Evaluating completion rates of COVID-19 contact tracing surveys in New York City.

IMPORTANCE: Contact tracing is the process of identifying people who have recently been in contact with someone diagnosed with an infectious disease. During an outbreak, data collected from contact tracing can inform interventions to reduce the spread of infectious diseases. Understanding factors associated with completion rates of contact tracing surveys can help design improved interview protocols for ongoing and future programs. OBJECTIVE: To identify factors associated with completion rates of COVID-19 contact tracing surveys in New York City (NYC) and evaluate the utility of a predictive model to improve completion rates, we analyze laboratory-confirmed and probable COVID-19 cases and their self-reported contacts in NYC from October 1st 2020 to May 10th 2021. METHODS: We analyzed 742,807 case investigation calls made during the study period. Using a log-binomial regression model, we examined the impact of age, time of day of phone call, and zip code-level demographic and socioeconomic factors on interview completion rates. We further developed a random forest model to predict the best phone call time and performed a counterfactual analysis to evaluate the change of completion rates if the predicative model were used. RESULTS: The percentage of contact tracing surveys that were completed was 79.4%, with substantial variations across ZIP code areas. Using a log-binomial regression model, we found that the age of index case (an individual who has tested positive through PCR or antigen testing and is thus subjected to a case investigation) had a significant effect on the completion of case investigation - compared with young adults (the reference group,24 years old < age < = 65 years old), the completion rate for seniors (age > 65 years old) were lower by 12.1% (95%CI: 11.1% - 13.3%), and the completion rate for youth group (age < = 24 years old) were lower by 1.6% (95%CI: 0.6% -2.6%). In addition, phone calls made from 6 to 9 pm had a 4.1% (95% CI: 1.8% - 6.3%) higher completion rate compared with the reference group of phone calls attempted from 12 and 3 pm. We further used a random forest algorithm to assess its potential utility for selecting the time of day of phone call. In counterfactual simulations, the overall completion rate in NYC was marginally improved by 1.2%; however, certain ZIP code areas had improvements up to 7.8%. CONCLUSION: These findings suggest that age and time of day of phone call were associated with completion rates of case investigations. It is possible to develop predictive models to estimate better phone call time for improving completion rates in certain communities.

Elevated glucocorticoids during the ovarian follicular phase predict conception in wild female chacma baboons.

Mating related behavior during ovarian cycling can be energetically demanding and constitute a significant stressor, requiring physiological responses to mediate investment in reproduction. To better understand the proximate mechanisms underlying these responses, we examine hormonal and behavioral variation across the ovarian cycle during conceptive and nonconceptive cycles in wild female chacma baboons (Papio ursinus). We quantified immunoreactive fecal estradiol, progesterone, and cortisol metabolites for 21 adult females, and calculated activity budgets and rates of received aggression from over 5000 15-min behavioral samples. We found conception to be associated with higher concentrations of both estradiol and cortisol during the follicular phase, but no difference in progesterone between conceptive and nonconceptive cycles for either the follicular or luteal phase. While females spent less time feeding during the follicular compared to the luteal phase, we found no difference in time spent feeding, moving, or copulating between conceptive and nonconceptive cycles of the same phase. Rates of received aggression also were similar across the ovarian cycle, with no difference between conceptive and nonconceptive cycles. Finally, we found positive associations between cortisol and estradiol, indicating that glucocorticoids (GCs) do not suppress hypothalamic-pituitary-gonadal (HPG) activity and reproductive function in this context. Overall, our results suggest that elevated GCs may play an adaptive role in mobilizing energy during sexually receptive periods of ovarian cycling.

Community transmission of SARS-CoV-2 during the Delta wave in New York City.

