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The current era of COVID-19 is characterized by emerging variants of concern, waning vaccine- and natural infection-induced immunity, debate over the timing and necessity of vaccine boosting, and the emergence of post-acute sequelae of SARS-CoV-2 infection. As a result, there is an ongoing need for research to promote understanding of the immunology of both natural infection and prevention, especially as SARS-CoV-2 immunology is a rapidly changing field, with new questions arising as the pandemic continues to grow in complexity. The next phase of COVID-19 immunology research will need focus on clearer characterization of the immune processes defining acute illness, development of a better understanding of the immunologic processes driving protracted symptoms and prolonged recovery (ie, post-acute sequelae of SARS-CoV-2 infection), and a growing focus on the impact of therapeutic and prophylactic interventions on the long-term consequences of SARS-CoV-2 infection. In this review, we address what is known about the long-term immune consequences of SARS-CoV-2 infection and propose how experience studying the translational immunology of other infections might inform the approach to some of the key questions that remain.

Background Despite the risks of immunosuppression, recommendations regarding screening for HIV infection prior to initiation of biologic therapies targeting common rheumatologic disorders, including inflammatory bowel disease (IBD) and inflammatory arthritides, are limited. Few cases of patients started on biologics while living with undiagnosed HIV infection have been reported. Methods We report three cases of patients initiated on biologics in the absence of recent or concurrent HIV screening who developed refractory disease or unanticipated complications and were later found to have undiagnosed chronic HIV infection. Results In Case 1, a 53-year-old MSM with negative HIV testing 2 years prior presented with presumed rheumatoid arthritis. He did not respond to methotrexate, so adalimumab was started. HIV testing to evaluate persistent symptoms was positive 9 months later; CD4+ T-cell count was 800 cells/μl. Antiretroviral therapy (ART) resulted in resolution of symptoms, which were attributed to HIV-associated arthropathy. In Case 2, a 55-year-old woman with injection drug use in remission and no prior HIV testing presented with hidradenitis suppurativa. She started infliximab and methotrexate therapy with good response. After she developed weight loss and lymphopenia, an HIV test was positive; CD4+ T-cell count was 334 cells/μl. Biologic hidradenitis suppurativa therapy was discontinued, with subsequent poor hidradenitis suppurativa control. In Case 3, a 32-year-old MSM with no prior HIV testing presented with presumed IBD; infliximab and steroids were started. Symptoms progressed despite IBD-directed therapy, and he was diagnosed with extensive Kaposi sarcoma with visceral and cutaneous involvement, likely exacerbated by immunosuppression. HIV testing was positive; CD4+ T-cell count was 250 cells/μl. Kaposi sarcoma initially worsened due to ART-associated immune reconstitution inflammatory syndrome. He is now improving with systemic chemotherapy and ART. HIV-associated Kaposi sarcoma is presumed to be the underlying diagnosis. Conclusion All three patients had elevated risk for HIV infection, and two had final diagnoses attributed to chronic HIV infection, not warranting therapeutic immunosuppression. Screening for HIV infection prior to initiation of biologic therapy should be incorporated into clinical practice guidelines.

Summary Background Most cohorts show similar or lower COVID-19 incidence among people living with HIV compared with the general population. However, incidence might be affected by lower testing rates among vulnerable populations. We aimed to compare SARS-CoV-2 IgG seroprevalence, disease severity, and neutralising antibody activity after infection among people with and without HIV receiving care in a county hospital system over a 3-month period. Methods In this matched case-control observational study, remnant serum samples were collected between Aug 1 and Oct 31, 2020, from all people living with HIV who underwent routine outpatient laboratory testing in a municipal health-care system (San Francisco General Hospital, CA, USA). Samples from people living with HIV were date of collection-matched (same day) and age-matched (±5 years) to samples from randomly selected adults (aged 18 years or older) without HIV receiving care for chronic conditions at the same hospital. We compared seroprevalence by HIV status via mixed-effects logistic regression models, accounting for the matched structure of the data (random effects for the matched group), adjusting for age, sex, race or ethnicity, and clinical factors (ie, history of cardiovascular or pulmonary disease, and type 2 diabetes). Severe COVID-19 was assessed in participants with past SARS-CoV-2 (IgG or PCR) infection by chart review and compared with multivariable mixed-effects logistic regression, adjusting for age and sex. SARS-CoV-2 IgG, neutralising antibody titres, and antibody avidity were measured in serum of participants with previous positive PCR tests and compared with multivariable mixed-effects models, adjusting for age, sex, and time since PCR-confirmed SARS-CoV-2 infection. Findings 1138 samples from 955 people living with HIV and 1118 samples from 1062 people without HIV were tested. SARS-CoV-2 IgG seroprevalence was 3·7% (95% CI 2·4 to 5·0) among people with HIV compared with 7·4% (5·7 to 9·2) among people without HIV (adjusted odds ratio 0·50, 95% CI 0·30 to 0·83). Among 31 people with HIV and 70 people without HIV who had evidence of past infection, the odds of severe COVID-19 were 5·52 (95% CI 1·01 to 64·48) times higher among people living with HIV. Adjusting for time since PCR-confirmed infection, SARS-CoV-2 IgG concentrations were lower (percentage change −53%, 95% CI −4 to −76), pseudovirus neutralising antibody titres were lower (−67%, −25 to −86), and avidity was similar (7%, −73 to 87) among people living with HIV compared with those without HIV. Interpretation Although fewer infections were detected by SARS-CoV-2 IgG testing among people living with HIV than among those without HIV, people with HIV had more cases of severe COVID-19. Among people living with HIV with past SARS-CoV-2 infection, lower IgG concentrations and pseudovirus neutralising antibody titres might reflect a diminished serological response to infection, and the similar avidity could be driven by similar time since infection. Funding US National Institute of Allergy and Infectious Diseases, US National Institutes of Health.

Total-body PET enables high-sensitivity imaging with dramatically improved signal-to-noise ratio. These enhanced performance characteristics allow for decreased PET scanning times acquiring data "total-body wide" and can be leveraged to decrease the amount of radiotracer required, thereby permitting more frequent imaging or longer imaging periods during radiotracer decay. Novel approaches to PET imaging of infectious diseases are emerging, including those that directly visualize pathogens invivo and characterize concomitant immune responses and inflammation. Efforts to develop these imaging approaches are hampered by challenges of traditional imaging platforms, which may be overcome by novel total-body PET strategies.

Objectives Immunomodulatory drugs (IMDs) are crucial for treating autoimmune, inflammatory, and oncologic conditions. Data regarding the safety of IMDs in people living with HIV (PLWH) are limited. We describe outcomes in all PLWH prescribed these agents from 2000--2019 at two academic medical centers. Design Retrospective cohort study. Methods We systematically identified and reviewed charts of all PLWH receiving IMDs. We defined a treatment episode as an uninterrupted period on an IMD regimen. We quantified infections, blips (detectable plasma HIV RNA following an undetectable result), and virologic failure (progression from plasma HIV RNA 200 copies/ml despite ART). Results Seventy-seven patients contributed 110 treatment episodes. Rheumatologic comorbidities were the most frequent indication. The most common IMD classes were TNF inhibitors, antimetabolites, and checkpoint inhibitors. Ninety percent of treatment episodes involved concomitant ART. Median pretreatment CD4 T-cell count was 609 cells/μl (IQR 375--861). Among 51 treatment episodes on ART with undetectable pretreatment plasma HIV RNA, HIV became detectable within 1 year in 21 of 51 cases (41.2%); there were no instances of virologic failure. Compared with other agents, treatment episodes involving checkpoint inhibitors were more likely to involve a blip (77.8 vs. 33.3%, P = 0.015). Thirteen treatment episodes (11.8%) were associated with concomitant infection; none was attributed to IMDs by the treating clinician. Conclusion PLWH treated with IMDs should be monitored carefully for virologic blips and incident infections. Checkpoint inhibitors may be associated with a higher rate of viral blips, although the clinical significance is unclear.

