Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty.

Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of critical epidemic drivers. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make months ahead projections of SARS-CoV-2 burden, totaling nearly 1.8 million national and state-level projections. Here, we find SMH performance varied widely as a function of both scenario validity and model calibration. We show scenarios remained close to reality for 22 weeks on average before the arrival of unanticipated SARS-CoV-2 variants invalidated key assumptions. An ensemble of participating models that preserved variation between models (using the linear opinion pool method) was consistently more reliable than any single model in periods of valid scenario assumptions, while projection interval coverage was near target levels. SMH projections were used to guide pandemic response, illustrating the value of collaborative hubs for longer-term scenario projections.

Informing pandemic response in the face of uncertainty. An evaluation of the U.S. COVID-19 Scenario Modeling Hub.

Our ability to forecast epidemics more than a few weeks into the future is constrained by the complexity of disease systems, our limited ability to measure the current state of an epidemic, and uncertainties in how human action will affect transmission. Realistic longer-term projections (spanning more than a few weeks) may, however, be possible under defined scenarios that specify the future state of critical epidemic drivers, with the additional benefit that such scenarios can be used to anticipate the comparative effect of control measures. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make 6-month ahead projections of the number of SARS-CoV-2 cases, hospitalizations and deaths. The SMH released nearly 1.8 million national and state-level projections between February 2021 and November 2022. SMH performance varied widely as a function of both scenario validity and model calibration. Scenario assumptions were periodically invalidated by the arrival of unanticipated SARS-CoV-2 variants, but SMH still provided projections on average 22 weeks before changes in assumptions (such as virus transmissibility) invalidated scenarios and their corresponding projections. During these periods, before emergence of a novel variant, a linear opinion pool ensemble of contributed models was consistently more reliable than any single model, and projection interval coverage was near target levels for the most plausible scenarios (e.g., 79% coverage for 95% projection interval). SMH projections were used operationally to guide planning and policy at different stages of the pandemic, illustrating the value of the hub approach for long-term scenario projections.

Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: A multi-model study.

Background: The COVID-19 Scenario Modeling Hub convened nine modeling teams to project the impact of expanding SARS-CoV-2 vaccination to children aged 5-11 years on COVID-19 burden and resilience against variant strains. Methods: Teams contributed state- and national-level weekly projections of cases, hospitalizations, and deaths in the United States from September 12, 2021 to March 12, 2022. Four scenarios covered all combinations of 1) vaccination (or not) of children aged 5-11 years (starting November 1, 2021), and 2) emergence (or not) of a variant more transmissible than the Delta variant (emerging November 15, 2021). Individual team projections were linearly pooled. The effect of childhood vaccination on overall and age-specific outcomes was estimated using meta-analyses. Findings: Assuming that a new variant would not emerge, all-age COVID-19 outcomes were projected to decrease nationally through mid-March 2022. In this setting, vaccination of children 5-11 years old was associated with reductions in projections for all-age cumulative cases (7.2%, mean incidence ratio [IR] 0.928, 95% confidence interval [CI] 0.880-0.977), hospitalizations (8.7%, mean IR 0.913, 95% CI 0.834-0.992), and deaths (9.2%, mean IR 0.908, 95% CI 0.797-1.020) compared with scenarios without childhood vaccination. Vaccine benefits increased for scenarios including a hypothesized more transmissible variant, assuming similar vaccine effectiveness. Projected relative reductions in cumulative outcomes were larger for children than for the entire population. State-level variation was observed. Interpretation: Given the scenario assumptions (defined before the emergence of Omicron), expanding vaccination to children 5-11 years old would provide measurable direct benefits, as well as indirect benefits to the all-age U.S. population, including resilience to more transmissible variants. Funding: Various (see acknowledgments).

Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination.

