Anal dysplasia and anal cancer screening practices among liver transplant centers in the United States: Results of an online survey.

BACKGROUND: Solid organ transplant recipients are at an increased risk for anogenital Human Papillomavirus (HPV)-related disease, including anal high-grade squamous intraepithelial lesions (HSIL) and anal squamous cell cancer (ASCC). Guidelines for ASCC screening in transplant recipients are limited. Our aim was to understand current practice of ASCC screening in adult liver transplant (LT) candidates and recipients at transplant centers across the United States. METHODS: We surveyed medical directors of 113 LT centers across the United States which had publicly available contact information. The survey evaluated center perceptions on cancer and HPV disease risk in transplant populations, ASCC screening, barriers and facilitators for ASCC screening and HPV vaccination practices. RESULTS: We received 26/113 (23%) responses, of which 24 were complete and included in the analysis. Eleven of 24 (46%) centers reported screening for ASCC and 3/24 (12.5%) centers reported having formal guidelines. Centers who perform ASCC screening were more likely to perform transplants in people living with HIV and were more aware of the burden of HPV disease in transplant populations. All respondents believed that additional data on the impact of screening on ASCC incidence would support screening decisions. Increased access to specialists for screening/high-resolution anoscopy was also perceived as a facilitator. Only 7/24 (29%) centers regularly evaluated HPV vaccination status of their patients. CONCLUSION: This national survey of LT centers reveals non-standardized ASCC screening practices, and identified data, educational and resource needs to improve prevention of ASCC in this population.

Orthopoxvirus-Specific T-Cell Responses in Convalescent Mpox Patients.

Orthopoxvirus-specific T-cell responses were analyzed in 10 patients who had recovered from Mpox including 7 people with human immunodeficiency virus (PWH). Eight participants had detectable virus-specific T-cell responses, including a PWH who was not on antiretroviral therapy and a PWH on immunosuppressive therapy. These 2 participants had robust polyfunctional CD4+ T-cell responses to peptides from the 121L vaccinia virus (VACV) protein. T-cells from 4 of 5 HLA-A2-positive participants targeted at least 1 previously described HLA-A2-restricted VACV epitope, including an epitope targeted in 2 participants. These results advance our understanding of immunity in convalescent Mpox patients.

Pathogenesis and Transmission Assessment of 3 Swine-Origin Influenza A(H3N2) Viruses With Zoonotic Risk to Humans Isolated in the United States, 2017-2020.

The sporadic occurrence of human infections with swine-origin influenza A(H3N2) viruses and the continual emergence of novel A(H3N2) viruses in swine herds underscore the necessity for ongoing assessment of the pandemic risk posed by these viruses. Here, we selected 3 recent novel swine-origin A(H3N2) viruses isolated between 2017 to 2020, bearing hemagglutinins from the 1990.1, 2010.1, or 2010.2 clades, and evaluated their ability to cause disease and transmit in a ferret model. We conclude that despite considerable genetic variances, all 3 contemporary swine-origin A(H3N2) viruses displayed a capacity for robust replication in the ferret respiratory tract and were also capable of limited airborne transmission. These findings highlight the continued public health risk of swine-origin A(H3N2) strains, especially in human populations with low cross-reactive immunity.

Risk Factors for Hospitalization and Effect of Immunosuppression on Clinical Outcomes Among an Urban Cohort of Patients With Mpox.