Background The biological processes associated with postacute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (PASC) are unknown. Methods We measured soluble markers of inflammation in a SARS-CoV-2 recovery cohort at early (90 days) timepoints. We defined PASC as the presence of 1 or more coronavirus disease 2019 (COVID-19)–attributed symptoms beyond 90 days. We compared fold-changes in marker values between those with and without PASC using mixed-effects models with terms for PASC and early and late recovery time periods. Results During early recovery, those who went on to develop PASC generally had higher levels of cytokine biomarkers including tumor necrosis factor–α (1.14-fold higher mean ratio [95% confidence interval {CI}, 1.01–1.28]; P = .028) and interferon-γ–induced protein 10 (1.28-fold higher mean ratio [95% CI, 1.01–1.62]; P = .038). Among those with PASC, there was a trend toward higher interleukin 6 levels during early recovery (1.29-fold higher mean ratio [95% CI, .98–1.70]; P = .07), which became more pronounced in late recovery (1.44-fold higher mean ratio [95% CI, 1.11–1.86]; P Conclusions Persistent immune activation may be associated with ongoing symptoms following COVID-19. Further characterization of these processes might identify therapeutic targets for those experiencing PASC.

BACKGROUNDShortness of breath, chest pain, and palpitations occur as post-acute sequelae of COVID-19 (PASC), but whether symptoms are associated with echocardiographic abnormalities, cardiac biomarkers, or markers of systemic inflammation remains unknown.METHODSIn a cross-sectional analysis, we assessed symptoms, performed echocardiograms, and measured biomarkers among adults >8 weeks after PCR-confirmed SARS-CoV-2 infection. We modeled associations between symptoms and baseline characteristics, echocardiographic findings, and biomarkers using logistic regression.RESULTSWe enrolled 102 participants at a median 7.2 months (IQR 4.1-9.1) following COVID-19 onset; 47 individuals reported dyspnea, chest pain, or palpitations. Median age was 52 years (range 24-86) and 41% were women. Female sex (OR 2.55, 95%CI 1.13-5.74) and hospitalization during acute infection (OR 3.25, 95%CI 1.08-9.82) were associated with symptoms. IgG antibody to SARS-CoV-2 receptor binding domain (OR 1.38 per doubling, 95%CI 1.38-1.84) and high-sensitivity C-reactive protein (OR 1.31 per doubling, 95%CI 1.00-1.71) were associated with symptoms. Regarding echocardiographic findings, 4/47 (9%) with symptoms had pericardial effusions compared to 0/55 without symptoms (p=0.038); those with pericardial effusions had a median 4 symptoms compared to 1 without (pCONCLUSIONSAmong adults in the post-acute phase of SARS-CoV-2 infection, SARS-CoV-2 RBD antibodies, markers of inflammation and, possibly, pericardial effusions are associated with cardiopulmonary symptoms. Investigation into inflammation as a mechanism underlying PASC is warranted.FUNDINGThis work was supported by the UCSF Division of Cardiology at Zuckerberg San Francisco General, and the National Institutes of Health/National Heart Lung Blood Institute and National Institute of Allergy and Infectious Diseases. MSD is supported by NIH 5K12HL143961. MJP is supported on NIH T32 AI60530-12. JDK is supported by NIH K23AI135037. TJH is supported by NIH/NIAID 3R01A1141003-03S1. PYH is supported by NIH/NAID 2K24AI112393-06. This publication was supported by the National Center for Advancing Translational Sciences, National Institutes of Health, through UCSF-CTSI Grant Number UL1TR001872. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH.GRAPHICAL ABSTRACT

BackgroundThe biologic mechanisms underlying neurologic post-acute-sequelae of SARS-CoV-2 infection (PASC) are incompletely understood.MethodsWe measured markers of neuronal injury (glial fibrillary acidic protein [GFAP], neurofilament light chain [NfL]) and soluble markers of inflammation among a cohort of people with prior confirmed SARS-CoV-2 infection at early and late recovery following the initial illness (defined as less than and greater than 90 days, respectively). The primary clinical outcome was the presence of self-reported central nervous system (CNS) PASC symptoms during the late recovery timepoint. We compared fold-changes in marker values between those with and without CNS PASC symptoms using linear mixed effects models and examined relationships between neurologic and immunologic markers using rank linear correlations.ResultsOf 121 individuals, 52 reported CNS PASC symptoms. During early recovery, those who went on to report CNS PASC symptoms had elevations in GFAP (1.3-fold higher mean ratio, 95% CI 1.04-1.63, p=0.02), but not NfL (1.06-fold higher mean ratio, 95% CI 0.89-1.26, p=0.54). During late recovery, neither GFAP nor NfL levels were elevated among those with CNS PASC symptoms. Although absolute levels of NfL did not differ, those who reported CNS PASC symptoms demonstrated a stronger downward trend over time in comparison to those who did not report CNS PASC symptoms (p=0.041). Those who went on to report CNS PASC also exhibited elevations in IL-6 (48% higher during early recovery and 38% higher during late recovery), MCP-1 (19% higher during early recovery), and TNF-alpha (19% higher during early recovery and 13% higher during late recovery). GFAP and NfL correlated with levels of several immune activation markers during early recovery; these correlations were attenuated during late recovery.ConclusionsSelf-reported neurologic symptoms present >90 days following SARS-CoV-2 infection are associated with elevations in markers of neurologic injury and inflammation at early recovery timepoints, suggesting that early injury can result in long-term disease. The correlation of GFAP and NfL with markers of systemic immune activation suggests one possible mechanism that might contribute to these symptoms. Additional work is needed to better characterize these processes and to identify interventions to prevent or treat this condition.Key PointsQuestionDo individuals with and without self-reported neurologic symptoms following SARS-CoV-2 infection have different levels of biomarkers of neurologic injury or immune activationãFindingsIn this cohort study of 121 adults, individuals reporting neurologic symptoms beyond 90 days following SARS-CoV-2 infection had higher levels of glial fibrillary acidic protein but not neurofilament light chain. Levels of several markers of inflammation including interleukin-6, tumor necrosis factor-alpha, and monocyte chemoattractant protein-1 were also elevated.MeaningPost-acute neurologic symptoms following SARS-CoV-2 infection are associated with significant differences in levels of certain biomarkers. Further investigation may provide clues to the biologic pathways underlying these symptoms.

BACKGROUNDThe biological processes associated with post-acute sequelae of SARS-CoV-2 infection (PASC) are unknown.METHODSWe measured soluble markers of inflammation in a SARS-CoV-2 recovery cohort at early (90 days) timepoints. We defined PASC as the presence of one or more COVID-19-attributed symptoms beyond 90 days. We compared fold-changes in marker values between those with and without PASC using mixed effects models with terms for PASC and early and late recovery time periods.RESULTSDuring early recovery, those who went on to develop PASC generally had higher levels of cytokine biomarkers including TNF-alpha (1.14-fold higher mean ratio, 95%CI 1.01-1.28, p=0.028) and IP-10 (1.28-fold higher mean ratio, 95%CI 1.01-1.62, p=0.038). Among those with PASC, there was a trend toward higher IL-6 levels during early recovery (1.28-fold higher mean ratio, 95%CI 0.98- 1.70, p=0.07) which became more pronounced in late recovery (1.44-fold higher mean ratio, 95%CI: 1.11-1.86, pCONCLUSIONSPersistent immune activation may be associated with ongoing symptoms following COVID-19. Further characterization of these processes might identify therapeutic targets for those experiencing PASC.

Suppression of plasma HIV RNA is most often attainable with effective antiretroviral therapy. Despite this, in some individuals, detection of HIV RNA remains evident in the cerebrospinal fluid (CSF) which is generally termed CSF HIV RNA escape. Defining CSF HIV RNA escape from a virological point of view, a symptomatology point of view and its management has many challenges with several different definitions being utilized. In this editorial, we outline proposed consensus definitions of CSF HIV RNA escape with consideration of virological, symptomatology and management aspects of this condition.

We report a patient with connective tissue disease who developed modest severe acute respiratory syndrome coronavirus 2 receptor binding domain–specific antibody levels and a lack of neutralization capacity, despite having received 3 mRNA coronavirus disease 2019 vaccines and holding anti-B-cell therapy for >7 months before vaccination. The patient developed virus-specific T-cell responses.

