performed. RESULTS: A total of 91 patients were enrolled in the study and provided blood sample for HIV type confirmatory testing including 13 (14.3%) HIV-2 mono-reactive and 78 (85.7%) HIV-1/HIV-2 dually-reactive based on the HIV testing National Algorithms. The first serological ELISA confirmatory test performed showed that 80 (78.9%) of the 91 participants were dually-reactive. The HIV-GSEIA performed on these 80 serum samples retrieve one 61 HIV-1/HIV-2 dually-reactive samples. HIV-1 and HIV-2 DNA PCR were performed on 54 of the 61 HIV-1/HIV-2 dually-reactive samples and 46 out of 61 (75.4%) samples were found HIV-1/HIV-2 coinfected. CONCLUSION: The contribution of type/group specific enzyme-immuno assay to accurately identify HIV-1/HIV-2 coinfections remain suboptimal, emphasizing the need for molecular diagnosis platforms in West Africa, to avail HIV DNA PCR test for the confirmation of HIV-1/HIV-2 co-infections.

Severity of SARS-CoV-2 Omicron variant infection in heart transplant recipients.

SARS-CoV-2 Omicron variant was first detected in France mid-November 2021 in wastewater treatment plants while cases started to increase at the beginning of December. The maximum incidence occurred in mid-January 2022. The Omicron wave spread rapidly throughout France in general population with lower case-fatality rate compared with previous waves. Little is known about infection with Omicron variant in heart transplant (HT) recipients. In this study, we examined incidence and mortality rate of COVID-19 in the general population and among 1,263 HT recipients during the period from June, 2021 to February, 2022, described characteristics of HT recipients infected with SARS-CoV-2 during Omicron (December 1st, 2021-February 7, 2022) and Delta (June 1st- November 30, 2021) periods, and compared hospital course of HT recipients with Omicron and Delta variant infection. Our findings contrast with the reported lower severity for Omicron variant infection compared with Delta variant infection in immunocompetent individuals.

Future of Antiretroviral Drugs and Evolution of HIV-1 Drug Resistance.

Highly active antiretroviral (ARV) therapy has been used for many years, but the use in low- and middle-income countries of antiretroviral drugs with low genetic barrier to resistance, combined with limited availability of viral load testing, has led to higher rates of acquired drug resistance, sustaining the rate of transmitted drug resistance. Here, we describe the evolution of ARV drugs with the ongoing development of injectable long-acting forms and the requirements regarding all new ARV drugs (i.e., no transmitted drug resistance, no cross-resistance and high genetic barrier to resistance). Then, we report the evolution of both transmitted and acquired resistance regarding new ARV drugs. The WHO has set very ambitious but motivating goals for HIV testing, treatment and viral suppression, aiming to achieve rates of 95% for all three by 2025. Reaching these goals requires a wide implementation and use of close virological monitoring in LMICs.

Agreement of respiratory viruses' detection between nasopharyngeal swab and bronchoalveolar lavage in adults admitted for pneumonia: a retrospective study.

OBJECTIVES: The COVID-19 pandemic has highlighted the high diagnostic accuracy of the nasopharyngeal swab (including in intensive care unit (ICU) patients). This study aimed to compare nasopharyngeal swab and bronchoalveolar lavage (BAL) results for non-SARS-CoV-2 viruses in patients with suspected pneumonia. METHODS: A retrospective analysis was performed in one French academic hospital on consecutive adults from 2012 to 2018 and tested nasopharyngeal swab and BAL within 24 hours by using multiplex PCR. The agreement in pathogen detection between nasopharyngeal swab and BAL was evaluated. RESULTS: Patients were primarily men (n = 178/276, 64.5%), with a median age of 60 years (IQR: 51-68 years). Of the 276 patients, 169 (61%) were admitted to the ICU for acute respiratory distress. We detected at least one respiratory virus in 34.4% of the nasopharyngeal swabs (n = 95/276) and 29.0% of BAL (n = 80/276). Two or more viruses were detected in 2.5% of the nasopharyngeal swabs (n = 7/276) and 2.2% of BAL (n = 6/276). Rhinovirus/enteroviruses were the most frequently detected viral group in 10.2% (n = 29/285) of the nasopharyngeal swabs and 9.5% (n = 27/285) of BAL, followed by influenza A, detected in 5.6% (n = 16/285) of the nasopharyngeal swabs and 4.9% (n = 14/285) of BAL. Overall agreement was 83.7% (n = 231/276 (95% CI [78.7%, 87.7%])) (i.e. same pathogen or pathogen combination was identified in the nasopharyngeal swab and BAL for 231 patients). Rhinovirus/enterovirus (n = 29/231) and respiratory syncytial virus (n = 13/231) had the lowest agreement of 62.1% (n = 18/29 (95% CI [42.4%-78.7%])) and 61.5% (n = 8/13 (95% CI [32.3%-84.9%])), respectively). CONCLUSIONS: There was a good agreement between nasopharyngeal swabs and BAL in detecting respiratory viruses among adult patients with suspected pneumonia. However, these data still encourage BAL in the case of a negative nasopharyngeal swab.