Background: During the 2022 mpox outbreak most patients were managed as outpatients, but some required hospitalization. Uncontrolled human immunodeficiency virus (HIV) has been identified as a risk factor for severe mpox. Methods: Patients with mpox diagnosed or treated within the Johns Hopkins Health System between 1 June and 15 December 2022 were included. The primary outcome of interest was risk of hospitalization. Demographic features, comorbid conditions, treatment, and clinical outcomes were determined. Results: A total of 353 patients were tested or treated for mpox; 100 had mpox diagnosed or treated (median age, 35.3 years; 97.0% male; 57.0% black and 10.0% Hispanic; 46.0% people with HIV [PWH]). Seventeen patients (17.0%) required hospitalization, 10 of whom were PWH. Age >40 years, race, ethnicity, HIV status, insurance status, and body mass index >30 (calculated as weight in kilograms divided by height in meters squared) were not associated with hospitalization. Eight of 9 patients (88.9%) with immunosuppression were hospitalized. Immunosuppression was associated with hospitalization in univariate (odds ratio, 69.3 [95% confidence interval, 7.8-619.7]) and adjusted analysis (adjusted odds ratio, 94.8 [8.5-1060.1]). Two patients (11.8%) who were hospitalized required intensive care unit admission and died; both had uncontrolled HIV infection and CD4 T-cell counts <50/µL. Median cycle threshold values for the first positive mpox virus sample did not differ between those who were hospitalized and those who were not. Conclusions: Immunosuppression was a significant risk factor for hospitalization with mpox. PWH with CD4 T-cell counts <50/µL are at high risk of death due to mpox infection. Patients who are immunosuppressed should be considered for early and aggressive treatment of mpox, given the increased risk of hospitalization.

Fourth-Generation HIV Testing.

A 72-year-old man presented to the emergency department with fevers, night sweats, and rash 3 days after condomless vaginal intercourse. Results of a fourth-generation HIV test were positive and HIV-1-/2 antibody differentiation testing was negative. How would you interpret these results?

Avian influenza A(H5) virus circulation in live bird markets in Vietnam, 2017-2022.

BACKGROUND: Highly pathogenic avian influenza A(H5) human infections are a global concern, with many A(H5) human cases detected in Vietnam, including a case in October 2022. Using avian influenza virus surveillance from March 2017-September 2022, we described the percent of pooled samples that were positive for avian influenza A, A(H5), A(H5N1), A(H5N6), and A(H5N8) viruses in live bird markets (LBMs) in Vietnam. METHODS: Monthly at each LBM, 30 poultry oropharyngeal swab specimens and five environmental samples were collected. Samples were pooled in groups of five and tested for influenza A, A(H5), A(H5N1), A(H5N6), and A(H5N8) viruses by real-time reverse-transcription polymerase chain reaction. Trends in the percent of pooled samples that were positive for avian influenza were summarized by LBM characteristics and time and compared with the number of passively detected avian influenza outbreaks using Spearman's rank correlation. RESULTS: A total of 25,774 pooled samples were collected through active surveillance at 167 LBMs in 24 provinces; 36.9% of pooled samples were positive for influenza A, 3.6% A(H5), 1.9% A(H5N1), 1.1% A(H5N6), and 0.2% A(H5N8). Influenza A(H5) viruses were identified January-December and at least once in 91.7% of sampled provinces. In 246 A(H5) outbreaks in poultry; 20.3% were influenza A(H5N1), 60.2% A(H5N6), and 19.5% A(H5N8); outbreaks did not correlate with active surveillance. CONCLUSIONS: In Vietnam, influenza A(H5) viruses were detected by active surveillance in LBMs year-round and in most provinces sampled. In addition to outbreak reporting, active surveillance for A(H5) viruses in settings with high potential for animal-to-human spillover can provide situational awareness.

Implementing a peer-supported, integrated strategy for substance use disorder care in an outpatient infectious disease clinic is associated with improved patient outcomes.