Novel mRNA-based vaccines have been proven to be powerful tools in combating the global pandemic caused by SARS-CoV-2, with BNT162b2 (trade name: Comirnaty) efficiently protecting individuals from COVID-19 across a broad age range. Still, it remains largely unknown how renal insufficiency and immunosuppressive medication affect development of vaccine-induced immunity. We therefore comprehensively analyzed humoral and cellular responses in kidney transplant recipients after the standard second vaccination dose. As opposed to all healthy vaccinees and the majority of hemodialysis patients, only 4 of 39 and 1 of 39 transplanted individuals showed IgA and IgG seroconversion at day 8 ± 1 after booster immunization, with minor changes until day 23 ± 5, respectively. Although most transplanted patients mounted spike-specific T helper cell responses, frequencies were significantly reduced compared with those in controls and dialysis patients and this was accompanied by a broad impairment in effector cytokine production, memory differentiation, and activation-related signatures. Spike-specific CD8(+) T cell responses were less abundant than their CD4(+) counterparts in healthy controls and hemodialysis patients and almost undetectable in transplant patients. Promotion of anti-HLA antibodies or acute rejection was not detected after vaccination. In summary, our data strongly suggest revised vaccination approaches in immunosuppressed patients, including individual immune monitoring for protection of this vulnerable group at risk of developing severe COVID-19.

Despite some inconsistent reporting of symptoms, studies have demonstrated that at least 20% of individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will remain asymptomatic. Although most global efforts have focused on understanding factors underlying severe illness in COVID-19 (coronavirus disease of 2019), the examination of asymptomatic infection provides a unique opportunity to consider early disease and immunologic features promoting rapid viral clearance. Owing to its critical role in the immune response, we postulated that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection. We enrolled 29,947 individuals registered in the National Marrow Donor Program for whom high-resolution HLA genotyping data were available in the UCSF Citizen Science smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n=1428) was comprised of unvaccinated, self-identified subjects who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci (HLA-A, -B, -C, -DRB1, -DQB1) with disease course and identified a strong association of HLA-B*15:01 with asymptomatic infection, and reproduced this association in two independent cohorts. Suggesting that this genetic association is due to pre-existing T-cell immunity, we show that T cells from pre-pandemic individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF, and 100% of the reactive cells displayed memory phenotype. Finally, we characterize the protein structure of HLA-B*15:01-peptide complexes, demonstrating that the NQKLIANQF peptide from SARS-CoV-2, and the highly homologous NQKLIANAF from seasonal coronaviruses OC43-CoV and HKU1-CoV, share similar ability to be stabilized and presented by HLA-B*15:01, providing the molecular basis for T-cell cross-reactivity and HLA-B*15:01-mediated pre-existing immunity.

Pharmacologic inhibition of the mammalian target of rapamycin (mTOR) in the setting of renal transplantation has previously been associated with lower human immunodeficiency virus 1 (HIV-1) DNA burden, and in vitro studies suggest that mTOR inhibition may lead to HIV transcriptional silencing. Because prospective clinical trials are lacking, we conducted an open-label, single-arm study to determine the impact of the broad mTOR inhibitor, everolimus, on residual HIV burden, transcriptional gene expression profiles, and immune responses in HIV-infected adult solid organ transplant (SOT) recipients on antiretroviral therapy. Whereas everolimus therapy did not have an overall effect on cell-associated HIV-1 DNA and RNA levels in the entire cohort, participants who maintained everolimus time-averaged trough levels >5ng/mL during the first 2months of therapy had significantly lower RNA levels up to 6months after the cessation of study drug. Time-averaged everolimus trough levels significantly correlated with greater inhibition of mTOR gene pathway transcriptional activity. Everolimus treatment also led to decreased PD-1 expression on certain T cell subsets. These data support the rationale for further study of the effects of mTOR inhibition on HIV transcriptional silencing in non-SOT populations, either alone or in combination with other strategies. Trial Registration: ClinicalTrials.gov NCT02429869.

Current serology tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies mainly take the form of enzyme-linked immunosorbent assays, chemiluminescent microparticle immunoassays or lateral flow assays, which are either laborious, expensive or lacking sufficient sensitivity and scalability. Here we present the development and validation of a rapid, low-cost, solution-based assay to detect antibodies in serum, plasma, whole blood and to a lesser extent saliva, using rationally designed split luciferase antibody biosensors. This new assay, which generates quantitative results in 30 min, substantially reduces the complexity and improves the scalability of coronavirus disease 2019 (COVID-19) antibody tests. This assay is well-suited for point-of-care, broad population testing, and applications in low-resource settings, for monitoring host humoral responses to vaccination or viral infection.

BACKGROUNDAs the coronavirus disease 2019 (COVID-19) pandemic continues and millions remain vulnerable to infection with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), attention has turned to characterizing post-acute sequelae of SARS-CoV-2 infection (PASC).METHODSFrom April 21 to December 31, 2020, we assembled a cohort of consecutive volunteers who a) had documented history of SARS-CoV-2 RNA-positivity; b) were ≥ 2 weeks past onset of COVID-19 symptoms or, if asymptomatic, first test for SARS-CoV-2; and c) were able to travel to our site in San Francisco. Participants learned about the study by being identified on medical center-based registries and being notified or by responding to advertisements. At 4-month intervals, we asked participants about physical symptoms that were new or worse compared to the period prior to COVID-19, mental health symptoms and quality of life. We described 4 time periods: 1) acute illness (0-3 weeks), 2) early recovery (3-10 weeks), 3) late recovery 1 (12-20 weeks), and 4) late recovery 2 (28-36 weeks). Blood and oral specimens were collected at each visit.RESULTSWe have, to date, enrolled 179 adults. During acute SARS-CoV-2 infection, 10 had been asymptomatic, 125 symptomatic but not hospitalized, and 44 symptomatic and hospitalized. In the acute phase, the most common symptoms were fatigue, fever, myalgia, cough and anosmia/dysgeusia. During the post-acute phase, fatigue, shortness of breath, concentration problems, headaches, trouble sleeping and anosmia/dysgeusia were the most commonly reported symptoms, but a variety of others were endorsed by at least some participants. Some experienced symptoms of depression, anxiety, and post-traumatic stress, as well as difficulties with ambulation and performance of usual activities. The median visual analogue scale value rating of general health was lower at 4 and 8 months (80, interquartile range [IQR]: 70-90; and 80, IQR 75-90) compared to prior to COVID-19 (85; IQR 75-90). Biospecimens were collected at nearly 600 participant-visits.CONCLUSIONAmong a cohort of participants enrolled in the post-acute phase of SARS-CoV-2 infection, we found many with persistent physical symptoms through 8 months following onset of COVID-19 with an impact on self-rated overall health. The presence of participants with and without symptoms and ample biological specimens will facilitate study of PASC pathogenesis. Similar evaluations in a population-representative sample will be needed to estimate the population-level prevalence of PASC.

We aimed to characterize the variability in the illness experience and recovery process from COVID-19. We conducted in-depth individual interviews with participants enrolled in the Long-term Immunological Impact of Novel Coronavirus (LIINC) cohort study in San Francisco, California from June through October of 2020. Participants were adults who had a previously confirmed positive SARV-CoV-2 nucleic acid amplification test result, had recovered or were recovering from acute infection, and underwent serial evaluations at our clinical research center. We purposefully sampled 24 English- and Spanish-speaking adults with asymptomatic, mild and severe symptomatic infection, including those who were hospitalized, and those with HIV co-infection. Half of our sample (50.0%) identified as Latinx/Hispanic and most of the participants were men (62.5%). We used thematic analysis to characterize the illness experience, recovery process, and mental health impact of experiencing COVID-19 and present clinical data for each participant. Emergent themes were: (1) across symptom profiles and severity, experiencing COVID-19 was associated with psychological distress, (2) among participants with symptomatic infection, the illness experience was characterized by uncertainty in terms of managing symptoms and recovery, and (3) despite wide-ranging illness experiences, participants shared many common characteristics, including health information-seeking behavior facilitated by access to medical care, and uncertainty regarding the course of their illness and recovery. COVID-19 was associated with elevated levels of psychological distress, regardless of symptoms.

