Global absence and targeting of protective immune states in severe COVID-19.

Although infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has pleiotropic and systemic effects in some individuals1-3, many others experience milder symptoms. Here, to gain a more comprehensive understanding of the distinction between severe and mild phenotypes in the pathology of coronavirus disease 2019 (COVID-19) and its origins, we performed a whole-blood-preserving single-cell analysis protocol to integrate contributions from all major immune cell types of the blood-including neutrophils, monocytes, platelets, lymphocytes and the contents of the serum. Patients with mild COVID-19 exhibit a coordinated pattern of expression of interferon-stimulated genes (ISGs)3 across every cell population, whereas these ISG-expressing cells are systemically absent in patients with severe disease. Paradoxically, individuals with severe COVID-19 produce very high titres of anti-SARS-CoV-2 antibodies and have a lower viral load compared to individuals with mild disease. Examination of the serum from patients with severe COVID-19 shows that these patients uniquely produce antibodies that functionally block the production of the ISG-expressing cells associated with mild disease, by activating conserved signalling circuits that dampen cellular responses to interferons. Overzealous antibody responses pit the immune system against itself in many patients with COVID-19, and perhaps also in individuals with other viral infections. Our findings reveal potential targets for immunotherapies in patients with severe COVID-19 to re-engage viral defence.

Plasma SARS-CoV-2 nucleocapsid antigen levels are associated with progression to severe disease in hospitalized COVID-19.

BACKGROUND: Studies quantifying SARS-CoV-2 have focused on upper respiratory tract or plasma viral RNA with inconsistent association with clinical outcomes. The association between plasma viral antigen levels and clinical outcomes has not been previously studied. Our aim was to investigate the relationship between plasma SARS-CoV-2 nucleocapsid antigen (N-antigen) concentration and both markers of host response and clinical outcomes. METHODS: SARS-CoV-2 N-antigen concentrations were measured in the first study plasma sample (D0), collected within 72 h of hospital admission, from 256 subjects admitted between March 2020 and August 2021 in a prospective observational cohort of hospitalized patients with COVID-19. The rank correlations between plasma N-antigen and plasma biomarkers of tissue damage, coagulation, and inflammation were assessed. Multiple ordinal regression was used to test the association between enrollment N-antigen plasma concentration and the primary outcome of clinical deterioration at one week as measured by a modified World Health Organization (WHO) ordinal scale. Multiple logistic regression was used to test the association between enrollment plasma N-antigen concentration and the secondary outcomes of ICU admission, mechanical ventilation at 28 days, and death at 28 days. The prognostic discrimination of an externally derived "high antigen" cutoff of N-antigen ≥ 1000 pg/mL was also tested. RESULTS: N-antigen on D0 was detectable in 84% of study participants. Plasma N-antigen levels significantly correlated with RAGE (r = 0.61), IL-10 (r = 0.59), and IP-10 (r = 0.59, adjusted p = 0.01 for all correlations). For the primary outcome of clinical status at one week, each 500 pg/mL increase in plasma N-antigen level was associated with an adjusted OR of 1.05 (95% CI 1.03-1.08) for worse WHO ordinal status. D0 plasma N-antigen ≥ 1000 pg/mL was 77% sensitive and 59% specific (AUROC 0.68) with a positive predictive value of 23% and a negative predictive value of 93% for a worse WHO ordinal scale at day 7 compared to baseline. D0 N-antigen concentration was independently associated with ICU admission and 28-day mechanical ventilation, but not with death at 28 days. CONCLUSIONS: Plasma N-antigen levels are readily measured and provide important insight into the pathogenesis and prognosis of COVID-19. The measurement of N-antigen levels early in-hospital course may improve risk stratification, especially for identifying patients who are unlikely to progress to severe disease.

Gaps in naloxone ownership among people who inject drugs during the fentanyl wave of the opioid overdose epidemic in New York City, 2018.