In Spring 2021, the highly transmissible SARS-CoV-2 Delta variant began to cause increases in cases, hospitalizations, and deaths in parts of the United States. At the time, with slowed vaccination uptake, this novel variant was expected to increase the risk of pandemic resurgence in the US in summer and fall 2021. As part of the COVID-19 Scenario Modeling Hub, an ensemble of nine mechanistic models produced 6-month scenario projections for July-December 2021 for the United States. These projections estimated substantial resurgences of COVID-19 across the US resulting from the more transmissible Delta variant, projected to occur across most of the US, coinciding with school and business reopening. The scenarios revealed that reaching higher vaccine coverage in July-December 2021 reduced the size and duration of the projected resurgence substantially, with the expected impacts was largely concentrated in a subset of states with lower vaccination coverage. Despite accurate projection of COVID-19 surges occurring and timing, the magnitude was substantially underestimated 2021 by the models compared with the of the reported cases, hospitalizations, and deaths occurring during July-December, highlighting the continued challenges to predict the evolving COVID-19 pandemic. Vaccination uptake remains critical to limiting transmission and disease, particularly in states with lower vaccination coverage. Higher vaccination goals at the onset of the surge of the new variant were estimated to avert over 1.5 million cases and 21,000 deaths, although may have had even greater impacts, considering the underestimated resurgence magnitude from the model.

Gecko: A time-series model for COVID-19 hospital admission forecasting.

During the COVID-19 pandemic, concerns about hospital capacity in the United States led to a demand for models that forecast COVID-19 hospital admissions. These short-term forecasts were needed to support planning efforts by providing decision-makers with insight about future demands for health care capacity and resources. We present a SARIMA time-series model called Gecko developed for this purpose. We evaluate its historical performance using metrics such as mean absolute error, predictive interval coverage, and weighted interval scores, and compare to alternative hospital admission forecasting models. We find that Gecko outperformed baseline approaches and was among the most accurate models for forecasting hospital admissions at the state and national levels from January-May 2021. This work suggests that simple statistical methods can provide a viable alternative to traditional epidemic models for short-term forecasting.

Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study.

Background: SARS-CoV-2 vaccination of persons aged 12 years and older has reduced disease burden in the United States. The COVID-19 Scenario Modeling Hub convened multiple modeling teams in September 2021 to project the impact of expanding vaccine administration to children 5-11 years old on anticipated COVID-19 burden and resilience against variant strains. Methods: Nine modeling teams contributed state- and national-level projections for weekly counts of cases, hospitalizations, and deaths in the United States for the period September 12, 2021 to March 12, 2022. Four scenarios covered all combinations of: 1) presence vs. absence of vaccination of children ages 5-11 years starting on November 1, 2021; and 2) continued dominance of the Delta variant vs. emergence of a hypothetical more transmissible variant on November 15, 2021. Individual team projections were combined using linear pooling. The effect of childhood vaccination on overall and age-specific outcomes was estimated by meta-analysis approaches. Findings: Absent a new variant, COVID-19 cases, hospitalizations, and deaths among all ages were projected to decrease nationally through mid-March 2022. Under a set of specific assumptions, models projected that vaccination of children 5-11 years old was associated with reductions in all-age cumulative cases (7.2%, mean incidence ratio [IR] 0.928, 95% confidence interval [CI] 0.880-0.977), hospitalizations (8.7%, mean IR 0.913, 95% CI 0.834-0.992), and deaths (9.2%, mean IR 0.908, 95% CI 0.797-1.020) compared with scenarios where children were not vaccinated. This projected effect of vaccinating children 5-11 years old increased in the presence of a more transmissible variant, assuming no change in vaccine effectiveness by variant. Larger relative reductions in cumulative cases, hospitalizations, and deaths were observed for children than for the entire U.S. population. Substantial state-level variation was projected in epidemic trajectories, vaccine benefits, and variant impacts. Conclusions: Results from this multi-model aggregation study suggest that, under a specific set of scenario assumptions, expanding vaccination to children 5-11 years old would provide measurable direct benefits to this age group and indirect benefits to the all-age U.S. population, including resilience to more transmissible variants.