Antibody detection of prior SARS-CoV-2 infection depends on severity, assay, and timing with implications for serosurveillance., Interpretation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serosurveillance studies is limited by poorly defined performance of antibody assays over time in individuals with different clinical presentations. We measured antibody responses in plasma samples from 128 individuals over 160 days using 14 assays. We found a consistent and strong effect of disease severity on antibody magnitude, driven by fever, cough, hospitalization, and oxygen requirement. Responses to spike protein versus nucleocapsid had consistently higher correlation with neutralization. Assays varied substantially in sensitivity during early convalescence and time to seroreversion. Variability was dramatic for individuals with mild infection, who had consistently lower antibody titers, with sensitivities at 6 months ranging from 33 to 98% for commercial assays. Thus, the ability to detect previous infection by SARS-CoV-2 is highly dependent on infection severity, timing, and the assay used. These findings have important implications for the design and interpretation of SARS-CoV-2 serosurveillance studies.

A detailed understanding of long-term SARS-CoV-2-specific T cell responses and their relationship to humoral immunity and markers of inflammation in diverse groups of individuals representing the spectrum of COVID-19 illness and recovery is urgently needed. Data are also lacking as to whether and how adaptive immune and inflammatory responses differ in individuals that experience persistent symptomatic sequelae months following acute infection compared to those with complete, rapid recovery. We measured SARS-CoV-2-specific T cell responses, soluble markers of inflammation, and antibody levels and neutralization capacity longitudinally up to 9 months following infection in a diverse group of 70 individuals with PCR-confirmed SARS-CoV-2 infection. The participants had varying degrees of initial disease severity and were enrolled in the northern California Long-term Impact of Infection with Novel Coronavirus (LIINC) cohort. Adaptive T cell responses remained remarkably stable in all participants across disease severity during the entire study interval. Whereas the magnitude of the early CD4+ T cell immune response is determined by the severity of initial infection (participants requiring hospitalization or intensive care), pre-existing lung disease was significantly associated with higher long-term SARS-CoV2-specific CD8+ T cell responses, independent of initial disease severity or age. Neutralizing antibody levels were strongly correlated with SARS-CoV-2-specific CD4+ T but not CD8+ T cell responses. Importantly, we did not identify substantial differences in long-term virus-specific T cell or antibody responses between participants with and without COVID-19-related symptoms that persist months after initial infection.

As cases of coronavirus disease 2019 (COVID-19) mount worldwide, attention is needed on potential long-term neurologic impacts for the majority of patients who experience mild to moderate illness managed as outpatients. To date, there has not been discussion of persistent neurocognitive deficits in patients with milder COVID-19. We present two cases of non-hospitalized patients recovering from COVID-19 with persistent neurocognitive symptoms. Commonly used cognitive screens were normal, while more detailed testing revealed working memory and executive functioning deficits. An observational cohort study of individuals recovering from COVID-19 (14 or more days following symptom onset) identified that among the first 100 individuals enrolled, 14 were non-hospitalized patients reporting persistent cognitive issues. These 14 participants had a median age of 39 years (interquartile range: 35–56), and cognitive symptoms were present for at least a median of 98 days (interquartile range: 71–120 following acute COVID-19 symptoms); no participants with follow-up evaluation reported symptom resolution. We discuss potential mechanisms to be explored in future studies, including direct viral effects, indirect consequences of immune activation, and immune dysregulation causing auto-antibody production.

As the SARS-CoV-2 pandemic continues, reports have demonstrated neurologic sequelae following COVID-19 recovery. Mechanisms to explain long-term neurological sequelae are unknown and need to be identified. Plasma from 24 individuals recovering from COVID-19 at 1 to 3 months after initial infection were collected for cytokine and antibody levels and neuronal-enriched extracellular vesicle (nEV) protein cargo analyses. Plasma cytokine IL-4 was increased in all COVID-19 participants. Volunteers with self-reported neurological problems (nCoV, n = 8) had a positive correlation of IL6 with age or severity of the sequalae, at least one co-morbidity and increased SARS-CoV-2 antibody compared to those COVID-19 individuals without neurological issues (CoV, n = 16). Protein markers of neuronal dysfunction including amyloid beta, neurofilament light, neurogranin, total tau, and p-T181-tau were all significantly increased in the nEVs of all participants recovering from COVID-19 compared to historic controls. This study suggests ongoing peripheral and neuroinflammation after COVID-19 infection that may influence neurological sequelae by altering nEV proteins. Individuals recovering from COVID-19 may have occult neural damage while those with demonstrative neurological symptoms additionally had more severe infection. Longitudinal studies to monitor plasma biomarkers and nEV cargo are warranted to assess persistent neurodegeneration and systemic effects.

Background: Most cohorts show similar or lower COVID-19 incidence among people living with HIV (PLWH) compared to the general population. However, incidence may be impacted by lower testing rates among vulnerable populations. We compared SARS-CoV-2 IgG seroprevalence, disease severity, and neutralizing antibody activity after infection among people with and without HIV receiving care within a county hospital system over a three-month period. Methods: From August through October 2020, remnant serum samples were collected from all PLWH who underwent routine outpatient laboratory testing in a municipal healthcare system which houses a large HIV clinic. Patients with HIV were date-of-collection and age-matched (same day, +/- 5 years respectively) to adults without HIV. SARS-CoV-2 IgG and neutralizing antibody titers were measured in serum. Severe disease was assessed by chart review. Findings: Overall, 2,256 samples from 955 PLWH and 1062 people without HIV were tested. Among PLWH, the seroprevalence was 3.7% as compared to 7.4% among people without HIV (adjusted odds ratio (AOR) 0·48; 95% Confidence Interval (CI): 0·34; 0·71). Among those with evidence of prior infection (IgG or PCR), the odds of severe disease were more than 5-fold higher among PLWH (OR 5·13 95% CI: 1·05; 38·9). Among those with past infection, SARS-CoV-2 IgG levels were 45% lower among PLWH vs. those without HIV (95% CI: 22%; 61%); neutralizing antibody titers were 63% lower among PLWH (2%-78%). Interpretation: Among PLWH, there were approximately 50% lower odds of past SARS-CoV-2 infection, possibly due to greater non-pharmaceutical intervention adherence among a population with experience of the HIV epidemic. However, in spite of fewer infections, PLWH experienced more cases of severe disease. Among PLWH with past SARS-CoV-2 infection, lower neutralizing antibody titers were observed and may lead to increased risk of severe COVID-19 disease or reinfection. PLWH should be followed after vaccination to ensure they mount and maintain sufficient responses. Funding Statement: This work was funded by NIH/NIAID R01AI158013. Declaration of Interests: MAS, DVG, TJH, MG, and LBB report funding from the NIH during conduct of the study. DVG reports personal fees from Gilead Sciences outside the submitted work. All other authors have nothing to declare. Ethics Approval Statement: As only remnant samples were used, the University of California, San Francisco IRB did not require informed consent for study participation.The UCSF IRB # is 20-30387.

Background: Limited data is available on whether there are differences in the humoral response to mRNA SARS-CoV-2 vaccination by HIV status. We compared surrogate virus neutralization tests (sVNT) and anti-receptor-binding-domain (RBD) IgG concentrations by HIV status, as well as if responses differed by mRNA vaccine type. Methods: Remnant serum samples were collected during the month of May 2021 from all people living with HIV (PLWH) undergoing outpatient laboratory testing in a U.S. municipal health-care system. Samples from 100 PLWH were then matched on the same number of days following second mRNA vaccination, age (+/- 5 years), birth sex, and type of mRNA vaccine to samples from 100 adults receiving care for chronic conditions at the same hospital. Antibody responses were measured using a previously validated sVNT and anti-RBD IgG, with non-response defined as the limit of detection at 200 copies/mL was associated with 89% lower titers (GMR 0.11; 95% CI=0.01-0.84). Interpretation: PLWH had lower than expected response to mRNA SARS-CoV-2 vaccines, particularly among those with low CD4+ T-cell counts, unsuppressed HIV RNA, and those who received the BNT162b2 vaccine. Funding: This research was supported by U.S. National Institute of Allergy and Infectious Diseases (NIAID) R01AI158013 (M.A.S. and M.G.), and U.S. NIAID P30AI027763 (M.G.) Declaration of Interest: DVG reports personal fees from Gilead Sciences outside the submitted work. All other authors declare no competing interests. Ethical Approval: As only remnant samples were used, the University of California, San Francisco IRB did not require informed consent for study participation. The UCSF IRB # is 20-30387.

