Contact tracing in NYC
The NYC Take a look at & Hint Corps initiative was launched in June 202020. Established as an operation to offer contact tracing, testing, and assets to help isolation and quarantine, the contact tracing program was built-in with a set of intervention efforts designed to restrict morbidity and mortality from COVID-19 in NYC (Supplementary Data). Contact tracing was carried out by means of telephone calls and textual content messages, able to reaching most residents of NYC. Particularly, contact tracers made telephone calls to confirmed instances and symptomatic contacts to conduct a case investigation. For kids beneath 18 years previous, dad and mom or authorized guardians have been contacted. Details about shut contacts throughout the infectious interval was elicited throughout the interview, and reported shut contacts have been then notified about their standing of publicity by means of telephone calls or textual content messages and are inspired to get examined. Each confirmed/most likely instances and their shut contacts have been monitored each day at some stage in their quarantine.
We analyzed knowledge obtained from case investigations and COVID-19 testing outcomes (molecular and antigen) collected between 1 October 2020 and 10 Could 2021 (Supplementary Fig. 1, Supplementary Data). Throughout this era, 691,834 confirmed and possible instances have been reported to the New York Metropolis Division of Well being and Psychological Hygiene (DOHMH)21. The circulating strains of SARS-CoV-2 in NYC have been dominated by the index virus pressure; nevertheless, the Iota (B.1.526) and Alpha (B.1.1.7) variants steadily changed the index virus throughout the spring of 2021 (Supplementary Fig. 2). After excluding instances residing in residential congregate settings, instances have been despatched to the NYC Take a look at & Hint Corps for contact tracing. Amongst these instances, 644,029 have been reached by tracers and 450,415 accomplished an interview. In complete, 779,011 contacts with confirmed and possible instances have been self-reported through case investigations, of whom 20.9% (162,659/779,011) have been subsequently examined. The general positivity charge amongst examined exposures is 55.8%. Nonetheless, as contaminated people have been extra more likely to search assessments, the precise secondary assault charge ought to be decrease. We additional disaggregated testing outcomes for various publicity varieties (healthcare facility contact, dwelling well being aide, family member, intimate associate, giant gathering contact, different shut proximity, office contact) (Supplementary Fig. 3). The positivity charge was highest for family members and lowest for office contacts. The median time from specimen assortment to reporting outcomes to DOHMH was 2 days. 97% of index sufferers have been referred to as by tracers inside two days of reporting to DOHMH (Fig. 1a) and 68.4% of contacts have been referred to as the day of reporting to the Take a look at & Hint group (Fig. 1b). Amongst examined contacts, 66.6% sought testing inside one week of notification (Fig. 1c). For traced symptomatic infections, 86.7% have been examined after symptom onset, and 13.3% have been examined earlier than symptom improvement (Fig. 1d).
a–d The distributions of: a time between reporting date for index instances and being referred to as by contact tracers; b time between calling index instances and notifying uncovered individuals; c time between notifying uncovered individuals and specimen sampling of notified people who have been examined; d time from symptom onset to specimen sampling for symptomatic COVID infections. A unfavorable worth implies that testing preceded symptom onset. Age distributions of index instances (e) and self-reported contacts (f). The contact mixing matrix (g) exhibits the whole variety of exposures amongst age teams reported throughout the research interval.
Adults aged 20 to 49 years previous constituted the vast majority of index instances (Fig. 1e), a discovering in settlement with the age distribution of confirmed infections in america22. Self-reported contacts have been extra uniformly distributed among the many inhabitants beneath 50 years previous (Fig. 1f). The age-stratified contact matrix highlights extra frequent interactions amongst people of comparable age and inter-generation mixing inside the family (Fig. 1g), a sample additionally noticed in different international locations23.
Publicity and transmission networks
We reconstructed the self-reported publicity community on the particular person stage for the research interval. The publicity community was extremely fragmented, with 947,042 people in 242,486 disjoint clusters. Cluster measurement confirmed appreciable heterogeneity (Fig. 2a), as did the variety of contacts reported by every index case (Fig. 2b). We visualize a number of giant publicity clusters in Fig. 2c, color-coded by the house borough of every particular person. Publicity clusters exhibit various buildings starting from hub-and-spoke networks with a single spreader to networks with a number of spreaders. Over half of the clusters proven in Fig. 2c have been in Queens and Brooklyn. Inside these giant publicity clusters in Fig. 2c, 1195 index sufferers (59.4%) reported contacts dwelling in the identical borough, however 817 (40.6%) cross-borough contacts have been additionally recorded.
a, b The distributions of cluster measurement and variety of shut contacts reported by every index case within the publicity community. Publicity clusters with greater than 35 people are visualized in (c). The publicity community is undirected. Index instances and reported shut contacts are related. Node measurement is proportional to the variety of related people. Colours point out the house location of every particular person (5 boroughs in NYC, exterior NYC, and unknown). The distributions of cluster measurement and the variety of secondary instances within the transmission community are proven in (d) and (e), respectively. f Visualizes transmission clusters with greater than six contaminated people. Node measurement represents the variety of secondary instances. Arrows point out the path of transmission.