Implementation of SARS-CoV-2 Monoclonal Antibody Infusion Sites at Three Medical Centers in the United States: Strengths and Challenges Assessment to Inform COVID-19 Pandemic and Future Public Health Emergency Use.

Monoclonal antibody therapeutics to treat coronavirus disease (COVID-19) have been authorized by the US Food and Drug Administration under Emergency Use Authorization (EUA). Many barriers exist when deploying a novel therapeutic during an ongoing pandemic, and it is critical to assess the needs of incorporating monoclonal antibody infusions into pandemic response activities. We examined the monoclonal antibody infusion site process during the COVID-19 pandemic and conducted a descriptive analysis using data from 3 sites at medical centers in the United States supported by the National Disaster Medical System. Monoclonal antibody implementation success factors included engagement with local medical providers, therapy batch preparation, placing the infusion center in proximity to emergency services, and creating procedures resilient to EUA changes. Infusion process challenges included confirming patient severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positivity, strained staff, scheduling, and pharmacy coordination. Infusion sites are effective when integrated into pre-existing pandemic response ecosystems and can be implemented with limited staff and physical resources.

Technologies Enabling Situational Awareness During Disaster Response: A Systematic Review.

Situational awareness (SA) is critical to mobilizing a rapid, efficient, and effective response to disasters. Limited by time and resources, response agencies must make decisions about rapidly evolving situations, which requires the collection, analysis, and sharing of actionable information across a complex landscape. Emerging technologies, if appropriately applied, can enhance SA and enable responders to make quicker, more accurate decisions. The aim of this systematic review is to identify technologies that can improve SA and assist decision-making across the United States Government and the domestic and international agencies they support during disaster response operations. A total of 1459 articles and 36 after-action reports were identified during literature searches. Following the removal of duplicates and application of inclusion/exclusion criteria, 302 articles and after-action reports were included in the review. Our findings suggest SA is constrained primarily due to unreliable and significantly delayed communications, time-intensive data analysis and visualization, and a lack of interoperable sensor networks and other capabilities providing data to shared platforms. Many of these challenges could be addressed by existing technologies. Bridging the divide between research and development efforts and the operational needs of response agencies should be prioritized.

Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination.

WHAT IS ALREADY KNOWN ABOUT THIS TOPIC?: The highly transmissible SARS-CoV-2 Delta variant has begun to cause increases in cases, hospitalizations, and deaths in parts of the United States. With slowed vaccination uptake, this novel variant is expected to increase the risk of pandemic resurgence in the US in July-December 2021. WHAT IS ADDED BY THIS REPORT?: Data from nine mechanistic models project substantial resurgences of COVID-19 across the US resulting from the more transmissible Delta variant. These resurgences, which have now been observed in most states, were projected to occur across most of the US, coinciding with school and business reopening. Reaching higher vaccine coverage in July-December 2021 reduces the size and duration of the projected resurgence substantially. The expected impact of the outbreak is largely concentrated in a subset of states with lower vaccination coverage. WHAT ARE THE IMPLICATIONS FOR PUBLIC HEALTH PRACTICE?: Renewed efforts to increase vaccination uptake are critical to limiting transmission and disease, particularly in states with lower current vaccination coverage. Reaching higher vaccination goals in the coming months can potentially avert 1.5 million cases and 21,000 deaths and improve the ability to safely resume social contacts, and educational and business activities. Continued or renewed non-pharmaceutical interventions, including masking, can also help limit transmission, particularly as schools and businesses reopen.

Real-world Effect of Monoclonal Antibody Treatment in COVID-19 Patients in a Diverse Population in the United States.