Individuals capable of naturally controlling HIV infection in the absence of ART represent both a diagnostic and a management challenge for the treating clinician. In this chapter, we review what is known about the epidemiology, biology, and clinical outcomes of individuals across the clinical spectrum of natural HIV control and provide suggestions for the management of such individuals in a clinical setting.

Author(s): Appa, Ayesha; Takahashi, Saki; Rodriguez-Barraquer, Isabel; Chamie, Gabriel; Sawyer, Aenor; Duarte, Elias; Hakim, Jill; Turcios, Keirstinne; Vinden, Joanna; Janson, Owen; Manglik, Aashish; Peluso, Michael J; Deeks, Steven G; Henrich, Timothy J; Torres, Leonel; Rodgers, Mary; Hackett, John; Chiu, Charles; Havlir, Diane; Greenhouse, Bryan | Abstract: BackgroundLimited systematic surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the early months of the US epidemic curtailed accurate appraisal of transmission intensity. Our objective was to perform case detection of an entire rural community to quantify SARS-CoV-2 transmission using polymerase chain reaction (PCR) and antibody testing.MethodsWe conducted a cross-sectional survey of SARS-CoV-2 infection in the rural town of Bolinas, California (population 1620), 4 weeks after shelter-in-place orders. Participants were tested between April 20 and 24, 2020. Prevalence by PCR and seroprevalence from 2 forms of antibody testing were performed in parallel (Abbott ARCHITECT immunoglobulin [Ig]G and in-house IgG enzyme-linked immunosorbent assay).ResultsOf 1891 participants, 1312 were confirmed Bolinas residents (g80% community ascertainment). Zero participants were PCR positive. Assuming 80% sensitivity, it would have been unlikely to observe these results (P l .05) if there were g3 active infections in the community. Based on antibody results, estimated prevalence of prior infection was 0.16% (95% credible interval [CrI], 0.02%-0.46%). The positive predictive value (PPV) of a positive result on both tests was 99.11% (95% CrI, 95.75%-99.94%), compared with PPV 44.19%-63.32% (95% CrI, 3.25%-98.64%) if 1 test was utilized.ConclusionsFour weeks after shelter-in-place, SARS-CoV-2 infection in a rural Northern California community was extremely rare. In this low-prevalence setting, use of 2 antibody tests increased seroprevalence estimate precision. This was one of the first community-wide studies to successfully implement synchronous PCR and antibody testing, particularly in a rural setting. Widespread testing remains an underpinning of effective disease control in conjunction with consistent uptake of public health measures.

Few interventional strategies lead to significant reductions in HIV-1 reservoir size or prolonged antiretroviral (ART)-free remission. Allogeneic stem cell transplantations (SCT) with or without donor cells harboring genetic mutations preventing functional expression of CCR5, an HIV coreceptor, lead to dramatic reductions in residual HIV burden. However, the mechanisms by which SCT reduces viral reservoirs and leads to a potential functional HIV cure are not well understood. A growing number of studies involving allogeneic SCT in people with HIV are emerging, including those with and without transplants involving CCR5Δ32/Δ32 mutations. Donor cells resistant to HIV entry are likely required in order to achieve permanent ART-free viral remission. However, dramatic reductions in the HIV reservoir secondary to beneficial graft-versus-host effects may lead to loss of HIV detection in blood and various tissues and lead to prolonged time to HIV rebound in individuals with wild-type CCR5 donors. Studies of SCT recipients and those who started very early ART during hyperacute infection suggest that dramatic reductions in reservoir size or restriction of initial reservoir seeding may lead to 8–10 months of time prior to eventual, and rapid, HIV recrudescence. Studies of allogeneic SCT in people with HIV have provided important insights into the size and nature of the HIV reservoir, and have invigorated other gene therapies to achieve HIV cure.

The coronavirus disease 2019 (COVID‐19) pandemic caused by SARS coronavirus 2 (SARS‐CoV‐2) has caused significant morbidity and mortality for patients and stressed healthcare systems worldwide. The clinical features, disease course, and serologic response of COVID‐19 among immunosuppressed patients such as solid organ transplant (SOT) recipients, who are at presumed risk for more severe disease, are not well characterized. We describe our institutional experience with COVID‐19 among ten SOT patients, including the clinical presentation, treatment modalities, and outcomes of seven renal transplant recipients, one liver transplant recipient, one heart transplant recipient, and one lung transplant recipient. In addition, we report the serologic response in SOT recipients, documenting a positive IgG response in all seven hospitalized patients. We also review the existing literature on COVID‐19 in SOT recipients to consolidate the current knowledge on COVID‐19 in the SOT population for the transplant community.

Author(s): Peluso, Michael J; Thanh, Cassandra; Prator, Cecilia A; Hogan, Louise E; Arechiga, Victor M; Stephenson, Sophie; Norris, Philip J; Di Germanio, Clara; Fuchs, Dietmar; Zetterberg, Henrik; Deeks, Steven G; Gisslen, Magnus; Price, Richard W; Henrich, Timothy J | Abstract: ObjectivesThe aim of this study was to assess soluble CD30 (sCD30), a protein that colocalises with HIV-1 RNA and DNA in lymphoid cells and tissues, in cerebrospinal fluid (CSF) as a marker of HIV-1 infection in the central nervous system (CNS).MethodsThis was a cross-sectional study using archived samples from two clinical cohorts. Soluble CD30 concentrations were measured in paired CSF and plasma from untreated viraemic individuals (n=52), individuals on suppressive antiretroviral therapy (ART) (n=33), HIV-1 controllers (n=10), participants with CSF HIV-1 'escape' (n=11) and controls without HIV-1 infection (n=16). Nonparametric tests were used to compare levels across groups and evaluate correlations with HIV-1 RNA, CSF neurofilament light chain protein (NFL) and neopterin.ResultsCompared with controls (median 30 ng/mL, interquartile range [IRQ] 23-50), plasma sCD30 levels were elevated in viraemic participants (75 ng/mL, 52-116; Pl0.001), but not in those on suppressive ART (38 ng/mL, 32-62). In contrast, CSF sCD30 levels were elevated in ART-suppressed individuals (34 ng/mL, 19-46; P=0.001) and in those with CSF 'escape' (33 ng/mL, 27-40; P=0.004) compared with controls (18 ng/mL, 11-23), but not in untreated viraemic individuals. No association was observed between CSF sCD30 and plasma HIV-1 RNA, concurrent or nadir CD4+ T cell count, duration of infection or plasma sCD30. CSF sCD30 correlated with CSF NFL (r=0.34, P=0.001).ConclusionsIn contrast to plasma, sCD30 levels are elevated in the CSF of individuals with HIV-1 infection who are on suppressive ART. Elevated levels of sCD30 in the CSF may be an indicator of persistent CNS HIV-1 infection, although the mechanism underlying this elevation warrants further investigation.

BACKGROUND: The relative stabilities of the intact and defective HIV genomes over time during effective antiretroviral therapy (ART) have not been fully characterized. METHODS: We used the intact proviral DNA assay (IPDA) to estimate the rate of change of intact and defective proviruses in HIV-infected adults on ART. We used linear spline models with a knot at seven years and a random intercept and slope up to the knot. We estimated the influence of covariates on rates of change. RESULTS: We studied 81 individuals for a median of 7.3 (IQR 5.9-9.6) years. Intact genomes declined more rapidly from initial suppression through seven years (15.7% per year decline; 95% CI -22.8%, -8.0%) and more slowly after seven years (3.6% per year; 95% CI -8.1%, +1.1%). The estimated half-life of the reservoir was 4.0 years (95% CI 2.7-8.3) until year seven and 18.7 years (95% CI 8.2-infinite) thereafter. There was substantial variability between individuals in the rate of decline until year seven. Intact provirus declined more rapidly than defective provirus (P < 0.001) and showed a faster decline in individuals with higher CD4(+) T cell nadirs. CONCLUSION: The biology of the replication-competent (intact) reservoir differs from that of the replication-incompetent (non-intact) pool of proviruses. The IPDA will likely be informative when investigating the impact of interventions targeting the reservoir. FUNDING: Delaney AIDS Research Enterprise, UCSF/Gladstone Institute of Virology & Immunology CFAR, CFAR Network of Integrated Systems, amfAR Institute for HIV Cure Research, I4C and Beat-HIV Collaboratories, Howard Hughes Medical Institute, Gilead Sciences, Bill and Melinda Gates Foundation.