We moreover reconstructed transmission chains between index instances and their shut contacts who have been confirmed constructive in laboratory assessments (molecular and antigen). Because of asymptomatic and pre-symptomatic shedding24,25,26, index instances weren’t essentially the supply of infections in these putative transmission occasions. To deduce the path of transmission, we estimated the an infection date of lab-positive instances. For symptomatic instances, an infection date was estimated utilizing an empirical incubation interval distribution obtained from a previous research18; for asymptomatic instances, we used specimen assortment date to estimate an infection date utilizing a mannequin of viral load dynamics coupled with a Bayesian inference (Supplementary Fig. 4)27. Particularly, for every index case and shut contact pair, we estimated their an infection occasions utilizing symptom onset date or specimen assortment date. The path of transmission was then decided by the estimated an infection occasions—the person contaminated earlier is the infector and the person contaminated later is the infectee. We sampled an ensemble of attainable transmission networks appropriate with the estimated chronological order of infections. For every sampled transmission community, we computed the chance of observing the community given transmission chances throughout age teams, estimated utilizing the check and hint knowledge (Supplementary Desk 1, Supplementary Fig. 5). The reconstructed community was chosen because the one which maximizes the chance among the many ensemble of attainable transmission networks. We additional carried out sensitivity analyses demonstrating that the community reconstruction is strong to potential bias of the incubation interval distribution28 (Supplementary Data). Extra particulars on the transmission community reconstruction are offered within the Supplementary Data.
In the course of the research interval, we recognized 58,474 potential transmission clusters fashioned by exposures that resulted in lab-confirmed infections. On common, these transmission clusters had a imply measurement of two.3 people, representing 19.6% (135,478/691,834) recorded instances throughout the research interval. Nonetheless, transmission cluster measurement and the variety of secondary instances linked to every index case had giant variance (Fig. 2nd, e)—solely 0.2% of transmission clusters concerned greater than 6 infections. The most important recognized transmission cluster consisted of 12 instances, and the utmost variety of secondary instances for a single index case was 7. Transmission clusters with at the least 6 infections are visualized in Fig. 2f.
To quantify the spatial unfold of SARS-CoV-2 in NYC at superb geographical scales, we mapped publicity and transmission networks throughout modified ZIP code tabulation areas (MODZCTAs, known as ZIP codes hereafter; Fig. 3a, b). Amongst 72,191 transmission occasions the place place of residence was recognized, 7826 (10.8%) included a number of ZIP codes. Amongst these cross-ZIP code transmission occasions, solely 2536 (32.4%) occurred between neighboring ZIP code areas, indicating that almost all of cross-ZIP code transmission drove non-local illness unfold. For 2187 cross-borough transmission occasions, solely 48 (2.2%) have been between neighboring ZIP code areas. We noticed a number of native clusters of ZIP codes that have been tightly interconnected by publicity and transmission, centered round places with excessive neighborhood prevalence. Infections in these high-prevalence ZIP code clusters have been linked to self-reported contacts in close by and much places (Fig. 3a), which can have facilitated the unfold of COVID-19 throughout town (Fig. 3b). Among the many cross-ZIP code transmission chains, we examined distributions of index instances who initiated transmission (Fig. 3c) and the contaminated contacts (Fig. 3d) throughout ZIP codes. A definite skew within the distribution means that sure ZIP codes have been extra concerned within the spatial unfold of COVID-19. Geographically, most cross-ZIP code transmission occasions occurred inside 10 km; nevertheless, long-distance transmission as much as 40 km was additionally evident (Fig. 3e).
a, b The exposures and transmission occasions throughout ZIP codes in NYC recognized from contact tracing knowledge. Arrows point out path of publicity (from index instances to reported shut contacts) and transmission (from index infections to contaminated contacts). Arrow thickness signifies the variety of exposures and transmission occasions. ZIP code space shade represents the cumulative variety of confirmed instances throughout the research interval (yellow to crimson—low to excessive). To higher visualize, publicity hyperlinks with lower than 30 occasions and transmission hyperlinks with <2 occasions should not proven on the maps. For cross-ZIP code transmission occasions, the distributions of index infections and contaminated contacts throughout ZIP code areas are introduced in c and d. e The distribution of distance between dwelling ZIP codes of index infections and contaminated contacts in cross-ZIP code transmission occasions. The inhabitants weighted centroids for ZIP code areas have been used to compute the gap.
Analysis of intervention measures
In the course of the interval from October 2020 to March 2021, a dynamic zone-based management technique was adopted in New York State to restrict viral unfold in communities with excessive case development charges whereas avoiding undue hurt to the financial system29. Three tiers of zones (yellow, orange, and crimson) have been recognized based mostly on a set of metrics, collectively outlined by check positivity charge, hospital admissions per capita, and hospital capability29,30. Native restrictions on enterprise and companies have been imposed based mostly on zone situations. Compliance to those restrictions might be mirrored by the variety of people visiting points-of-interest (POIs, e.g., eating places, grocery shops, gyms, and bars) in every ZIP code. In December 2020, vaccines turned accessible to the inhabitants at highest danger for extreme outcomes related to COVID-19 in NYC and have been subsequently accessible to all eligible people over 15 years previous throughout early April 2021. With the help of the detailed contact tracing knowledge, we evaluated the influence of those public well being interventions on neighborhood transmission of SARS-CoV-2 in NYC.