BACKGROUND: Monoclonal antibodies (mAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are a promising treatment for limiting the progression of coronavirus disease 2019 (COVID-19) and decreasing strain on hospitals. Their use, however, remains limited, particularly in disadvantaged populations. METHODS: Electronic health records were reviewed from SARS-CoV-2 patients at a single medical center in the United States that initiated mAb infusions in January 2021 with the support of the US Department of Health and Human Services' National Disaster Medical System. Patients who received mAbs were compared with untreated patients from the time period before mAb availability who met eligibility criteria for mAb treatment. We used logistic regression to measure the effect of mAb treatment on the risk of hospitalization or emergency department (ED) visit within 30 days of laboratory-confirmed COVID-19. RESULTS: Of 598 COVID-19 patients, 270 (45%) received bamlanivimab and 328 (55%) were untreated. Two hundred thirty-one patients (39%) were Hispanic. Among treated patients, 5/270 (1.9%) presented to the ED or required hospitalization within 30 days of a positive SARS-CoV-2 test, compared with 39/328 (12%) untreated patients (P < .001). After adjusting for age, gender, and comorbidities, the risk of ED visit or hospitalization was 82% lower in mAb-treated patients compared with untreated patients (95% CI, 56%-94%). CONCLUSIONS: In this diverse, real-world COVID-19 patient population, mAb treatment significantly decreased the risk of subsequent ED visit or hospitalization. Broader treatment with mAbs, including in disadvantaged patient populations, can decrease the burden on hospitals and should be facilitated in all populations in the United States to ensure health equity.

Modeling of Future COVID-19 Cases, Hospitalizations, and Deaths, by Vaccination Rates and Nonpharmaceutical Intervention Scenarios - United States, April-September 2021.

After a period of rapidly declining U.S. COVID-19 incidence during January-March 2021, increases occurred in several jurisdictions (1,2) despite the rapid rollout of a large-scale vaccination program. This increase coincided with the spread of more transmissible variants of SARS-CoV-2, the virus that causes COVID-19, including B.1.1.7 (1,3) and relaxation of COVID-19 prevention strategies such as those for businesses, large-scale gatherings, and educational activities. To provide long-term projections of potential trends in COVID-19 cases, hospitalizations, and deaths, COVID-19 Scenario Modeling Hub teams used a multiple-model approach comprising six models to assess the potential course of COVID-19 in the United States across four scenarios with different vaccination coverage rates and effectiveness estimates and strength and implementation of nonpharmaceutical interventions (NPIs) (public health policies, such as physical distancing and masking) over a 6-month period (April-September 2021) using data available through March 27, 2021 (4). Among the four scenarios, an accelerated decline in NPI adherence (which encapsulates NPI mandates and population behavior) was shown to undermine vaccination-related gains over the subsequent 2-3 months and, in combination with increased transmissibility of new variants, could lead to surges in cases, hospitalizations, and deaths. A sharp decline in cases was projected by July 2021, with a faster decline in the high-vaccination scenarios. High vaccination rates and compliance with public health prevention measures are essential to control the COVID-19 pandemic and to prevent surges in hospitalizations and deaths in the coming months.

Staffing and Capacity Planning for SARS-CoV-2 Monoclonal Antibody Infusion Facilities: A Performance Estimation Calculator Based on Discrete-Event Simulations.

Background: The COVID-19 pandemic has significantly stressed healthcare systems. The addition of monoclonal antibody (mAb) infusions, which prevent severe disease and reduce hospitalizations, to the repertoire of COVID-19 countermeasures offers the opportunity to reduce system stress but requires strategic planning and use of novel approaches. Our objective was to develop a web-based decision-support tool to help existing and future mAb infusion facilities make better and more informed staffing and capacity decisions. Materials and Methods: Using real-world observations from three medical centers operating with federal field team support, we developed a discrete-event simulation model and performed simulation experiments to assess performance of mAb infusion sites under different conditions. Results: 162,000 scenarios were evaluated by simulations. Our analyses revealed that it was more effective to add check-in staff than to add additional nurses for middle-to-large size sites with ≥2 infusion nurses; that scheduled appointments performed better than walk-ins when patient load was not high; and that reducing infusion time was particularly impactful when load on resources was only slightly above manageable levels. Discussion: Physical capacity, check-in staff, and infusion time were as important as nurses for mAb sites. Health systems can effectively operate an infusion center under different conditions to provide mAb therapeutics even with relatively low investments in physical resources and staff. Conclusion: Simulations of mAb infusion sites were used to create a capacity planning tool to optimize resource utility and allocation in constrained pandemic conditions, and more efficiently treat COVID-19 patients at existing and future mAb infusion sites.

