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.

Interventions to Reduce Risk for Pathogen Spillover and Early Disease Spread to Prevent Outbreaks, Epidemics, and Pandemics.

The pathogens that cause most emerging infectious diseases in humans originate in animals, particularly wildlife, and then spill over into humans. The accelerating frequency with which humans and domestic animals encounter wildlife because of activities such as land-use change, animal husbandry, and markets and trade in live wildlife has created growing opportunities for pathogen spillover. The risk of pathogen spillover and early disease spread among domestic animals and humans, however, can be reduced by stopping the clearing and degradation of tropical and subtropical forests, improving health and economic security of communities living in emerging infectious disease hotspots, enhancing biosecurity in animal husbandry, shutting down or strictly regulating wildlife markets and trade, and expanding pathogen surveillance. We summarize expert opinions on how to implement these goals to prevent outbreaks, epidemics, and pandemics.

Consequences of Undervaccination - Measles Outbreak, New York City, 2018-2019.

BACKGROUND: Measles was declared eliminated in the United States in 2000, but the risk of outbreaks owing to international importations remains. An outbreak of measles in New York City began when one unvaccinated child returned home from Israel with measles; onset of rash occurred on September 30, 2018, 9 days after the child returned home. METHODS: We investigated suspected cases of measles by conducting interviews, reviewing medical and immunization records, identifying exposed persons, and performing diagnostic testing. Measles-mumps-rubella (MMR) vaccine (given as either MMR or measles-mumps-rubella-varicella vaccine and collectively referred to as MMR vaccine) uptake was monitored with the use of the Citywide Immunization Registry. The total direct cost to the New York City Department of Health and Mental Hygiene was calculated. RESULTS: A total of 649 cases of measles were confirmed, with onsets of rash occurring between September 30, 2018, and July 15, 2019. A majority of the patients (93.4%) were part of the Orthodox Jewish community, and 473 of the patients (72.9%) resided in the Williamsburg area of Brooklyn, New York. The median age was 3 years; 81.2% of the patients were 18 years of age or younger, and 85.8% of the patients with a known vaccination history were unvaccinated. Serious complications included pneumonia (in 37 patients [5.7%]) and hospitalization (in 49 patients [7.6%]); among the patients who were hospitalized, 20 (40.8%) were admitted to an intensive care unit. As a result of efforts to promote vaccination, the percentage of children in Williamsburg who received at least one dose of MMR vaccine increased from 79.5% to 91.1% among children 12 to 59 months of age. As of September 9, 2019, a total of 559 staff members at the Department of Health and Mental Hygiene (7% of the agency) had been involved in the measles response. The cost of the Department of Health and Mental Hygiene response was $8.4 million. CONCLUSIONS: Importation of measles and vaccination delays among young children led to an outbreak of measles in New York City. The outbreak response was resource intensive and caused serious illness, particularly among unvaccinated children.

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.

Integrating Contact Tracers Into Point-of-Care Testing Workflow to Accelerate the Tracing of People With Exposure to COVID-19, August-December 2020, New York City.

OBJECTIVES: We assessed the timeliness of contact tracing following rapid-positive COVID-19 test result at point-of-care testing (POCT) sites in New York City (NYC). DESIGN: Interviewed case-patients to elicit exposed contacts and conducted COVID-19 exposure notifications. SETTINGS: Twenty-two COVID-19 POCT sites in NYC, the 2 NYC international airports, and 1 ferry terminal. PARTICIPANTS: Case-patients with rapid-positive COVID-19 test results and their named contacts. MAIN OUTCOME MEASURES: We quantified the proportions of interviewed individuals with COVID-19 and notified contacts and assessed the timeliness between the dates of the rapid-positive COVID-19 test results and the interviews or notifications. RESULTS: In total, 11 683 individuals with rapid-positive COVID-19 test results were referred for contact tracing on the day of their diagnosis; 8878 (76) of whom were interviewed within 1 day of diagnosis, of whom 5499 (62%) named 11 486 contacts. A median of 1.24 contacts were identified from each interview. The odds of eliciting contacts were significantly higher among individuals reporting COVID-19 symptoms than among persons with no symptoms (51% vs 36%; adjusted odds ratio [aOR] = 1.37; 95% confidence interval [CI], 1.11-1.70) or living with 1 or more persons than living alone (89% vs 38%; aOR = 12.11; 95% CI, 10.73-13.68). Among the 8878 interviewed case-patients, 8317 (94%) were interviewed within 1 day of their rapid-positive COVID-19 test results and 91% of contact notifications were completed within 1 day of contact identification. The median interval from test result to interview date and from case investigation interview to contact notification were both 0 days (IQR = 0). CONCLUSIONS: The integration of contact tracers into COVID-19 POCT workflow achieved timely case investigation and contact notification. Accelerated contact tracing can be used to curb COVID-19 transmission during local outbreaks.