We assessed the associations of the numbers of non-household within- and cross-ZIP code transmission occasions throughout NYC with demographic, socioeconomic, illness surveillance, vaccination protection, and human mobility options (Supplementary Data, Supplementary Figs. 6–7). Right here cross-ZIP code transmission occasions embody each instructions, i.e., transmission for which both infector or infectee lived in a sure ZIP code. As non-household transmission contributed to the enlargement of SARS-CoV-2 exterior the family, we centered on 4642 non-household transmission occasions, representing 7% of all transmission occasions. We used aggregated foot visitors information derived from cell phone knowledge31 documenting weekly numbers of POI guests in every ZIP code as an indicator of human mobility and compliance with the zone-based native restrictions (Supplementary Data, Supplementary Fig. 7). We used conditional autoregressive (CAR) fashions32 to evaluate the results of the above components on within- and cross-ZIP code transmission (Fig. 4). Particularly, for each within- and cross-ZIP code transmission, we fitted Poisson generalized linear combined fashions (GLMM) with random results and CAR priors to account for the inherent spatial-temporal autocorrelation in illness transmission knowledge32,33 (Supplementary Data, Supplementary Figs. 8–9).
Incidence charge ratios (exponentiated coefficients) for non-household within-ZIP code transmission and cross-ZIP code transmission are proven for 12 covariates in a and b, respectively (Deviance data criterion, DIC = 6342 for a and DIC = 12,644 for b). Coefficients have been estimated utilizing a Poisson generalized linear combined mannequin controlling for spatial-temporal autocorrelations. We used the log-transformed inhabitants because the offset within the regression mannequin. Covariates have been standardized and are proven on the y-axis. The incidence charge ratio quantifies the multiplicative change within the variety of transmission occasions per every covariate enhance of 1 customary deviation, controlling for different covariates. The violin plots present the distributions of incidence charge ratios. Black dots and horizontal black traces spotlight the median estimates and 95% CIs. Distributions in a and b have been obtained utilizing (n={{{{mathrm{20,000}}}}}) MCMC samples of the posterior estimates.
We discovered that larger vaccination protection and fewer POI guests have been related to diminished non-household within- and cross-ZIP code transmission in the identical week (Fig. 4). Estimates of coefficients are offered in Supplementary Desk 2. The mannequin identifies a robust impact of vaccination on SARS-CoV-2 transmission: throughout the early section of vaccine rollout that aligns with the research interval, a 12.5% newly vaccinated inhabitants was related to reductions of 28.0% (95% CI: 14.0%–40.0%) and 14.8% (1.7%–26.4%) for within- and cross-ZIP code non-household transmission occasions, respectively. This marginal profit could diminish for larger vaccine protection as we anticipate the impact is nonlinear when the vaccinated inhabitants is close to 100%. In distinction, a 78.1% enhance of POI guests per capita (ratio of the variety of POI guests to the inhabitants of every ZIP code) was related to will increase of 9.6% (0.3%–19.3%) and 14.4% (8.7%–20.2%) for within- and cross-ZIP code transmission exterior households, respectively. Within the foot visitors knowledge, the POI class with the most important variety of guests was eating places and bars. It’s attainable, however not recognized, whether or not gathering in these locations could contribute extra to cross-ZIP code transmission than to within-ZIP code transmission. We additional discovered that each within- and cross-ZIP code transmission had sturdy constructive associations with log weekly instances per capita. A 13.5% enhance of log weekly instances per capita was related to will increase of 158.8% (126.5%–196.4%) and 117.3% (97.7%–137.9%) for non-household within- and cross-ZIP code transmission. Increased proportion of Hispanic residents and decrease cumulative instances per capita have been related to larger non-household transmission (see power of impact in Supplementary Desk 2). For cross-ZIP code transmission, cumulative instances per capita had a stronger impact than vaccination and POI guests (Fig. 4b, Supplementary Desk 2), indicating that prior infections could end in diminished cross-ZIP code transmission in places with the next assault charge. These findings reveal how well being inequities associated to COVID-19 manifest throughout NYC communities. Outcomes additionally point out that selling vaccination and capability limits or non permanent limits on native companies, colleges, and different POIs in high-prevalence communities have been efficient in lowering SARS-CoV-2 transmission in NYC. These findings have been corroborated with an alternate random-effect mannequin (Supplementary Data) and testing of impact lags of 1 week and two weeks (Supplementary Figs. 10–12). Findings have been additionally discovered sturdy to attainable diminished response charge involved tracing amongst kids and aged (Supplementary Fig. 13).
