COVID-19 Case Investigation and Contact Tracing in New York City, June 1, 2020, to October 31, 2021.

Importance: Contact tracing is a core strategy for preventing the spread of many infectious diseases of public health concern. Better understanding of the outcomes of contact tracing for COVID-19 as well as the operational opportunities and challenges in establishing a program for a jurisdiction as large as New York City (NYC) is important for the evaluation of this strategy. Objective: To describe the establishment, scaling, and maintenance of Trace, NYC's contact tracing program, and share data on outcomes during its first 17 months. Design, Setting, and Participants: This cross-sectional study included people with laboratory test-confirmed and probable COVID-19 and their contacts in NYC between June 1, 2020, and October 31, 2021. Trace launched on June 1, 2020, and had a workforce of 4147 contact tracers, with the majority of the workforce performing their jobs completely remotely. Data were analyzed in March 2022. Main Outcomes and Measures: Number and proportion of persons with COVID-19 and contacts on whom investigations were attempted and completed; timeliness of interviews relative to symptom onset or exposure for symptomatic cases and contacts, respectively. Results: Case investigations were attempted for 941 035 persons. Of those, 840 922 (89.4%) were reached and 711 353 (75.6%) completed an intake interview (women and girls, 358 775 [50.4%]; 60 178 [8.5%] Asian, 110 636 [15.6%] Black, 210 489 [28.3%] Hispanic or Latino, 157 349 [22.1%] White). Interviews were attempted for 1 218 650 contacts. Of those, 904 927 (74.3%) were reached, and 590 333 (48.4%) completed intake (women and girls, 219 261 [37.2%]; 47 403 [8.0%] Asian, 98 916 [16.8%] Black, 177 600 [30.1%] Hispanic or Latino, 116 559 [19.7%] White). Completion rates were consistent over time and resistant to changes related to vaccination as well as isolation and quarantine guidance. Among symptomatic cases, median time from symptom onset to intake completion was 4.7 days; a median 1.4 contacts were identified per case. Median time from contacts' last date of exposure to intake completion was 2.3 days. Among contacts, 30.1% were tested within 14 days of notification. Among cases, 27.8% were known to Trace as contacts. The overall expense for Trace from May 6, 2020, through October 31, 2021, was approximately $600 million. Conclusions and Relevance: Despite the complexity of developing a contact tracing program in a diverse city with a population of over 8 million people, in this case study we were able to identify 1.4 contacts per case and offer resources to safely isolate and quarantine to over 1 million cases and contacts in this study period.

Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases.

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes global epidemics of debilitating disease worldwide. To gain functional insight into the host cellular genes required for virus infection, we performed whole-blood RNA-seq, 37-plex mass cytometry of peripheral blood mononuclear cells (PBMCs), and serum cytokine measurements of acute- and convalescent-phase samples obtained from 42 children naturally infected with CHIKV Semi-supervised classification and clustering of single-cell events into 57 sub-communities of canonical leukocyte phenotypes revealed a monocyte-driven response to acute infection, with the greatest expansions in "intermediate" CD14++CD16+ monocytes and an activated subpopulation of CD14+ monocytes. Increases in acute-phase CHIKV envelope protein E2 expression were highest for monocytes and dendritic cells. Serum cytokine measurements confirmed significant acute-phase upregulation of monocyte chemoattractants. Distinct transcriptomic signatures were associated with infection timepoint, as well as convalescent-phase anti-CHIKV antibody titer, acute-phase viremia, and symptom severity. We present a multiscale network that summarizes all observed modulations across cellular and transcriptomic levels and their interactions with clinical outcomes, providing a uniquely global view of the biomolecular landscape of human CHIKV infection.

Associations between antiretroviral use and subclinical coronary atherosclerosis.

OBJECTIVES: HIV infection is associated with increased prevalence of subclinical coronary plaque. The extent to which such plaque reflects effects of HIV infection or effects of long-term antiretroviral therapy (ART) use remains unclear and was the goal of this analysis. DESIGN AND METHODS: We compared the prevalence and extent of coronary plaque and stenosis between users of specific ART drugs or drug classes using coronary computed tomography (CT) among HIV-infected men in the Multicenter AIDS Cohort Study. To account for time-dependent confounders, including cardiovascular disease risk factors and time-varying reasons for using specific treatments, we conducted fully adjusted logistic and linear models with inverse probability of treatment weighting. RESULTS: There were 618 men who underwent noncontrast coronary CT; 450 also underwent coronary CT angiography. At the time of scanning, 81% had undetectable plasma HIV RNA. In fully adjusted models, cumulative use of zidovudine, abacavir, darunavir, and protease inhibitors as a drug class were inconsistently associated with specific forms of plaque presence or extent. CONCLUSION: Among virally suppressed HIV-infected men with extensive ART exposure, no consistent associations between use of specific ART drugs and both subclinical coronary plaque presence and extent were apparent. Our findings support the hypothesis that, among virally suppressed persons, type of ART used is not in general a major determinant of subclinical coronary plaque risk.

Community-associated methicillin-resistant Staphylococcus aureus colonization in high-risk groups of HIV-infected patients.

BACKGROUND: We examined the epidemiology of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) nasal colonization among 3 groups of human immunodeficiency virus (HIV)-infected and 1 group of HIV-negative outpatients. METHODS: We determined prevalence and risk factors associated with MRSA colonization among women, recently incarcerated, and Hispanic HIV-infected patients and HIV-negative patients; isolates were typed by pulsed-field gel electrophoresis. Relative prevalence was calculated using Poisson regression, and logistic regression was used for multivariate analysis. RESULTS: Of 601 patients, 9.3% were colonized with MRSA; 11% of HIV-infected and 4.2% of HIV-negative patients were colonized (relative prevalence, 2.6; 95% confidence interval [CI], 1.12-6.07; P = .03). Among HIV-infected patients, recently incarcerated patients had the highest colonization prevalence (15.6%) followed by women (12%); Hispanic patients had the lowest (2.8%). Eighty percent of confirmed MRSA isolates were identified as USA300. On multivariate analysis, history of incarceration or residence in alternative housing (odds ratio [OR], 2.3; 95% CI, 1.1-4.7; P = .03) was associated with MRSA colonization; Hispanic ethnicity was negatively associated (OR, 0.3; 95% CI, .11-.98; P = .045). There was a trend (OR, 1.6; 95% CI, .9-3.0; P = .097) toward geographic location of residence being associated with colonization. After controlling for incarceration, residence, and geography, HIV status was no longer significantly associated with colonization. CONCLUSIONS: The CA-MRSA and HIV epidemics have intersected. Examination of networks of individuals released from incarceration, both HIV positive and negative, is needed to assess the role of social networks in spread of CA-MRSA and inform prevention strategies.