Review of Biomarkers and Analytical Methods for Organophosphate Pesticides and Applicability to Nerve Agents.

INTRODUCTION: Recent malicious use of chemical warfare agents (CWAs) is a reminder of their severity and ongoing threat. One of the main categories of CWAs is the organophosphate (OP) nerve agents. Presently, there is an urgent need to identify and evaluate OP nerve agent biomarkers that can facilitate identification of exposed individuals post-CWA incident. While exposures to OP nerve agents may be scenario-specific, the public is commonly exposed to OP compounds through the ubiquitous use of OP pesticides, which are chemically related to nerve agents. Therefore, a systematic literature review and methodological quality assessment were conducted for OP pesticide biomarker studies to serve as a baseline to assess if these approaches may be adapted to OP nerve agent exposures. MATERIALS AND METHODS: We conducted a systematic literature review to identify biomarkers of OP pesticide exposures. English language studies of any design that reported primary data on biomarkers for exposures in nonhuman primates or adult human study participants were eligible for inclusion. Using standard criteria for assessing the completeness of reported analytical methods, the quality of study methods was critically evaluated. RESULTS: A total of 1,044 studies of biomarkers of OP pesticide exposure were identified, of which 75 articles satisfied the inclusion and exclusion criteria. These studies described 143 different analyte/sample matrix combinations: 99 host-based biomarkers, 28 metabolites, 12 pesticides, and 4 adducts. The most commonly reported biomarkers were dialkyl phosphate urinary metabolites (22 studies), blood acetylcholinesterase, and plasma butyrylcholinesterase (26 studies each). None of the assessed quality review criteria were fully addressed by all identified studies, with almost all criteria scoring less than 50%. CONCLUSION: Cholinesterase activity may have utility for identifying individuals with exposures surpassing a given threshold of OP nerve agent, but further investigation of how acetylcholinesterase and butyrylcholinesterase levels correlate with observed patient symptoms may be required to ensure accuracy of results. As CWAs and nerve agents are more readily used, more standardized reporting of biomarker measurements are needed to develop new approaches for OP nerve agent biomarkers.

Effect of an Intervention Package and Teamwork Training to Prevent Healthcare Personnel Self-contamination During Personal Protective Equipment Doffing.

BACKGROUND: More than 28 000 people were infected with Ebola virus during the 2014-2015 West African outbreak, resulting in more than 11 000 deaths. Better methods are needed to reduce the risk of self-contamination while doffing personal protective equipment (PPE) to prevent pathogen transmission. METHODS: A set of interventions based on previously identified failure modes was designed to mitigate the risk of self- contamination during PPE doffing. These interventions were tested in a randomized controlled trial of 48 participants with no prior experience doffing enhanced PPE. Contamination was simulated using a fluorescent tracer slurry and fluorescent polystyrene latex spheres (PLSs). Self-contamination of scrubs and skin was measured using ultraviolet light visualization and swabbing followed by microscopy, respectively. Doffing sessions were videotaped and reviewed to score standardized teamwork behaviors. RESULTS: Participants in the intervention group contaminated significantly fewer body sites than those in the control group (median [interquartile range], 6 [3-8] vs 11 [6-13], P = .002). The median contamination score was lower for the intervention group than the control group when measured by ultraviolet light visualization (23.15 vs 64.45, P = .004) and PLS swabbing (72.4 vs 144.8, P = .001). The mean teamwork score was greater in the intervention group (42.2 vs 27.5, P < .001). CONCLUSIONS: An intervention package addressing the PPE doffing task, tools, environment, and teamwork skills significantly reduced the amount of self-contamination by study participants. These elements can be incorporated into PPE guidance and training to reduce the risk of pathogen transmission.