BACKGROUND: Substance use disorder (SUD) and infectious disease (ID) care integration may lead to improvements in SUD and ID outcomes. We assessed implementation of integrating peer-supported SUD care in an outpatient ID setting. METHODS: In this implementation study, we describe REcovery in Specialty care Through medication and OutREach (RESTORE), a low-threshold SUD program implemented in a Baltimore outpatient ID clinic. Key program components were clinician training and support in SUD care, prescription of SUD treatment medications, and peer-based psychosocial support provided by peer recovery specialists. We assessed clinician adoption of RESTORE and compared patient outcomes from baseline to 6 months. RESULTS: Between January 2019 and January 2022, the number of ID clinicians (N=61) who prescribed buprenorphine increased eightfold from 3 (5%) to 24 (39%). Of 258 ID patients referred to RESTORE, 182 (71%) engaged, 137 consented to study participation. Mean age in the study sample was 52.1 (SD=10.4), 63% were male, 84% were Black/African-American. Among 127 (93%) who completed 6-month follow-up, fewer participants reported illicit/non-prescribed opioid use in the past 30 days at follow-up (32%) compared to baseline (52%; p<0.001). Similar reductions were noted for cocaine use (47% to 34%; p=0.006), emergency department visits (23% to 9%; p=0.002), and inpatient hospitalizations (15% to 7%; p=0.025). CONCLUSION: SUD care integration into an outpatient ID care setting using a peer-supported implementation strategy was adopted by clinicians and improved clinical outcomes for patients. This strategy is a promising approach to treating people with infectious diseases and SUD.

Antiviral susceptibility of clade 2.3.4.4b highly pathogenic avian influenza A(H5N1) viruses isolated from birds and mammals in the United States, 2022.

Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) A(H5N1) viruses that are responsible for devastating outbreaks in birds and mammals pose a potential threat to public health. Here, we evaluated their susceptibility to influenza antivirals. Of 1,015 sequences of HPAI A(H5N1) viruses collected in the United States during 2022, eight viruses (∼0.8%) had a molecular marker of drug resistance to an FDA-approved antiviral: three adamantane-resistant (M2-V27A), four oseltamivir-resistant (NA-H275Y), and one baloxavir-resistant (PA-I38T). Additionally, 31 viruses contained mutations that may reduce susceptibility to inhibitors of neuraminidase (NA) (n = 20) or cap-dependent endonuclease (CEN) (n = 11). A panel of 22 representative viruses was tested phenotypically. Overall, clade 2.3.4.4b A(H5N1) viruses lacking recognized resistance mutations were susceptible to FDA-approved antivirals. Oseltamivir was least potent at inhibiting NA activity, while the investigational NA inhibitor AV5080 was most potent, including against NA mutants. A novel NA substitution T438N conferred 12-fold reduced inhibition by zanamivir, and in combination with the known marker N295S, synergistically affected susceptibility to all five NA inhibitors. In cell culture-based assays HINT and IRINA, the PA-I38T virus displayed 75- to 108-fold and 37- to 78-fold reduced susceptibility to CEN inhibitors, baloxavir and the investigational AV5116, respectively. Viruses with PA-I38M or PA-A37T showed 5- to 10-fold reduced susceptibilities. As HPAI A(H5N1) viruses continue to circulate and evolve, close monitoring of drug susceptibility is needed for risk assessment and to inform decisions regarding antiviral stockpiling.

Lessons learned from U.S. rapid antiretroviral therapy initiation programs.

BACKGROUND: Rapid antiretroviral therapy initiation (R-ART) for treatment of HIV has been recommended since 2017, however it has not been adopted widely across the US. PURPOSE: The study purpose was to understand facilitators and barriers to R-ART implementation in the U.S. RESEARCH DESIGN: This was a qualitative design involving semi-structured interviews. STUDY SAMPLE: The study sample was comprised of the medical leadership of nine US HIV clinics that were early implementers of R-ART. DATA COLLECTION AND ANALYSIS: In-depth, semi-structured interviews were performed. The Consolidated Framework for Implementation Research (CFIR) was used to guide thematic analysis. RESULTS: We identified three main content areas: strong scientific rationale for R-ART, buy-in from multiple key stakeholders, and the condensed timeline of R-ART. The CFIR construct of Evidence Strength and Quality was cited as an important factor in R-ART implementation. Buy-in from key stakeholders and immediate access to medications ensured the success of R-ART implementation. Patient acceptance of the condensed timeline for ART initiation was facilitated when presented in a patient-centered manner, including empathetic communication and addressing other patient needs concurrently. The condensed timeline of R-ART presented logistical challenges and opportunities for the development of intense patient-provider relationships. CONCLUSIONS: Results from the analysis showed that R-ART implementation should address the following: 1) logistical planning to implement HIV treatment with a condensed timeline 2) patients' mixed reactions to a new HIV diagnosis and 3) the high cost of HIV medications.