Bat and Lyssavirus Exposure among Humans in Area that Celebrates Bat Festival, Nigeria, 2010 and 2013.

Using questionnaires and serologic testing, we evaluated bat and lyssavirus exposure among persons in an area of Nigeria that celebrates a bat festival. Bats from festival caves underwent serologic testing for phylogroup II lyssaviruses (Lagos bat virus, Shimoni bat virus, Mokola virus). The enrolled households consisted of 2,112 persons, among whom 213 (10%) were reported to have ever had bat contact (having touched a bat, having been bitten by a bat, or having been scratched by a bat) and 52 (2%) to have ever been bitten by a bat. Of 203 participants with bat contact, 3 (1%) had received rabies vaccination. No participant had neutralizing antibodies to phylogroup II lyssaviruses, but >50% of bats had neutralizing antibodies to these lyssaviruses. Even though we found no evidence of phylogroup II lyssavirus exposure among humans, persons interacting with bats in the area could benefit from practicing bat-related health precautions.

Hospitalizations Involving an Intensive Care Unit Admission Among Patients Aged 65 Years and Older Within New York City Hospitals During 2000-2014.

OBJECTIVE: To describe hospitalizations involving an intensive care unit (ICU) admission among patients aged 65 years and older within New York City (NYC) hospitals during 2000-2014. DESIGN: Observational study using an all-payer hospital discharge dataset. SETTING: The setting was in NYC hospitals. PATIENTS: Patients aged 65 years and older admitted to an ICU within a NYC hospital during 2000-2014. INTERVENTIONS: No interventions were carried out. MEASUREMENTS AND MAIN RESULTS: We calculated the mean annual number of hospitalizations involving an ICU admission. We also examined characteristics of hospitalizations, including the occurrence of in-hospital death and principal diagnosis. There were 5,338,577 hospitalizations of patients aged ≥65 years within NYC hospitals during 2000-2014, of which 765,084 (14.3%) involved an ICU admission. The mean annual number of hospitalizations involving an ICU admission for this age group decreased from 57,938 during 2000-2002 to 45,785 during 2012-2014. The proportion of hospitalizations involving an ICU admission in which in-hospital death occurred decreased from 15.9% during 2000-2002 to 14.5% during 2012-2014. During 2000-2002, 11.6% of hospitalizations involving an ICU admission listed an "infectious" principal diagnosis, increasing to 20.7% during 2012-2014. Listing of a "cardiovascular" principal diagnosis decreased from 46.4% to 33.4% between these time periods. "Infectious" principal diagnoses accounted for 31.0% of all hospitalizations involving an ICU admission in which in-hospital death occurred during the entire study period, while "cardiovascular" principal diagnoses accounted for 21.3%. CONCLUSIONS: This investigation provides a clearer understanding of ICU utilization among patients aged 65 years and older in NYC. Ongoing monitoring is warranted given projections that the proportion of New Yorkers aged 65 years and older will increase in coming years. In particular, in light of the observed increase of infectious principal diagnoses during the study period, further investigation is needed into the role of infectious disease in causing critical illness in NYC.

Cost Comparison Between 2 Responses to Hepatitis A Virus Incidents in Restaurant Food Handlers-New York City, 2015 and 2017.

CONTEXT: While the New York City Department of Health and Mental Hygiene (DOHMH) can use agency-wide emergency activation to respond to a hepatitis A virus-infected food handler, there is a need to identify alternative responses that conserve scarce resources. OBJECTIVE: To compare the costs incurred by DOHMH of responding to a hepatitis A case in restaurant food handlers using an agency-wide emergency activation (2015) versus the cost of collaborating with a private network of urgent care clinics (2017). DESIGN: We partially evaluate the costs incurred by DOHMH of responding to a hepatitis A case in a restaurant food handler using agency-wide emergency activation (2015) with the cost of collaborating with a private network of urgent care clinics (2017) estimated for a scenario in which DOHMH incurred the retail cost of services rendered. RESULTS: Costs incurred by DOHMH for emergency activation were $65 831 ($238 per restaurant employee evaluated) of which DOHMH personnel services accounted for 85% ($55 854). Costs of collaboration would have totaled $50 914 ($253 per restaurant employee evaluated) of which personnel services accounted for 6% ($3146). CONCLUSIONS: Accounting for incident size, collaborating with the clinic network was more expensive than agency-wide emergency activation, though required fewer DOHMH personnel services.