Development and Comparison of Complementary Methods to Study Potential Skin and Inhalational Exposure to Pathogens During Personal Protective Equipment Doffing.

BACKGROUND: Fluorescent tracers are often used with ultraviolet lights to visibly identify healthcare worker self-contamination after doffing of personal protective equipment (PPE). This method has drawbacks, as it cannot detect pathogen-sized contaminants nor airborne contamination in subjects' breathing zones. METHODS: A contamination detection/quantification method was developed using 2-µm polystyrene latex spheres (PSLs) to investigate skin contamination (via swabbing) and potential inhalational exposure (via breathing zone air sampler). Porcine skin coupons were used to estimate the PSL swabbing recovery efficiency and limit of detection (LOD). A pilot study with 5 participants compared skin contamination levels detected via the PSL vs fluorescent tracer methods, while the air sampler quantified potential inhalational exposure to PSLs during doffing. RESULTS: Average PSL skin swab recovery efficiency was 40% ± 29% (LOD = 1 PSL/4 cm2 of skin). In the pilot study, all subjects had PSL and fluorescent tracer skin contamination. Two subjects had simultaneously located contamination of both types on a wrist and hand. However, for all other subjects, the PSL method enabled detection of skin contamination that was not detectable by the fluorescent tracer method. Hands/wrists were more commonly contaminated than areas of the head/face (57% vs 23% of swabs with PSL detection, respectively). One subject had PSLs detected by the breathing zone air sampler. CONCLUSIONS: This study provides a well-characterized method that can be used to quantitate levels of skin and inhalational contact with simulant pathogen particles. The PSL method serves as a complement to the fluorescent tracer method to study PPE doffing self-contamination.

Identifying Potential Provider and Environmental Contamination on a Clinical Biocontainment Unit Using Aerosolized Pathogen Simulants.

The Johns Hopkins Hospital created a biocontainment unit (BCU) to care for patients with highly infectious diseases while assuring healthcare worker safety. Research to date for BCU protocols and practices are based on case reports and lessons learned from patient care and exercises. This study seeks to be the first to explore the influences of healthcare worker movement and personal protective equipment (PPE) doffing on the transport of simulant pathogen particles in a BCU. A cough device released 1 µm fluorescent polystyrene beads (PSLs) in the patient room. PSL transport was then examined under 2 scenarios: (1) PSL release only, no healthcare workers; and (2) PSL release during 5-minute simulated activity by healthcare workers. Airborne PSL concentrations were quantified every second for 30 minutes per scenario by 7 optical particle sensors located throughout the BCU. PSLs were not detected in the donning room at any time nor in the doffing room during the first test scenario where no healthcare worker was present. The main difference detected between the tested scenarios was the presence of PSLs in the doffing room when healthcare workers were removing PPE, potentially due to re-aerosolization of PSLs off the exterior PPE surface or opening of the patient room door. Future work will further explore the potential for re-aerosolization of particles off of PPE during doffing. The present study provides the groundwork for a systematic method for evaluating the BCU and doffing procedures for their respective safety, and it also pilots a systematic method for evaluating potential pathogen exposure pathways for BCU healthcare workers.

Inflammation and Immune Activation in Antiretroviral-Treated Human Immunodeficiency Virus Type 1-Infected African Infants and Rotavirus Vaccine Responses.