Enhanced fitness of SARS-CoV-2 B.1.617.2 Delta variant in ferrets.

Competition assays were conducted in vitro and in vivo to examine how the Delta (B.1.617.2) variant displaced the prototype Washington/1/2020 (WA/1) strain. While WA/1 virus exhibited a moderately increased proportion compared to that in the inoculum following co-infection in human respiratory cells, Delta variant possessed a substantial in vivo fitness advantage as this virus becoming predominant in both inoculated and contact animals. This work identifies critical traits of the Delta variant that likely played a role in it becoming a dominant variant and highlights the necessities of employing multiple model systems to assess the fitness of newly emerged SARS-CoV-2 variants.

Leveraging mHealth and Patient Supporters for African Americans' and Latinxs' Engagement in HIV Care (LEAN): Protocol for a Randomized, Controlled, Effectiveness-Implementation Trial.

BACKGROUND: Despite substantial investments in ending the HIV epidemic, disparities in HIV care persist, and there is an urgent need to evaluate novel and scalable approaches to improving HIV care engagement and viral suppression in real-world settings. OBJECTIVE: This paper aims to describe a study protocol for a pragmatic type II hybrid effectiveness-implementation randomized controlled trial comparing existing standard of care clinic HIV linkage, adherence, and retention (LAR) protocols to a mobile health (mHealth)-enhanced linkage, adherence, and retention (mLAR) intervention. METHODS: The study will enroll 450 participants from clinics in Baltimore City. Eligibility criteria include being ≥18 years of age, having a new HIV diagnosis or being HIV-positive and out of care, or being HIV-positive and deemed by clinic staff as someone who could benefit from linkage and retention services. Participants randomized to the intervention receive mHealth-supported patient navigation for 12 months. Participants in the control group receive the referring clinic's standard of care patient support. The primary outcome is HIV virologic suppression at 12 months. A subset of participants will be interviewed at 12 months to learn about their HIV care experiences and, for those in the intervention arm, their experiences with the mLAR intervention. This protocol was developed in collaboration with the Baltimore City Health Department (BCHD) and the Maryland Department of Health (MDH) and with input from a community advisory board. RESULTS: Enrollment began on February 25, 2020. As of August 11, 2022, 411 of the 450 target participants had been enrolled. CONCLUSIONS: Pragmatic implementation science trials designed with input from key stakeholders, including health departments and community members, can help evaluate the evidence for mHealth interventions to reduce HIV health disparities. TRIAL REGISTRATION: ClinicalTrials.gov NCT03934437; https://clinicaltrials.gov/ct2/show/NCT03934437. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/42691.

Telemedicine Use Among People With HIV in 2021: The Hybrid-Care Environment.

BACKGROUND: Telemedicine use for the care of people with HIV (PWH) significantly expanded during the COVID-19 pandemic. During 2021, vaccine uptake increased and patients were encouraged to resume in-person care, resulting in a mixture of in-person and telemedicine visits. We studied how different patient populations used telemedicine in this hybrid-care environment. METHODS: Using observational data from patients enrolled in the Johns Hopkins HIV Clinical Cohort, we analyzed all in-person and telemedicine HIV primary care visits completed in an HIV clinic from January 1st, 2021, to December 31st, 2021. We used log-binomial regression to investigate the association between patient characteristics and the probability of completing a telemedicine versus in-person visit and the probability of completing a video versus telephone visit. RESULTS: A total of 5518 visits were completed by 1884 patients; 4282 (77.6%) visits were in-person, 800 (14.5%) by phone, and 436 (7.9%) by video. The relative risk (RR) of completing telemedicine vs. in-person visits was 0.65 (95% Confidence Interval (CI): 0.47, 0.91) for patients age 65 years or older vs. age 20-39 years; 0.84 (95% CI: 0.72, 0.98) for male patients vs. female patients; 0.81 (95% CI: 0.66, 0.99) for Black vs. White patients; 0.62 (95% CI: 0.49, 0.79) for patients in the highest vs. lowest quartile of Area Deprivation Index; and 1.52 (95% CI: 1.26, 1.84) for patients >15 miles vs. <5 miles from clinic. CONCLUSIONS: In the second year of the pandemic, overall in-person care was used more than telemedicine and significant differences persist across subgroups in telemedicine uptake.