Despite the success of antiretroviral therapy (ART) in reducing HIV-1–related morbidity and mortality, viral reservoirs persist in infected cells in individuals on suppressive ART. Unfortunately, very few therapeutic strategies have led to a substantial decrease in the number of these persistently infected cells, and novel approaches to eliminate or reduce HIV reservoir burden are urgently needed.1 One such high-priority strategy is the identification of cell-surface markers of either quiescent or HIV-1 transcriptionally active cells that may be targeted with therapeutics such as cytotoxic antibody-drug conjugates (ADCs).2,3 Whereas the search for targetable biomarkers on quiescent, latently infected cells has remained elusive, an alternative approach involves targeting and clearing viral reactivated cells following in vivo HIV-1 latency reversal, thereby providing the “kill” component to the “shock-and-kill” approach to achieving a functional HIV-1 cure or long-term ART-free remission.2,3 We recently reported that CD4+ T cells expressing CD30, a cell-surface membrane protein and a member of the tumor necrosis factor receptor superfamily, were enriched in HIV-1 RNA, and that CD30 and HIV-1 transcriptional activity strongly colocalized in gut tissue from ART-suppressed individuals.2 Furthermore, HIV-1–infected individuals, either viremic or on suppressive ART, had significantly higher percentages of memory CD4+ T cells that expressed CD30 compared with uninfected controls.2 Prior studies also demonstrated a link between HIV-1 plasma RNA and disease progression with soluble plasma CD30 levels.4-8 CD30 is usually expressed on tumor cells involved with Hodgkin or aggressive lymphomas, but is otherwise expressed in very few cells from healthy, HIV-1–uninfected individuals,9,10 making it an enticing target. We have also observed that ex vivo treatment of peripheral blood mononuclear cells (PBMCs) from ART-suppressed individuals with brentuximab vedotin, an anti-CD30 ADC,11 led to a decrease in HIV-1 DNA levels in samples from 4 of 7 participants tested.2 However, the direct, longitudinal impact of brentuximab vedotin therapy on measures of HIV-1 persistence in vivo is not known and proof-of-concept studies are urgently needed. Therefore, we studied the impact of 3 doses of brentuximab vedotin therapy for Hodgkin lymphoma on HIV-1 persistence and immune phenotype in a newly identified HIV-1–infected individual on long-term ART.

We describe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cell responses, soluble markers of inflammation, and antibody levels and neutralization capacity longitudinally in 70 individuals with PCR-confirmed SARS-CoV-2 infection. Participants represent a spectrum of illness and recovery, including some with persistent viral shedding in saliva and many experiencing post-acute sequelae of SARS-CoV-2 infection (PASC). T cell responses remain stable for up to 9 months. Whereas the magnitude of early CD4+ T cell immune responses correlates with severity of initial infection, pre-existing lung disease is independently associated with higher long-term SARS-CoV-2-specific CD8+ T cell responses. Among participants with PASC 4 months following coronavirus disease 2019 (COVID-19) symptom onset, we observe a lower frequency of CD8+ T cells expressing CD107a, a marker of degranulation, in response to Nucleocapsid (N) peptide pool stimulation, and a more rapid decline in the frequency of N-specific interferon-γ-producing CD8+ T cells. Neutralizing antibody levels strongly correlate with SARS-CoV-2-specific CD4+ T cell responses., Graphical abstract, CD4+ and CD8+ T cell responses following natural infection with COVID-19 are stable over 8 months. Individuals with PASC demonstrate a lower frequency of CD8+ T cells expressing CD107a, a marker of degranulation, and a more rapid decline in the frequency of N-specific interferon-γ-producing CD8+ T cells.

Background Identification of nonviral markers of human immunodeficiency virus (HIV) infection that increase before viral rebound during analytical treatment interruption (ATI) may affect HIV persistence research. We previously showed that HIV ribonucleic acid (RNA) is enriched in CD30+CD4+ T cells in many individuals. Here, we studied CD30+CD4+ T-cell dynamics before ATI, during ATI (before detectable plasma RNA), and after HIV rebound. Methods Peripheral blood mononuclear cells from 23 participants collected longitudinally from 5 Adult AIDS Clinical Trials Group studies incorporating ATI were included in this study. Flow cytometric characterization of expression of CD30 and markers of T-cell activation and exhaustion were performed along with HIV-1 RNA and deoxyribonucleic acid quantification and measurement of soluble plasma CD30 and CD30 ligand. Results The percentage of CD4+ T cells expressing CD30 significantly increased from pre-ATI to postinterruption time points before detectible viremia (1.65 mean relative increase, P = .005). Seventy-seven percent of participants experienced an increase in CD30+ cells before viral rebound. In contrast, there were no significant differences between pre-ATI and postinterruption pre-rebound time points in percentages of lymphocytes expressing CD69, CD38/HLA-DR, or PD-1 until after HIV recrudescence. Conclusions CD30 may be a surrogate marker of early replication or viral transcriptional activity before detection by routine peripheral blood sampling.

Elite controllers (EC), a small subset of the HIV-positive population ( 1%), suppress HIV viremia below the limit of quantification of clinical viral load assays in the absence of antiretroviral therapy (ART). However, there is a paucity of longitudinal data detailing the viral and immune dynamics or HIV reservoir seeding during acute infection in individuals that go on to become Elite Controllers.In this report, we describe a case of a 42 year old woman diagnosed during acute infection who rapidly and permanently suppressed her viremia in the absence of antiretroviral therapy (ART). Rapid antibody/antigen testing was either negative or equivocal during acute infection, despite subsequent viral load testing at that time point with 71,550 plasma HIV RNA copies/mL, making initial diagnosis challenging. The patient subsequently developed detectable anti-HIV antibodies and an increase in HIV-specific CD8+ T cell responses to overlapping subtype C HIV gag peptide; very low-level plasma viremia (0.84 RNA copies/mL) was detected by an ultrasensitive assay 2 years following infection. Subsequently, she was started on ART for multifocal furunculosis despite continued suppression of virus and stable CD4+ T cell counts. Following ART initiation, HIV specific antibody levels and CD8+ T cell responses increased, but no HIV DNA or RNA was able to be isolated from large numbers of peripheral blood CD4+ T cells.This case provides important information regarding the establishment of elite HIV control during acute infection and also demonstrates an increase in HIV-specific immune responses following ART despite undetectable peripheral blood cellular measures of HIV persistence. This case also highlights the challenges in diagnosing acute HIV infection without the use of viral load testing in this rare elite controller phenotype.

A major obstacle to HIV eradication is the presence of infected cells that persist despite suppressive antiretroviral therapy (ART). HIV largely resides outside of the peripheral circulation, and thus, numerous anatomical and lymphoid compartments that have the capacity to harbor HIV are inaccessible to routine sampling. As a result, there is a limited understanding of the tissue burden of HIV infection or anatomical distribution of HIV transcriptional and translational activity. Novel, non-invasive, in vivo methods are urgently needed to address this fundamental gap in knowledge. In this review, we discuss past and current nuclear imaging approaches that have been applied to HIV infection with an emphasis on current strategies to implement positron emission tomography (PET)-based imaging to directly visualize and characterize whole-body HIV burden. These imaging approaches have various limitations, such as the potential for limited PET sensitivity and specificity in the setting of ART suppression or low viral burden. However, recent advances in high-sensitivity, total-body PET imaging platforms and development of new radiotracer technologies that may enhance anatomical penetration of target-specific tracer molecules are discussed. Potential strategies to image non-viral markers of HIV tissue burden or focal immune perturbation are also addressed. Overall, emerging nuclear imaging techniques and platforms may play an important role in the development of novel therapeutic and HIV reservoir eradication strategies.