Human Exposure to Novel Bartonella Species from Contact with Fruit Bats.

Twice a year in southwestern Nigeria, during a traditional bat festival, community participants enter designated caves to capture bats, which are then consumed for food or traded. We investigated the presence of Bartonella species in Egyptian fruit bats (Rousettus aegyptiacus) and bat flies (Eucampsipoda africana) from these caves and assessed whether Bartonella infections had occurred in persons from the surrounding communities. Our results indicate that these bats and flies harbor Bartonella strains, which multilocus sequence typing indicated probably represent a novel Bartonella species, proposed as Bartonella rousetti. In serum from 8 of 204 persons, we detected antibodies to B. rousetti without cross-reactivity to other Bartonella species. This work suggests that bat-associated Bartonella strains might be capable of infecting humans.

Human infection with a zoonotic orthopoxvirus in the country of Georgia.

During 2013, cutaneous lesions developed in two men in the country of Georgia after they were exposed to ill cows. The men had never received vaccination against smallpox. Tests of lesion material with the use of a quantitative real-time polymerase-chain-reaction assay for non-variola virus orthopoxviruses were positive, and DNA sequence analysis implicated a novel orthopoxvirus species. During the ensuing epidemiologic investigation, no additional human cases were identified. However, serologic evidence of exposure to an orthopoxvirus was detected in cows in the patients' herd and in captured rodents and shrews. A third case of human infection that occurred in 2010 was diagnosed retrospectively during testing of archived specimens that were originally submitted for tests to detect anthrax. Orthopoxvirus infection should be considered in persons in whom cutaneous lesions develop after contact with animals.

Potential Confounding of Diagnosis of Rabies in Patients with Recent Receipt of Intravenous Immune Globulin.

Rabies is an acute encephalitis that is nearly always fatal. It is caused by infection with viruses of the genus Lyssavirus, the most common of which is Rabies lyssavirus. The Council of State and Territorial Epidemiologists (CSTE) defines a confirmed human rabies case as an illness compatible with rabies that meets at least one of five different laboratory criteria.* Four of these criteria do not depend on the patient's rabies vaccination status; however, the remaining criterion, "identification of Lyssavirus-specific antibody (i.e. by indirect fluorescent antibody…test or complete [Rabies lyssavirus] neutralization at 1:5 dilution) in the serum," is only considered diagnostic in unvaccinated patients. Lyssavirus-specific antibodies include Rabies lyssavirus-specific binding immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies and Rabies lyssavirus neutralizing antibodies (RLNAs). This report describes six patients who were tested for rabies by CDC and who met CSTE criteria for confirmed human rabies because they had illnesses compatible with rabies, had not been vaccinated for rabies, and were found to have serum RLNAs (with complete Rabies lyssavirus neutralization at a serum dilution of 1:5). An additional four patients are described who were tested for rabies by CDC who were found to have serum RLNAs (with incomplete Rabies lyssavirus neutralization at a serum dilution of 1:5) despite having not been vaccinated for rabies. None of these 10 patients received a rabies diagnosis; rather, they were considered to have been passively immunized against rabies through recent receipt of intravenous immune globulin (IVIG). Serum RLNA test results should be interpreted with caution in patients who have not been vaccinated against rabies but who have recently received IVIG.

Retrospective Proteomic Analysis of Serum After Akhmeta Virus Infection: New Suspect Case Identification and Insights Into Poxvirus Humoral Immunity.

Serologic cross-reactivity, a hallmark of orthopoxvirus (OPXV) infection, makes species-specific diagnosis of infection difficult. In this study, we used a variola virus proteome microarray to characterize and differentiate antibody responses to nonvaccinia OPXV infections from smallpox vaccination. The profile of 2 case patients infected with newly discovered OPXV, Akhmeta virus, exhibited antibody responses of greater intensity and broader recognition of viral proteins and includes the B21/22 family glycoproteins not encoded by vaccinia virus strains used as vaccines. An additional case of Akhmeta virus, or nonvaccinia OPXV infection, was identified through community surveillance of individuals with no or uncertain history of vaccination and no recent infection. The results demonstrate the utility of microarrays for high-resolution mapping of antibody response to determine the nature of OPXV exposure.

Zika Virus Knowledge among Pregnant Women Who Were in Areas with Active Transmission.

We surveyed women in New York, New York, USA, who were in areas with active Zika virus transmission while pregnant. Of 99 women who were US residents, 30 were unaware of the government travel advisory to areas with active Zika virus transmission while pregnant, and 37 were unaware of their pregnancies during travel.

Prevalence and Clinical Attributes of Congenital Microcephaly - New York, 2013-2015.