Detection of Airborne Influenza A and SARS-CoV-2 Virus Shedding following Ocular Inoculation of Ferrets.

Despite reports of confirmed human infection following ocular exposure with both influenza A virus (IAV) and SARS-CoV-2, the dynamics of virus spread throughout oculonasal tissues and the relative capacity of virus transmission following ocular inoculation remain poorly understood. Furthermore, the impact of exposure route on subsequent release of airborne viral particles into the air has not been examined previously. To assess this, ferrets were inoculated by the ocular route with A(H1N1)pdm09 and A(H7N9) IAVs and two SARS-CoV-2 (early pandemic Washington/1 and Delta variant) viruses. Virus replication was assessed in both respiratory and ocular specimens, and transmission was evaluated in direct contact or respiratory droplet settings. Viral RNA in aerosols shed by inoculated ferrets was quantified with a two-stage cyclone aerosol sampler (National Institute for Occupational Safety and Health [NIOSH]). All IAV and SARS-CoV-2 viruses mounted a productive and transmissible infection in ferrets following ocular inoculation, with peak viral titers and release of virus-laden aerosols from ferrets indistinguishable from those from ferrets inoculated by previously characterized intranasal inoculation methods. Viral RNA was detected in ferret conjunctival washes from all viruses examined, though infectious virus in this specimen was recovered only following IAV inoculation. Low-dose ocular-only aerosol exposure or inhalation aerosol exposure of ferrets to IAV similarly led to productive infection of ferrets and shedding of aerosolized virus. Viral evolution during infection was comparable between all inoculation routes examined. These data support that both IAV and SARS-CoV-2 can establish a high-titer mammalian infection following ocular exposure that is associated with rapid detection of virus-laden aerosols shed by inoculated animals. IMPORTANCE Documented human infection with influenza viruses and SARS-CoV-2 has been reported among individuals wearing respiratory protection in the absence of eye protection, highlighting the capacity of these respiratory tract-tropic viruses to exploit nonrespiratory routes of exposure to initiate productive infection. However, comprehensive evaluations of how ocular exposure may modulate virus pathogenicity and transmissibility in mammals relative to respiratory exposure are limited and have not investigated multiple virus families side by side. Using the ferret model, we show that ocular exposure with multiple strains of either coronaviruses or influenza A viruses leads to an infection that results in shedding of detectable aerosolized virus from inoculated animals, contributing toward onward transmission of both viruses to susceptible contacts. Collectively, these studies support that the ocular surface represents a susceptible mucosal surface that, if exposed to a sufficient quantity of either virus, permits establishment of an infection which is similarly transmissible as that following respiratory exposure.

Human monkeypox virus infection in women and non-binary individuals during the 2022 outbreaks: a global case series.

