Strengthening the WHO Regional Office for Africa (WHO AFRO) COVID-19 vaccination information system.

This manuscript describes the process and impact of strengthening the WHO Regional Office for Africa (WHO AFRO)'s COVID-19 vaccination information system. This system plays a critical role in tracking vaccination coverage, guiding resource allocation and supporting vaccination campaign roll-out for countries in the African region. Recognising existing data management issues, including complex reporting prone to human error, compromised data quality and underutilisation of collected data, WHO AFRO introduced significant system improvements during the COVID-19 pandemic. These improvements include shifting from an Excel-based to an online Azure-based data collection system, automating data processing and validation, and expansion of collected data. These changes have led to improvements in data quality and quantity including a decrease in data non-validity, missingness, and record duplication, and expansion of data collection forms to include a greater number of data fields, offering a more comprehensive understanding of vaccination efforts. Finally, the creation of accessible information products-including an interactive public dashboard, a weekly data pack and a public monthly bulletin-has improved data use and reach to relevant partners. These resources provide crucial insights into the region's vaccination progress at national and subnational levels, thereby enabling data-driven decision-making to improve programme performance. Overall, the strengthening of the WHO AFRO COVID-19 vaccination information system can serve as a model for similar efforts in other WHO regions and contexts. The impact of system strengthening on data quality demonstrated here underscores the vital role of robust data collection, capacity building and management systems in achieving high-quality data on vaccine distribution and coverage. Continued investment in information systems is essential for effective and equitable public health efforts.

Quantifying the relationship between arboviral infection prevalence and human mobility patterns among participants of the Communities Organized to Prevent Arboviruses cohort (COPA) in southern Puerto Rico.

Human movement is increasingly being recognized as a major driver of arbovirus risk and dissemination. The Communities Organized to Prevent Arboviruses (COPA) study is a cohort in southern Puerto Rico to measure arboviral prevalence, evaluate interventions, and collect mobility data. To quantify the relationship between arboviral prevalence and human mobility patterns, we fit multilevel logistic regression models to estimate odds ratios for mobility-related predictors of positive chikungunya IgG or Zika IgM test results collected from COPA, assuming mobility data does not change substantially from year to year. From May 8, 2018-June 8, 2019, 39% of the 1,845 active participants during the study period had a positive arboviral seroprevalence result. Most (74%) participants reported spending five or more weekly hours outside of their home. A 1% increase in weekly hours spent outside the home was associated with a 4% (95% confidence interval (CI): 2-7%) decrease in the odds of testing positive for arbovirus. After adjusting for age and whether a person had air conditioning (AC) at home, any time spent in a work location was protective against arbovirus infection (32% decrease, CI: 9-49%). In fact, there was a general decreased prevalence for individuals who visited locations that were inside and had AC or screens, regardless of the type of location (32% decrease, CI: 12-47%). In this population, the protective characteristics of locations visited appear to be the most important driver of the relationship between mobility and arboviral prevalence. This relationship indicates that not all mobility is the same, with elements like screens and AC providing protection in some locations. These findings highlight the general importance of AC and screens, which are known to be protective against mosquitoes and mosquito-transmitted diseases.

Implementation of data triangulation and dashboard development for COVID-19 vaccine adverse event following immunisation (AEFI) data in Nigeria.

Nigeria began administering COVID-19 vaccines on 5 March 2021 and is working towards the WHO's African regional goal to fully vaccinate 70% of their eligible population by December 2022. Nigeria's COVID-19 vaccination information system includes a surveillance system for COVID-19 adverse events following immunisation (AEFI), but as of April 2021, AEFI data were being collected and managed by multiple groups and lacked routine analysis and use for action. To fill this gap in COVID-19 vaccine safety monitoring, between April 2021 and June 2022, the US Centers for Disease Control and Prevention, in collaboration with other implementing partners led by the Institute of Human Virology Nigeria, supported the Government of Nigeria to triangulate existing COVID-19 AEFI data. This paper describes the process of implementing published draft guidelines for data triangulation for COVID-19 AEFI data in Nigeria. Here, we focus on the process of implementing data triangulation rather than analysing the results and impacts of triangulation. Work began by mapping the flow of COVID-19 AEFI data, engaging stakeholders and building a data management system to intake and store all shared data. These datasets were used to create an online dashboard with key indicators selected based on existing WHO guidelines and national guidance. The dashboard went through an iterative review before dissemination to stakeholders. This case study highlights a successful example of implementing data triangulation for rapid use of AEFI data for decision-making and emphasises the importance of stakeholder engagement and strong data governance structures to make data triangulation successful.