Background: Community distribution of naloxone, a medication that reverses opioid overdose, is an effective public health strategy to prevent overdose deaths. However, data are limited on who has naloxone during the current fentanyl wave of the opioid overdose epidemic in the United States. We aim to determine correlates of naloxone ownership among a community sample of people who inject drugs (PWID) from New York City (NYC). Methods: Data were drawn from the National HIV Behavioral Surveillance Study among PWID. Participants were recruited via respondent-driven sampling. Eligible participants completed an interviewer-administered survey. Log-linked Poisson regression was used to determine adjusted prevalence ratios (aPR) and 95% confidence intervals (CIs) current naloxone ownership. Results: Of 503 PWID, 60% currently owned naloxone. In the past 12 months, 74% witnessed an opioid overdose and 25% experienced one. Those who experienced current homelessness were less likely to own naloxone (aPR: 0.79; 95% CI: 0.68, 0.91), as were those who had been recently incarcerated (aPR: 0.83; 95% CI: 0.71, 0.97). Respondents who reported recent known or possible fentanyl use were more likely to own naloxone (aPR: 1.23; 95% CI: 1.07, 1.43) as were those who experienced an opioid overdose in the past 12 months (aPR: 1.33; 95% CI: 1.15, 1.53). Conclusions: The prevalence of naloxone ownership among PWID in NYC was high, potentially due to widespread community naloxone distribution programs; however, gaps in naloxone ownership existed. Interventions that further ease access to naloxone, such as reclassifying naloxone as an over-the-counter medication and making it available "off the shelf," should be considered. More research is needed to identify barriers to access, uptake, and sustained possession within this group to maximize the impact of naloxone distribution during the ongoing fentanyl wave of the opioid overdose epidemic.

Trends in Methamphetamine Use Among Men Who Have Sex with Men in New York City, 2004-2017.

Methamphetamine (meth) use among men who have sex with men (MSM) has been documented to be associated with HIV transmission among those who are HIV-negative and worsening HIV outcomes among those who are HIV-positive. Recent media reports have suggested recent increases in meth use in New York City (NYC), particularly among Hispanic/Latino and Black MSM. Using serial cross-sectional data from 2004 to 2017, we aim to describe trends in meth use and describe racial/ethnic patterns among MSM in NYC. Overall, we observed a decrease in meth use among MSM from 2004 to 2011 and an increase from 2011 to 2017. When stratified by race/ethnicity, use among White MSM decreased. Beginning in 2008, use among both Hispanic/Latino and Black MSM increased over time. These data provide more evidence that meth use may be increasing in Hispanic/Latino and Black MSM. Culturally-tailored and status-neutral interventions should be explored.

Implementing Respondent-Driven Sampling to Recruit Women Who Exchange Sex in New York City: Factors Associated with Recruitment and Lessons Learned.

Respondent-driven sampling (RDS) relies on productive peer recruitment to capture hidden populations. Domestic studies have identified characteristics of productive recruitment among RDS samples of men who have sex with men and persons who use drugs, but not of women who exchange sex, a group vulnerable to HIV infection. We examined sociodemographic-, behavioral-, exchange-sex-, and protocol-related factors associated with recruitment among seeds (n = 25) and peers (n = 297) in the 2016 New York City National HIV Behavioral Surveillance Study cycle focused on women who exchange sex. Recruiter productivity was significantly associated with not having been recently incarcerated, lower rate of HIV testing, and larger exchange sex networks among seeds, and with HIV-prevention services usage among peers. We describe challenges and lessons learned from implementing RDS in this population. Our study identifies seed characteristics and protocol improvements researchers can utilize when implementing future RDS studies among women who exchange sex.

Estimating the size of populations at risk for malaria: a case study in cattle herders and agricultural workers in Northern Namibia.

Cattle herders and agricultural workers have been identified has key high-risk populations for malaria in northern Namibia. Population size estimates for these groups are lacking but are important for planning, monitoring and evaluating the effectiveness of targeted strategies towards malaria elimination in the region. In this analysis, we extend population size estimation methods routinely used in HIV research, specifically social mapping and multiple source capture-recapture, to the context of malaria to estimate how many cattle herders and agricultural workers lived in two regions of northern Namibia over the course of the 2019-2020 malaria season. Both methods estimated two to three times more agricultural workers than cattle herders but size estimates based on the multiple source capture-recapture method were two to three times greater than the mapping-based, highlighting important methodological considerations to apply such methods to these highly mobile populations. In particular, we compared open versus closed populations assumptions for the capture-recapture method and assessed the impact of sensitivity analyses on the procedure to link records across multiple data sources on population size estimates. Our results are important for national control programs to target their resources and consider integrating routine population size estimation of high risk populations in their surveillance activities.

Individual, Environmental, and Early Life Factors Associated With Client-Perpetrated Violence Among Women Who Exchange Sex in New York City, 2016.