BACKGROUND: Between May and November, 2022, global outbreaks of human monkeypox virus infection have been reported in more than 78 000 people worldwide, predominantly in men who have sex with men. We describe the epidemiological and clinical characteristics of monkeypox virus infection in cisgender (cis) and transgender (trans) women and non-binary individuals assigned female sex at birth to improve identification and understanding of risk factors. METHODS: International collaborators in geographical locations with high numbers of diagnoses of monkeypox virus infection were approached and invited to contribute data on women and non-binary individuals with confirmed monkeypox virus infection. Contributing centres completed deidentified structured case-report spreadsheets, adapted and developed by participating clinicians, to include variables of interest relevant to women and non-binary individuals assigned female at birth. We describe the epidemiology and clinical course observed in the reported infections. FINDINGS: Collaborators reported data for a total of 136 individuals with monkeypox virus infection who presented between May 11 and Oct 4, 2022, across 15 countries. Overall median age was 34 years (IQR 28-40; range 19-84). The cohort comprised 62 trans women, 69 cis women, and five non-binary individuals (who were, because of small numbers, grouped with cis women to form a category of people assigned female at birth for the purpose of comparison). 121 (89%) of 136 individuals reported sex with men. 37 (27%) of all individuals were living with HIV, with a higher proportion among trans women (31 [50%] of 62) than among cis women and non-binary individuals (six [8%] of 74). Sexual transmission was suspected in 55 (89%) trans women (with the remainder having an unknown route of transmission) and 45 (61%) cis women and non-binary individuals; non-sexual routes of transmission (including household and occupational exposures) were reported only in cis women and non-binary individuals. 25 (34%) of 74 cis women and non-binary individuals submitted to the case series were initially misdiagnosed. Overall, among individuals with available data, rash was described in 124 (93%) of 134 individuals and described as anogenital in 95 (74%) of 129 and as vesiculopustular in 105 (87%) of 121. Median number of lesions was ten (IQR 5-24; range 1-200). Mucosal lesions involving the vagina, anus, or oropharynx or eye occurred in 65 (55%) of 119 individuals with available data. Vaginal and anal sex were associated with lesions at those sites. Monkeypox virus DNA was detected by PCR from vaginal swab samples in all 14 samples tested. 17 (13%) individuals were hospitalised, predominantly for bacterial superinfection of lesions and pain management. 33 (24%) individuals were treated with tecovirimat and six (4%) received post-exposure vaccinations. No deaths were reported. INTERPRETATION: The clinical features of monkeypox in women and non-binary individuals were similar to those described in men, including the presence of anal and genital lesions with prominent mucosal involvement. Anatomically, anogenital lesions were reflective of sexual practices: vulvovaginal lesions predominated in cis women and non-binary individuals and anorectal features predominated in trans women. The prevalence of HIV co-infection in the cohort was high. FUNDING: None.

Comparative Assessment of Severe Acute Respiratory Syndrome Coronavirus 2 Variants in the Ferret Model.

The continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans necessitates evaluation of variants for enhanced virulence and transmission. We used the ferret model to perform a comparative analysis of four SARS-CoV-2 strains, including an early pandemic isolate from the United States (WA1), and representatives of the Alpha, Beta, and Delta lineages. While Beta virus was not capable of pronounced replication in ferrets, WA1, Alpha, and Delta viruses productively replicated in the ferret upper respiratory tract, despite causing only mild disease with no overt histopathological changes. Strain-specific transmissibility was observed; WA1 and Delta viruses transmitted in a direct contact setting, whereas Delta virus was also capable of limited airborne transmission. Viral RNA was shed in exhaled air particles from all inoculated animals but was highest for Delta virus. Prior infection with SARS-CoV-2 offered varied protection against reinfection with either homologous or heterologous variants. Notable genomic variants in the spike protein were most frequently detected following WA1 and Delta virus infection. IMPORTANCE Continued surveillance and risk assessment of emerging SARS-CoV-2 variants are critical for pandemic response and preparedness. As such, in vivo evaluations are indispensable for early detection of variants with enhanced virulence and transmission. Here, we used the ferret model to compare the pathogenicity and transmissibility of an original SARS-CoV-2 isolate (USA-WA1/2020 [WA1]) to those of a panel of Alpha, Beta, and Delta variants, as well as to evaluate protection from homologous and heterologous reinfection. We observed strain-specific differences in replication kinetics in the ferret respiratory tract and virus load emitted into the air, revealing enhanced transmissibility of the Delta virus relative to previously detected strains. Prior infection with SARS-CoV-2 provided varied levels of protection from reinfection, with the Beta strain eliciting the lowest level of protection. Overall, we found that ferrets represent a useful model for comparative assessments of SARS-CoV-2 infection, transmission, and reinfection.