Congenital Zika virus infection can cause microcephaly and other severe fetal neurological anomalies (1). To inform microcephaly surveillance efforts and assess ascertainment sources, the New York State Department of Health and the New York City Department of Health and Mental Hygiene sought to determine the prevalence of microcephaly in New York during 2013-2015, before known importation of Zika virus infections. Suspected newborn microcephaly diagnoses were identified from 1) reports submitted by birth hospitals in response to a request and 2) queries of a hospital administrative discharge database for newborn microcephaly diagnoses. Anthropometric measurements, maternal demographics, and pregnancy characteristics were abstracted from newborn records from both sources. Diagnoses were classified using microcephaly case definitions developed by CDC and the National Birth Defects Prevention Network (NBDPN) (2). During 2013-2015, 284 newborns in New York met the case definition for severe congenital microcephaly (prevalence = 4.2 per 10,000 live births). Most newborns with severe congenital microcephaly were identified by both sources; 263 (93%) were identified through hospital requests and 256 (90%) were identified through administrative discharge data. The proportions of newborns with severe congenital microcephaly who were black (30%) or Hispanic (31%) were higher than the observed proportions of black (15%) or Hispanic (23%) infants among New York live births. Fifty-eight percent of newborns with severe congenital microcephaly were born to mothers with pregnancy complications or who had in utero or perinatal infections or teratogenic exposures, genetic disorders, or family histories of birth defects.

Active Monitoring of Travelers Arriving from Ebola-Affected Countries - New York City, October 2014-April 2015.

The Ebola virus disease (Ebola) outbreak in West Africa has claimed approximately 11,300 lives (1), and the magnitude and course of the epidemic prompted many nonaffected countries to prepare for Ebola cases imported from affected countries. In October 2014, CDC and the Department of Homeland Security (DHS) implemented enhanced entry risk assessment and management at five U.S. airports: John F. Kennedy (JFK) International Airport in New York City (NYC), O'Hare International Airport in Chicago, Newark Liberty International Airport in New Jersey, Hartsfield-Jackson International Airport in Atlanta, and Dulles International Airport in Virginia (2). Enhanced entry risk assessment began at JFK on October 11, 2014, and at the remaining airports on October 16 (3). On October 21, DHS exercised its authority to direct all travelers flying into the United States from an Ebola-affected country to arrive at one of the five participating airports. At the time, the Ebola-affected countries included Guinea, Liberia, Mali, and Sierra Leone. On October 27, CDC issued updated guidance for monitoring persons with potential Ebola virus exposure (4), including recommending daily monitoring of such persons to ascertain the presence of fever or symptoms for a period of 21 days (the maximum incubation period of Ebola virus) after the last potential exposure; this was termed "active monitoring." CDC also recommended "direct active monitoring" of persons with a higher risk for Ebola virus exposure, including health care workers who had provided direct patient care in Ebola-affected countries. Direct active monitoring required direct observation of the person being monitored by the local health authority at least once daily (5). This report describes the operational structure of the NYC Department of Health and Mental Hygiene's (DOHMH) active monitoring program during its first 6 months (October 2014-April 2015) of operation. Data collected on persons who required direct active monitoring are not included in this report.

Zika Virus Surveillance and Preparedness - New York City, 2015-2016.

Zika virus has rapidly spread through the World Health Organization's Region of the Americas since being identified in Brazil in early 2015. Transmitted primarily through the bite of infected Aedes species mosquitoes, Zika virus infection during pregnancy can cause spontaneous abortion and birth defects, including microcephaly (1,2). New York City (NYC) is home to a large number of persons who travel frequently to areas with active Zika virus transmission, including immigrants from these areas. In November 2015, the NYC Department of Health and Mental Hygiene (DOHMH) began developing and implementing plans for managing Zika virus and on February 1, 2016, activated its Incident Command System. During January 1-June 17, 2016, DOHMH coordinated diagnostic laboratory testing for 3,605 persons with travel-associated exposure, 182 (5.0%) of whom had confirmed Zika virus infection. Twenty (11.0%) confirmed patients were pregnant at the time of diagnosis. In addition, two cases of Zika virus-associated Guillain-Barré syndrome were diagnosed. DOHMH's response has focused on 1) identifying and diagnosing suspected cases; 2) educating the public and medical providers about Zika virus risks, transmission, and prevention strategies, particularly in areas with large populations of immigrants from areas with ongoing Zika virus transmission; 3) monitoring pregnant women with Zika virus infection and their fetuses and infants; 4) detecting local mosquito-borne transmission through both human and mosquito surveillance; and 5) modifying existing Culex mosquito control measures by targeting Aedes species of mosquitoes through the use of larvicides and adulticides.