Women who exchange sex are at an increased risk of violence from both clients and nonpaying intimate partners. This study utilizes data from the 2016 New York City National HIV Behavioral Surveillance Study cycle focused on high-risk women to examine factors associated with experiencing client-perpetrated violence (CPV). Women who exchanged sex for money or drugs (n = 330) were recruited via respondent-driven sampling. Adjusted log-linked Poisson regression was used to analyze individual, environmental, and early-life factors associated with experiencing CPV in the past 12 months. Compared with women who did not experience CPV, women who experienced CPV were more likely to have a household income of <$10,000 (adjusted prevalence ratio [aPR]: 2.15; 95% confidence interval [CI]: [1.29, 3.57]), have a same-sex partnership (aPR: 2.31; 95% CI: [1.23, 4.33]), have > 2 male exchange sex partners (aPR: 2.76; 95% CI: [1.28, 5.99]), find clients on the street (aPR: 2.10; 95% CI: [1.05, 3.99]), have been refused help from or avoided the police due to exchange sex (aPR: 1.88; 95% CI: [1.06, 3.32]) and to have experienced sexual violence as a minor (aPR: 2.16; 95% CI: [1.29, 3.30]). Multilevel approaches to violence prevention among women who exchange sex, particularly those who find clients on the street, should be considered.

Prevalence of U = U Awareness and Its Association with Anticipated HIV Stigma Among Low-Income Heterosexually Active Black and Latino Adults in New York City, 2019.

The fact that people with HIV (PWH) who have an undetectable viral load cannot sexually transmit HIV has been disseminated under the messaging "Undetectable = Untransmittable" (U = U). U = U messaging intends to destigmatize HIV by demonstrating that PWH can have healthy sexual lives. Among a sample of low-income heterosexually active Black and Latino adults, we aimed to (1) measure the prevalence of U = U awareness and (2) determine its association with anticipated HIV stigma. Low-income heterosexually active adults were recruited through respondent-driven sampling in New York City. Among Black and Latino participants who self-reported not having HIV, multiple linear regression was used to determine the association between U = U awareness with the following types of anticipated HIV stigma, as determined by principal component analyses: (1) general; (2) dating related; and (3) sex related. Of 485 participants, 35% were aware of U = U. Those who were aware reported less dating-related [adjusted B: -0.20; 95% confidence interval (CI): -0.37 to -0.03] and sex-related (adjusted B: -0.15; 95% CI: -0.29 to -0.002) anticipated HIV stigma. Although the prevalence of U = U awareness was much lower than reported in other populations (e.g., gender and sexual minorities and PWH), prevalence was moderate in our sample, given that awareness efforts have generally not focused on heterosexually active adults. Our findings provide preliminary evidence that U = U awareness may have an impact on anticipated HIV stigma related to dating and sex. Additional methods to disseminate U = U messaging and dismantle HIV stigma in this population should be explored.

Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.

Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing (scRNA-seq) we assessed lower respiratory tract immune responses and microbiome dynamics in 28 COVID-19 patients, 15 of whom developed VAP, and eight critically ill uninfected controls. Two days before VAP onset we observed a transcriptional signature of bacterial infection. Two weeks prior to VAP onset, following intubation, we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.

Impaired immune signaling and changes in the lung microbiome precede secondary bacterial pneumonia in COVID-19.

Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections including in patients with coronavirus disease 2019 (COVID-19). Using a combination of tracheal aspirate bulk and single-cell RNA sequencing we assessed lower respiratory tract immune responses and microbiome dynamics in 23 COVID-19 patients, 10 of whom developed VAP, and eight critically ill uninfected controls. At a median of three days (range: 2-4 days) before VAP onset we observed a transcriptional signature of bacterial infection. At a median of 15 days prior to VAP onset (range: 8-38 days), we observed a striking impairment in immune signaling in COVID-19 patients who developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients with VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. These findings suggest that COVID-19 patients who develop VAP have impaired antibacterial immune defense detectable weeks before secondary infection onset.

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a wholeblood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferonstimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies with multiple patterns of specificity against interferon-stimulated cells and that those antibodies functionally block the production of the mild disease-associated ISG-expressing cells. Overzealous and autodirected antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense.

Global Absence and Targeting of Protective Immune States in Severe COVID-19.

While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies with multiple patterns of specificity against interferon-stimulated cells and that those antibodies functionally block the production of the mild disease-associated ISG-expressing cells. Overzealous and auto-directed antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense. ONE SENTENCE SUMMARY: In severe COVID-19 patients, the immune system fails to generate cells that define mild disease; antibodies in their serum actively prevents the successful production of those cells.