Replication-competent HIV-1 in human alveolar macrophages and monocytes despite nucleotide pools with elevated dUTP.

BACKGROUND: Although CD4+ memory T cells are considered the primary latent reservoir for HIV-1, replication competent HIV has been detected in tissue macrophages in both animal and human studies. During in vitro HIV infection, the depleted nucleotide pool and high dUTP levels in monocyte derived macrophages (MDM) leads to proviruses with high levels of dUMP, which has been implicated in viral restriction or reduced transcription depending on the uracil base excision repair (UBER) competence of the macrophage. Incorporated dUMP has also been detected in viral DNA from circulating monocytes (MC) and alveolar macrophages (AM) of HIV infected patients on antiretroviral therapy (ART), establishing the biological relevance of this phenotype but not the replicative capacity of dUMP-containing proviruses. RESULTS: As compared to in vitro differentiated MDM, AM from normal donors had sixfold lower levels of dTTP and a sixfold increased dUTP/dTTP, indicating a highly restrictive dNTP pool for reverse transcription. Expression of uracil DNA glycosylase (UNG) was eightfold lower in AM compared to the already low levels in MDM. Accordingly, ~ 80% of HIV proviruses contained dUMP, which persisted for at least 14-days due to low UNG excision activity. Unlike MDM, AM expression levels of UNG and SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) increased over 14 days post-HIV infection, while dUTP nucleotidohydrolase (DUT) expression decreased. These AM-specific effects suggest a restriction response centered on excising uracil from viral DNA copies and increasing relative dUTP levels. Despite the restrictive nucleotide pools, we detected rare replication competent HIV in AM, peripheral MC, and CD4+ T cells from ART-treated donors. CONCLUSIONS: These findings indicate that the potential integration block of incorporated dUMP is not realized during in vivo infection of AM and MC due to the near absence of UBER activity. In addition, the increased expression of UNG and SAMHD1 in AM post-infection is too slow to prevent integration. Accordingly, dUMP persists in integrated viruses, which based on in vitro studies, can lead to transcriptional silencing. This possible silencing outcome of persistent dUMP could promote viral latency until the repressive effects of viral dUMP are reversed.

Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines.

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the emergence of new variant lineages that have exacerbated the COVID-19 pandemic. Some of those variants were designated as variants of concern/interest (VOC/VOI) by national or international authorities based on many factors including their potential impact on vaccine-mediated protection from disease. To ascertain and rank the risk of VOCs and VOIs, we analyze the ability of 14 variants (614G, Alpha, Beta, Gamma, Delta, Epsilon, Zeta, Eta, Theta, Iota, Kappa, Lambda, Mu, and Omicron) to escape from mRNA vaccine-induced antibodies. The variants show differential reductions in neutralization and replication by post-vaccination sera. Although the Omicron variant (BA.1, BA.1.1, and BA.2) shows the most escape from neutralization, sera collected after a third dose of vaccine (booster sera) retain moderate neutralizing activity against that variant. Therefore, vaccination remains an effective strategy during the COVID-19 pandemic.

Sexually Transmitted Infections Among Men and Transgender Women Using HIV Pre-exposure Prophylaxis in a Large Integrated Health System-A Cohort Study.

BACKGROUND: Sexually transmitted infections (STIs) are common in people using pre-exposure prophylaxis (PrEP). We examined risk and factors associated with STIs in a cohort of PrEP users in an integrated health system in the United States. SETTING: The Kaiser Permanente Southern California is a large integrated health system that provides comprehensive medical services to approximately 4.7 million demographically diverse members. METHODS: We identified men and transgender women initiating PrEP between January 1, 2014, and June 1, 2018, and followed through December 31, 2018. Demographic and clinical factors potentially associated with the risk of bacterial STIs during PrEP use were evaluated using Poisson regression models. RESULTS: Among 5042 individuals tested for STIs with 7198 person-years of follow-up, 1709 (33.9%) had at least one new STI. The estimated incidence of STIs was 48.3 per 100 person-years, and the most common STI was rectal chlamydia. Most repeat STIs (61.4%) occurred <180 days apart. In a multivariable analysis, an history of STIs in the prior 6 months through 7 days after the PrEP initiation was the most prominent risk factor of STIs during PrEP use (adjusted risk ratio: 1.78, 95% confidence intervals: 1.65 to 1.93). Other risk factors included younger age (<35 years), being Hispanic, and having a history of alcohol use disorder or drug use disorder. CONCLUSIONS: Quarterly STI testing and targeted intervention to mitigate STI risk are warranted for young and racial minority PrEP users, particularly for those with prior history of STIs and substance use disorders.