BACKGROUND: Understanding community transmission of SARS-CoV-2 variants of concern (VOCs) is critical for disease control in the post pandemic era. The Delta variant (B.1.617.2) emerged in late 2020 and became the dominant VOC globally in the summer of 2021. While the epidemiological features of the Delta variant have been extensively studied, how those characteristics shaped community transmission in urban settings remains poorly understood. METHODS: Using high-resolution contact tracing data and testing records, we analyze the transmission of SARS-CoV-2 during the Delta wave within New York City (NYC) from May 2021 to October 2021. We reconstruct transmission networks at the individual level and across 177 ZIP code areas, examine network structure and spatial spread patterns, and use statistical analysis to estimate the effects of factors associated with COVID-19 spread. RESULTS: We find considerable individual variations in reported contacts and secondary infections, consistent with the pre-Delta period. Compared with earlier waves, Delta-period has more frequent long-range transmission events across ZIP codes. Using socioeconomic, mobility and COVID-19 surveillance data at the ZIP code level, we find that a larger number of cumulative cases in a ZIP code area is associated with reduced within- and cross-ZIP code transmission and the number of visitors to each ZIP code is positively associated with the number of non-household infections identified through contact tracing and testing. CONCLUSIONS: The Delta variant produced greater long-range spatial transmission across NYC ZIP code areas, likely caused by its increased transmissibility and elevated human mobility during the study period. Our findings highlight the potential role of population immunity in reducing transmission of VOCs. Quantifying variability of immunity is critical for identifying subpopulations susceptible to future VOCs. In addition, non-pharmaceutical interventions limiting human mobility likely reduced SARS-CoV-2 spread over successive pandemic waves and should be encouraged for reducing transmission of future VOCs.

Social status and helminth infections in female forest guenons (Cercopithecus mitis).

OBJECTIVE: When resource competition within primate social groups is effective, high-ranking individuals generally gain fitness benefits. Contrary to expectations, female Cercopithecus mitis form linear dominance hierarchies without evidence for rank-related variation in fitness-relevant measures, raising questions about the evolution of guenon social structure. Here, we test whether social status predicts gastrointestinal helminth infections, known to influence health and morbidity in other mammalian hosts. In addition, we assess whether infections contribute to stress responses as indicated by fecal glucocorticoid (fGC) levels. METHODS: We quantified infections and hormone levels in 382 fecal samples from 11 adult female Sykes' monkeys (C. m. albogularis) over four months in one wild study group at Gede Ruins, Kenya. Using a generalized estimating equations technique, we modeled the odds of infection, relative infection intensity, and fGC variation. RESULTS: High-ranking females were less likely infected with Trichuris and Trichostrongylus, had lower fecal egg counts for both taxa, and overall lower helminth richness than low-ranking females. An inverse relationship between rank and Trichuris egg counts existed also in a study population of blue monkeys (C. m. stuhlmanni), where we collected comparable data over a shorter period. Regardless of rank, lactating females were more likely than non-lactating females to be infected with Trichuris, and had higher fecal egg counts for both Trichuris and Oesophagostomum. Lastly, we report evidence that Trichuris infections exacerbated energetic stress and that food supplementation by tourists increased infection levels. CONCLUSION: Our findings suggest that high-rank may provide long-term health and energetic benefits for female C. mitis, with potential fitness implications.

Personality traits, rank attainment, and siring success throughout the lives of male chimpanzees of Gombe National Park.

Personality traits in many taxa correlate with fitness. Several models have been developed to try to explain how variation in these traits is maintained. One model proposes that variation persists because it is linked to trade-offs between current and future adaptive benefits. Tests of this model's predictions, however, are scant in long-lived species. To test this model, we studied male chimpanzees living in Gombe National Park, Tanzania. We operationalized six personality traits using ratings on 19 items. We used 37 years of behavioral and genetic data to assemble (1) daily rank scores generated from submissive vocalizations and (2) records of male siring success. We tested whether the association between two personality traits, Dominance and Conscientiousness, and either rank or reproductive success, varied over the life course. Higher Dominance and lower Conscientiousness were associated with higher rank, but the size and direction of these relationships did not vary over the life course. In addition, independent of rank at the time of siring, higher Dominance and lower Conscientiousness were related to higher siring success. Again, the size and direction of these relationships did not vary over the life course. The trade-off model, therefore, may not hold in long-lived and/or slowly reproducing species. These findings also demonstrate that ratings are a valid way to measure animal personality; they are related to rank and reproductive success. These traits could therefore be used to test alternative models, including one that posits that personality variation is maintained by environmental heterogeneity, in studies of multiple chimpanzee communities.

Correlates of bushmeat hunting among remote rural households in Gabon, Central Africa.