Biomarkers of inflammation and immune activation were correlated with rotavirus vaccine responses in 68 human immunodeficiency virus type 1 (HIV-1)­infected (and 116 HIV-exposed but uninfected (HEU) African infants receiving pentavalent rotavirus vaccine (RV5) in a clinical trial. Prevaccination, HIV-1+ infants had significantly higher concentrations of interferon γ (IFNγ), interleukin1ß, interleukin 2, interleukin 6, interleukin 10 (IL-10), and soluble CD14 compared with HEU infants. Postvaccination concentrations of neutralizing antibodies to RV5 were negatively correlated with prevaccination concentrations of IL-10 (RV5 surface proteins G1 and P1) and IFNγ (G1) in the HIV-1+ infants, whereas antirotavirus immunoglobulin A (IgA) levels were not. Heightened inflammation and immune activation in HIV-1+ infants did not alter IgA responses associated with protection from rotavirus disease.

Paucity of Intact Non-Induced Provirus with Early, Long-Term Antiretroviral Therapy of Perinatal HIV Infection.

The latent reservoir is a major barrier to HIV eradication. Reservoir size is emerging as an important biomarker to assess the likelihood of HIV remission in the absence of antiretroviral therapy (ART) and may be reduced by earlier initiation of ART that restricts HIV spread into CD4+ T cells. Reservoir size is traditionally measured with a quantitative viral outgrowth assay (QVOA) that induces replication-competent HIV production through in vitro stimulation of resting CD4+ T cells. However, the recent identification of replication-intact, non-induced proviral genomes (NIPG) suggests the QVOA significantly underestimates (by 62-fold) latent reservoir size in chronically-infected adults. Whether formation and persistence of Intact, NIPG is thwarted by early ART initiation and long-term virologic suppression in perinatal infection is unclear. Here, we show that the latent reservoir in 11 early treated, long-term suppressed perinatally infected children and adolescents was not inducible by QVOA and dominated by defective, NIPG. Single genome analysis of 164 NIPG from 232 million cultured resting CD4+ T cells revealed no replication-intact, near-full length sequences. Forty-three (26%) NIPG contained APOBEC3G-mediated hypermutation, 115 (70%) NIPG contained large internal deletions, one NIPG contained nonsense mutations and indels, and 5 (3%) NIPG were assigned as "Not Evaluable" due to multiple failed sequencing attempts that precluded further classification. The lack of replication competent inducible provirus and intact NIPG in this cohort indicate early, long-term ART of perinatal infection leads to marked diminution of replication-competent HIV-1 reservoirs, creating a favorable state towards interventions aimed at virologic remission.

Measles and Rubella Seroprevalence Among HIV-infected and Uninfected Zambian Youth.

BACKGROUND: Measles and congenital rubella syndrome remain significant causes of morbidity and mortality despite available vaccines. HIV-infected youth may be at increased risk of measles because of greater waning immunity after vaccination. At a population level, they constitute a potentially large pool of susceptibles to measles and rubella. More data among HIV-infected youth in sub-Saharan Africa are needed to guide vaccination policy and control strategies. METHODS: This cross-sectional study was nested within 2 ongoing studies of malaria and HIV in Zambia. Dried blood spot cards from youth (5-15 years) in these studies from 2009 to 2013 were tested for IgG antibodies to measles and rubella viruses. HIV-uninfected youth, HIV-infected treatment-naive youth and HIV-infected youth receiving antiretroviral therapy (ART) were compared. RESULTS: A total of 617 HIV-uninfected, 144 HIV-infected treatment-naive and 128 HIV-infected youth receiving ART were included in this study. The proportion seropositive for measles virus was significantly higher among HIV-uninfected youth (92.5%) compared with HIV-infected treatment-naive youth (74.1%) and HIV-infected youth receiving ART (71.9%). No differences by age were observed. The proportion seropositive for rubella virus was significantly higher among HIV-uninfected youth (54.7%) compared with HIV-infected treatment-naive youth (41.7%) and HIV-infected youth receiving ART (49.6%), with increases observed by age for all groups. CONCLUSIONS: Measles seroprevalence was lower among HIV-infected than uninfected youth, consistent with waning immunity after measles vaccination. HIV-infected youth would benefit from revaccination. Half of all youth in rural Zambia were susceptible to rubella and may need targeting for catch-up rubella campaigns when measles-rubella vaccine is introduced.