Development of label-free, highly sensitive, miniaturized surface plasmon resonance sensors enables real-time quantification of biomolecule interactions at atomic-levels, desirable for medical diagnostics and which will allow rapid clinical decisions. However, multi-target diagnostic assays require skilled labor, expensive materials, lengthy manual steps, as well as complicated analysis steps. Here, we develop a microfluidic-integrated digital optical disc (DVD) grating as a metasurface, which is coated with titanium-silver-gold (Ti-Ag-Au, 10, 30, and 15nm) for real-time monitoring of biomolecular interactions and binding affinities. Device fabrication process consists of poly (methyl methacrylate) (PMMA) microfluidic channel assembly on nanoplasmonic DVD surface gratings via double side adhesive (DSA) layers. Compared with other nano- and micro-fabrication methods, DVD-based sensor fabrication is relatively simple, cost-effective, and enables large-scale fabrication with minimum efforts. The plasmonic microfluidic chip surface was illuminated with a broadband light source and the normal reflection signal was monitored using a customized optical-setup. Maximum bulk sensitivity (337 nm/RIU) was observed with 30 seconds of etching period and low glycerol concentration (5%, v/v). Red-shifts of peak-wavelength (~16 nm) upon glycerol concentrations were observed as a function of time (seconds). A 0.6 nm peak-wavelength shift was observed in the step of EDC/NHS coupling and continuous protein A/G and G binding resulted in 0.353 ± 0.211 nm and 0.667 ± 0.116 nm (n=3, p

Background Despite the risks of immunosuppression, recommendations regarding screening for HIV infection prior to initiation of biologic therapies targeting common autoimmune disorders, including inflammatory bowel disease (IBD) and inflammatory arthritides, are limited. Few cases of patients started on biologics while living with undiagnosed HIV have been reported. Methods We report 3 cases of patients initiated on biologics in the absence of recent or concurrent HIV screening who developed refractory disease or unanticipated complications and were later found to have undiagnosed chronic HIV infection. Results In Case 1, a 53-year-old man who has sex with men (MSM) with negative HIV testing 10 years prior presented with presumed rheumatoid arthritis. He did not respond to methotrexate (MTX), so adalimumab (ADA) was started. HIV testing to evaluate persistent symptoms was positive 9 months later; CD4 was 800 cells/uL. Antiretroviral therapy (ART) resulted in resolution of symptoms, which were attributed to HIV-associated arthropathy. In Case 2, a 55-year-old woman with injection drug use in remission and no prior HIV testing presented with Hidradenitis Suppurativa (HS). She was initiated on infliximab (IFX) and MTX with good response. After she developed weight loss and lymphopenia, an HIV test was positive; CD4 was 334 cells/uL. Biologic HS therapy was discontinued, with subsequent poor HS control. In Case 3, a 32-year-old MSM with no prior HIV testing presented with presumed IBD; IFX and steroids were started. Symptoms progressed despite IBD-directed therapy, and he was diagnosed with extensive Kaposi Sarcoma (KS) with visceral and cutaneous involvement likely exacerbated by immunosuppression. HIV testing was positive; CD4 was 250 cells/uL. KS initially worsened due to ART-associated immune reconstitution inflammatory syndrome. He is now improving with systemic chemotherapy and ART. HIV-associated KS is presumed to be hte underlying diagnosis. Conclusion All 3 patients had elevated risk for HIV infection, and 2 had final diagnoses attributed to chronic HIV infection, not warranting therapeutic immunosuppression. Screening for HIV infection prior to initiation of biologic therapy should be incorporated into clinical practice guidelines. Disclosures All Authors: No reported disclosures

Metasurfaces are engineered nanostructured interfaces that extend the photonic behavior of natural materials, and they spur many breakthroughs in multiple fields, including quantum optics, optoelectronics, and biosensing. Recent advances in metasurface nanofabrication enable precise manipulation of light-matter interactions at subwavelength scales. However, current fabrication methods are costly and time-consuming and have a small active area with low reproducibility due to limitations in lithography, where sensing nanosized rare biotargets requires a wide active surface area for efficient binding and detection. Here, a plastic-templated tunable metasurface with a large active area and periodic metal-dielectric layers to excite plasmonic Fano resonance transitions providing multimodal and multiplex sensing of small biotargets, such as proteins and viruses, is introduced. The tunable Fano resonance feature of the metasurface is enabled via chemical etching steps to manage nanoperiodicity of the plastic template decorated with plasmonic layers and surrounding dielectric medium. This metasurface integrated with microfluidics further enhances the light-matter interactions over a wide sensing area, extending data collection from 3D to 4D by tracking real-time biomolecular binding events. Overall, this work resolves cost- and complexity-related large-scale fabrication challenges and improves multilayer sensitivity of detection in biosensing applications.

Background The use of immunomodulatory drugs (IMDs) is increasingly common. However, data on outcomes of IMD use in people living with HIV (PLWH) are limited and may be biased due to selective reporting of certain outcomes. Institution-level data reflecting patient-time at risk have not been described. Methods We systematically identified all PLWH prescribed non-steroidal IMDs from 2012 to 2019 at two centers. We defined a treatment episode (TE) as an uninterrupted period on a particular IMD regimen. Patients contributed multiple TEs if interrupting or switching therapy. We excluded those with lymphoproliferative disorders or transplants. We quantified infections and blips, defined as a detectable viral load following an undetectable result. Results 35 patients contributed 55 TEs comprising 24,020 patient-days at risk. 29/35 (83%) were male, median age was 53 (IQR 39–59), median CD4 nadir was 197 (IQR 100–314), and 12/35 (34%) had a prior opportunistic infection. TEs utilized TNF inhibitors (19/55, 35%), PD-1 inhibitors (11/55, 20%), antimetabolites (7/55, 13%), interleukin inhibitors (7/55, 13%), and other agents (7/55, 13%). 4/55 (7%) involved in dual therapy. 32/35 (94%) patients were on antiretroviral therapy (ART) at IMD initiation; one was off therapy, one already on IMDs-acquired HIV, and one was an elite controller. Median CD4 count was 472 (IQR 337–807); CD4 was < 500 in 28/55 TEs (51%). Preceding plasma HIV RNA was undetectable in 36/55 (65%) TEs. Of these, 18 (50%) were associated with a viral blip within 1 year; one blip was >200 copies and none resulted in sustained viremia. Compared with other agents, PD-1 inhibitors were associated with a higher blip rate (incidence rate ratio 4.3, 1.3–12.3). 17/55 (32%) TEs were initiated with detectable plasma HIV RNA, which declined on ART in 13/15 (87%) TEs with follow-up testing; one patient stopped ART and one later suppressed. 9/55 (16%) TEs involved an infectious complication (7 soft-tissue infections, 2 pneumonias), although none was clearly attributed to IMDs. 36/55 (65%) TEs had good therapeutic response. Conclusion IMDs can be used without major complications in PLWH on ART, including those not yet suppressed or with CD4 counts < 500. PD-1 inhibitors may be associated with a higher rate of viral blips, although the clinical significance is unclear. Disclosures All authors: No reported disclosures.

A person infected with HIV who was treated for blood cancer with a stem-cell transplant has gone into viral remission, with no trace of the virus in their blood. A similar outcome in 2009 hadn’t been replicated until now. A person’s HIV infection became undetectable after a stem-cell transplant.

Objectives To determine viral and immune factors involved in transmission and control of HIV-1 infection in persons without functional CCR5. Design Understanding transmission and control of HIV-1 in persons homozygous for CCR5(Δ32) is important given efforts to develop HIV-1 curative therapies aimed at modifying or disrupting CCR5 expression. Methods We identified two HIV-infected CCR5(Δ32/Δ32) individuals among a cohort of patients with spontaneous control of HIV-1 infection without antiretroviral therapy and determined coreceptor usage of the infecting viruses. We assessed genetic evolution of full-length HIV-1 envelope sequences by single-genome analysis from one participant and his sexual partner, and explored HIV-1 immune responses and HIV-1 mutations following virologic escape and disease progression. Results Both participants experienced viremia of less than 4000 RNA copies/ml with preserved CD4(+) T-cell counts off antiretroviral therapy for at least 3.3 and 4.6 years after diagnosis, respectively. One participant had phenotypic evidence of X4 virus, had no known favorable human leukocyte antigen alleles, and appeared to be infected by minority X4 virus from a pool that predominately used CCR5 for entry. The second participant had virus that was unable to use CXCR4 for entry in phenotypic assay but was able to engage alternative viral coreceptors (e.g., CXCR6) in vitro. Conclusion Our study demonstrates that individuals may be infected by minority X4 viruses from a population that predominately uses CCR5 for entry, and that viruses may bypass traditional HIV-1 coreceptors (CCR5 and CXCR4) completely by engaging alternative coreceptors to establish and propagate HIV-1 infection.