Hunted wild animals (i.e., bushmeat) are a main source of protein for many rural populations in the tropics, and the unsustainable harvest of these animals puts both human food security and ecosystem functioning at risk. To understand the correlates of bushmeat consumption, we surveyed 1219 households in 121 rural villages near three newly established national parks in Gabon. Through the surveys we gathered information on bushmeat consumption, income, and material assests. In addition, we quantified land cover in a 5-km radius around the village center and distance of the village center to the nearest park boundary. Bushmeat was not a source of income for most households, but it was the primary animal protein consumed. Ninety-seven percent of households consumed bushmeat at least once during a survey period of 12 days. Income or wealth, land cover, distance of village to the nearest park boundary, and level of education of the head of the household were among the factors that significantly related to the likelihood of consuming any of the 10 most commonly consumed species of bushmeat. Household size was the predictor most strongly associated with quantities of bushmeat consumed and was negatively related to consumption. Total bushmeat consumption per adult male equivalent increased as household wealth increased and decreased as distance of villages to park boundaries increased. Bushmeat consumption at the household level was not related to unit values (i.e., price estimates for a good that typically does not have a market value; estimates derived from willingness to sell or trade the good for items of known price) of bushmeat or the price of chicken and fish as potential substitutes. The median consumption of bushmeat at the village level, however, was negatively related to village mean unit values of bushmeat across all species. Our results suggest that a lack of alternative protein sources motivated even the wealthiest among surveyed households to consume bushmeat. Providing affordable, alternative protein sources to all households would likely reduce unsustainable levels of bushmeat consumption in rural Gabon.

Contact tracing reveals community transmission of COVID-19 in New York City.

Understanding SARS-CoV-2 transmission within and among communities is critical for tailoring public health policies to local context. However, analysis of community transmission is challenging due to a lack of high-resolution surveillance and testing data. Here, using contact tracing records for 644,029 cases and their contacts in New York City during the second pandemic wave, we provide a detailed characterization of the operational performance of contact tracing and reconstruct exposure and transmission networks at individual and ZIP code scales. We find considerable heterogeneity in reported close contacts and secondary infections and evidence of extensive transmission across ZIP code areas. Our analysis reveals the spatial pattern of SARS-CoV-2 spread and communities that are tightly interconnected by exposure and transmission. We find that locations with higher vaccination coverage and lower numbers of visitors to points-of-interest had reduced within- and cross-ZIP code transmission events, highlighting potential measures for curtailing SARS-CoV-2 spread in urban settings.

Contact tracing reveals community transmission of COVID-19 in New York City.

Understanding SARS-CoV-2 transmission within and among communities is critical for tailoring public health policies to local context. However, analysis of community transmission is challenging due to a lack of high-resolution surveillance and testing data. Here, using contact tracing records for 644,029 cases and their contacts in New York City during the second pandemic wave, we provide a detailed characterization of the operational performance of contact tracing and reconstruct exposure and transmission networks at individual and ZIP code scales. We find considerable heterogeneity in reported close contacts and secondary infections and evidence of extensive transmission across ZIP code areas. Our analysis reveals the spatial pattern of SARS-CoV-2 spread and communities that are tightly interconnected by exposure and transmission. We find that higher vaccination coverage and reduced numbers of visitors to points-of-interest are associated with fewer within- and cross-ZIP code transmission events, highlighting potential measures for curtailing SARS-CoV-2 spread in urban settings.

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.

Social behavior, foraging strategies, and fecal glucocorticoids in female blue monkeys (Cercopithecus mitis): potential fitness benefits of high rank in a forest guenon.

Socioecological theory predicts that aggressive feeding competition is associated with linear dominance hierarchies and reproductive advantages for high-ranking females. Female blue monkeys contest fruits and have a linear dominance hierarchy, yet previous research has shown no evidence that high-ranking females benefit from greater feeding success or fertility. Here, we assess whether individuals differ in fecal glucocorticoid (fGC) excretion and examine proximate determinants of such differences to infer potential fitness correlates of rank, using data collected from two study groups in the Kakamega Forest, Kenya. We found that higher ranking females had preferential access to fruits in both groups, although the behavioral mechanisms leading to this effect varied between groups. Despite a consistent rank difference in feeding on fruits, an overall rank effect on fGCs emerged in only one group; females of this group spent comparatively more time feeding on fruits, fruits accounted for a greater proportion of the diet, and females engaged in more frequent food-related agonism. In addition, more females in this group were lactating during a period of low fruit availability, when rank effects on fGCs were particularly strong. Regardless of fruit availability, among lactating females of both groups higher rank was associated with lower fGC levels, indicating lower energetic stress in higher ranking females when energy demands were particularly high. Individual rates of agonism, a potential psychological stressor, were unrelated to fGCs at all times. After we accounted for rates of agonism and feeding on fruits, females of one group who groomed others more had lower fGCs, suggesting that variable social coping behavior can contribute to fGC variation in some groups. This study provides the first empirical evidence that high-ranking female blue monkeys may obtain fitness benefits from their social status, by gaining priority of access to fruits during critical times in the reproductive cycle.