Pathogenesis and transmission of human seasonal and swine-origin A(H1) influenza viruses in the ferret model.

Influenza A viruses (IAVs) in the swine reservoir constantly evolve, resulting in expanding genetic and antigenic diversity of strains that occasionally cause infections in humans and pose a threat of emerging as a strain capable of human-to-human transmission. For these reasons, there is an ongoing need for surveillance and characterization of newly emerging strains to aid pandemic preparedness efforts, particularly for the selection of candidate vaccine viruses and conducting risk assessments. Here, we performed a parallel comparison of the pathogenesis and transmission of genetically and antigenically diverse swine-origin A(H1N1) variant (v) and A(H1N2)v, and human seasonal A(H1N1)pdm09 IAVs using the ferret model. Both groups of viruses were capable of replication in the ferret upper respiratory tract; however, variant viruses were more frequently isolated from the lower respiratory tract as compared to the human-adapted viruses. Regardless of virus origin, observed clinical signs of infection differed greatly between strains, with some viruses causing nasal discharge, sneezing and, in some instances, diarrhea in ferrets. The most striking difference between the viruses was the ability to transmit through the air. Human-adapted viruses were capable of airborne transmission between all ferret pairs. In contrast, only one out of the four tested variant viruses was able to transmit via the air as efficiently as the human-adapted viruses. Overall, this work highlights the need for sustained monitoring of emerging swine IAVs to identify strains of concern such as those that are antigenically different from vaccine strains and that possess adaptations required for efficient respiratory droplet transmission in mammals.

Time Between Viral Loads for People With HIV During the COVID-19 Pandemic.

BACKGROUND: During the COVID-19 pandemic, patients experienced significant care disruptions, including laboratory monitoring. We investigated changes in the time between viral load (VL) checks for people with HIV (PWH) associated with the pandemic. SETTING AND METHODS: This was an observational analysis of VLs of PWH in routine care at a large subspecialty clinic. At pandemic onset, the clinic temporarily closed its onsite laboratory. The exposure was time period (time varying): prepandemic (January 1, 2019-March 15, 2020); pandemic laboratory closed (March 16-July 12, 2020); and pandemic laboratory open (July 13-December 31, 2020). We estimated time from an index VL to a subsequent VL, stratified by whether the index VL was suppressed (≤200 copies/mL). We also calculated cumulative incidence of a nonsuppressed VL following a suppressed index VL, and of resuppression following a loss of viral suppression. RESULTS: Compared with prepandemic, hazard ratios for next VL check were 0.34 (95% CI: 0.30 to 0.37, laboratory-closed) and 0.73 (CI: 0.68 to 0.78, laboratory-open) for suppressed patients, and 0.56 (CI: 0.42 to 0.79, laboratory-closed) and 0.92 (95% CI: 0.76 to 1.10, laboratory-open) for nonsuppressed patients. The 12-month cumulative incidence of loss of suppression was the same in the pandemic laboratory-open (4%) and prepandemic (4%) period. The hazard of resuppression following the loss of suppression was lower during the pandemic laboratory-open versus the prepandemic period (hazard ratio: 0.68, 95% CI: 0.50 to 0.92). CONCLUSIONS: Early pandemic restrictions and laboratory closure significantly delayed VL monitoring. Once the laboratory reopened, nonsuppressed patients resumed normal monitoring. Suppressed patients still had a delay but no significant loss of suppression.