In the wake of reports of an HIV cure for Timothy Brown (the Berlin patient) after two haemopoietic stem cell transplantations (HSCT) from a donor homozygous for the CCR5Δ32 mutation, at least four other individuals have had antiretroviral therapy (ART) stopped as analytical treatment interruptions after similar procedures. Only one of those patients received stem cells from a donor homozygous for CCR5Δ32, and three of the recipients were heterozygous for CCR5Δ32. The clinical outcome after each of these interruptions has been disappointing, with pronounced viral rebound and associated morbidity. What if remission among a minority of patients is possible after HSCT, such as that experienced by some patients after treatment during acute infection? 3 Given such discouraging outcomes so far, can analytical treatment interruptions after HSCT be ethically appropriate? This is a crucially important issue, because many patients with HIV will have HSCT, with or without a donor homozygous for CCR5Δ32, and efforts continue to optimise the possibility of using the procedure to achieve HIV remission.

Background It is unknown if extremely early initiation of antiretroviral therapy (ART) may lead to long-term ART-free HIV remission or cure. As a result, we studied 2 individuals recruited from a pre-exposure prophylaxis (PrEP) program who started prophylactic ART an estimated 10 days (Participant A; 54-year-old male) and 12 days (Participant B; 31-year-old male) after infection with peak plasma HIV RNA of 220 copies/mL and 3,343 copies/mL, respectively. Extensive testing of blood and tissue for HIV persistence was performed, and PrEP Participant A underwent analytical treatment interruption (ATI) following 32 weeks of continuous ART. Methods and findings Colorectal and lymph node tissues, bone marrow, cerebral spinal fluid (CSF), plasma, and very large numbers of peripheral blood mononuclear cells (PBMCs) were obtained longitudinally from both participants and were studied for HIV persistence in several laboratories using molecular and culture-based detection methods, including a murine viral outgrowth assay (mVOA). Both participants initiated PrEP with tenofovir/emtricitabine during very early Fiebig stage I (detectable plasma HIV-1 RNA, antibody negative) followed by 4-drug ART intensification. Following peak viral loads, both participants experienced full suppression of HIV-1 plasma viremia. Over the following 2 years, no further HIV could be detected in blood or tissue from PrEP Participant A despite extensive sampling from ileum, rectum, lymph nodes, bone marrow, CSF, circulating CD4+ T cell subsets, and plasma. No HIV was detected from tissues obtained from PrEP Participant B, but low-level HIV RNA or DNA was intermittently detected from various CD4+ T cell subsets. Over 500 million CD4+ T cells were assayed from both participants in a humanized mouse outgrowth assay. Three of 8 mice infused with CD4+ T cells from PrEP Participant B developed viremia (50 million input cells/surviving mouse), but only 1 of 10 mice infused with CD4+ T cells from PrEP Participant A (53 million input cells/mouse) experienced very low level viremia (201 copies/mL); sequence confirmation was unsuccessful. PrEP Participant A stopped ART and remained aviremic for 7.4 months, rebounding with HIV RNA of 36 copies/mL that rose to 59,805 copies/mL 6 days later. ART was restarted promptly. Rebound plasma HIV sequences were identical to those obtained during acute infection by single-genome sequencing. Mathematical modeling predicted that the latent reservoir size was approximately 200 cells prior to ATI and that only around 1% of individuals with a similar HIV burden may achieve lifelong ART-free remission. Furthermore, we observed that lymphocytes expressing the tumor marker CD30 increased in frequency weeks to months prior to detectable HIV-1 RNA in plasma. This study was limited by the small sample size, which was a result of the rarity of individuals presenting during hyperacute infection. Conclusions We report HIV relapse despite initiation of ART at one of the earliest stages of acute HIV infection possible. Near complete or complete loss of detectable HIV in blood and tissues did not lead to indefinite ART-free HIV remission. However, the small numbers of latently infected cells in individuals treated during hyperacute infection may be associated with prolonged ART-free remission., Timothy Henrich and colleagues study the effect of very early antiretroviral treatment on the reservoir of HIV-infected cells in two patients., Author summary Why was this study done? Early initiation of ART following infection may limit the total body burden of HIV. It is not known if starting ART extremely early after HIV infection will lead to ART-free remission or cure. We studied 2 individuals who started ART an estimated 10 and 12 days after HIV infection with very low peak viral load measurement; extensive testing of blood and tissue for HIV persistence was performed. One participant stopped ART in order to test if and when HIV would rebound. What did the researchers find? No HIV could be definitively detected for up to 2 years in the participant who initiated ART approximately 10 days after HIV infection. Intermittent, very low levels of HIV were detected in blood but not tissue in the participant who initiated ART an estimated 12 days following infection. The participant with no detectable HIV following ART experienced viral rebound 225 days after stopping ART. What do these findings mean? HIV relapsed despite initiation of ART at one of the earliest stages of acute HIV infection possible. Near complete loss of detectable HIV in blood and tissues did not lead to indefinite ART-free HIV remission.

Background Human Herpes Virus 8 (HHV8) can cause Kaposi’s Sarcoma (KS) in immunosuppressed individuals. However, little is known about the association between chemotherapy or hematopoietic stem cell transplantation (HSCT), circulating HHV8 DNA levels, and clinical KS in HIV-1-infected individuals with various malignancies. Therefore, we examined the associations between various malignancies, systemic cancer chemotherapy, T cell phenotypes, and circulating HHV8 DNA in 29 HIV-1-infected participants with concomitant KS or other cancer diagnoses. Methods We quantified HHV8 plasma viral loads and cell-associated HHV8 DNA and determined the relationship between circulating HHV8 DNA and lymphocyte counts, and markers of early and late lymphocyte activation, proliferation and exhaustion. Results There were no significant differences in plasma HHV8 DNA levels between baseline and post-chemotherapy time points or with the presence or absence of clinical KS. However, in two participants circulating HHV8 DNA increased following treatment for KS or HSCT for lymphoma,. We observed an approximately 2-log10 reduction in plasma HHV8 DNA in an individual with KS and multicentric Castleman disease following rituximab monotherapy. Although individuals with clinical KS had lower mean CD4+ T cell counts and percentages as expected, there were no significant associations with these factors and plasma HHV8 levels. We identified increased proportions of CD8+ and CD4+ T cells expressing CD69 (P = 0.01 & P = 0.04 respectively), and increased CD57 expression on CD4+ T cells (P = 0.003) in participants with detectable HHV8. Conclusion These results suggest there is a complex relationship between circulating HHV8 DNA and tissue-based disease in HIV-1 and HHV8 co-infected individuals with various malignancies.

Background Systemic chemotherapies for various malignancies have been shown to significantly, yet transiently, decrease numbers of CD4+ T lymphocytes, a major reservoir for human immunodeficiency virus type 1 (HIV-1) infection. However, little is known about the impact of cytoreductive chemotherapy on HIV-1 reservoir dynamics, persistence, and immune responses. Methods We investigated the changes in peripheral CD4+ T-cell-associated HIV-1 DNA and RNA levels, lymphocyte activation, viral population structure, and virus-specific immune responses in a longitudinal cohort of 15 HIV-1-infected individuals receiving systemic chemotherapy or subsequent autologous stem cell transplantation for treatment of hematological malignancies and solid tumors. Results Despite a transient reduction in CD4+ T cells capable of harboring HIV-1, a 1.7- and 3.3-fold increase in mean CD4+ T-cell-associated HIV-1 RNA and DNA, respectively, were observed months following completion of chemotherapy in individuals on antiretroviral therapy. We also observed changes in CD4+ T-cell population diversity and clonal viral sequence expansion during CD4+ T-cell reconstitution following chemotherapy cessation. Finally, HIV-1 DNA was preferentially, and in some cases exclusively, detected in cytomegalovirus (CMV)- and Epstein-Barr virus (EBV)-responsive CD4+ T cells following chemotherapy. Conclusions Expansion of HIV-infected CMV/EBV-specific CD4 + T cells may contribute to maintenance of the HIV DNA reservoir following chemotherapy.