CDC's COVID-19 International Vaccine Implementation and Evaluation Program and Lessons from Earlier Vaccine Introductions.

The US Centers for Disease Control and Prevention (CDC) supports international partners in introducing vaccines, including those against SARS-CoV-2 virus. CDC contributes to the development of global technical tools, guidance, and policy for COVID-19 vaccination and has established its COVID-19 International Vaccine Implementation and Evaluation (CIVIE) program. CIVIE supports ministries of health and their partner organizations in developing or strengthening their national capacities for the planning, implementation, and evaluation of COVID-19 vaccination programs. CIVIE's 7 priority areas for country-specific technical assistance are vaccine policy development, program planning, vaccine confidence and demand, data management and use, workforce development, vaccine safety, and evaluation. We discuss CDC's work on global COVID-19 vaccine implementation, including priorities, challenges, opportunities, and applicable lessons learned from prior experiences with Ebola, influenza, and meningococcal serogroup A conjugate vaccine introductions.

Outcomes after Acute Malnutrition Program Adaptations to COVID-19, Uganda, Ethiopia, and Somalia.

At the onset of the COVID-19 pandemic, protocols for community-based management of acute malnutrition (CMAM) were implemented to support continuity of essential feeding services while mitigating COVID-19 transmission. To assess correlations between adaptation timing and CMAM program indicators, we evaluated routine program data in Uganda, Ethiopia, and Somalia for children 6-59 months of age. We specifically analyzed facility-level changes in total admissions, average length of stay (ALOS), total children screened for admission, and recovery rates before and after adaptations. We found no statistically significant changes in program indicators after adaptations. For Somalia, we also analyzed child-level changes in ALOS and in weight and mid-upper arm circumference at admission and discharge. ALOS significantly increased immediately after adaptations and then decreased to preadaptation levels. We found no meaningful changes in either weight or mid-upper arm circumference at admission or discharge. These findings indicate that adapted CMAM programs can remain effective.

Household characteristics associated with surface contamination of SARS-CoV-2 and frequency of RT-PCR and viral culture positivity-California and Colorado, 2021.

While risk of fomite transmission of SARS-CoV-2 is considered low, there is limited environmental data within households. This January-April 2021 investigation describes frequency and types of surfaces positive for SARS-CoV-2 by real-time reverse transcription polymerase chain reaction (RT-PCR) among residences with ≥1 SARS-CoV-2 infection, and associations of household characteristics with surface RT-PCR and viable virus positivity. Of 1232 samples from 124 households, 27.8% (n = 342) were RT-PCR positive with nightstands (44.1%) and pillows (40.9%) most frequently positive. SARS-CoV-2 lineage, documented household transmission, greater number of infected persons, shorter interval between illness onset and sampling, total household symptoms, proportion of infected persons ≤12 years old, and persons exhibiting upper respiratory symptoms or diarrhea were associated with more positive surfaces. Viable virus was isolated from 0.2% (n = 3 samples from one household) of all samples. This investigation suggests that while SARS-CoV-2 on surfaces is common, fomite transmission risk in households is low.

Distance to public transit predicts spatial distribution of dengue virus incidence in Medellín, Colombia.

Dengue is a growing global threat in some of the world's most rapidly growing landscapes. Research shows that urbanization and human movement affect the spatial dynamics and magnitude of dengue outbreaks; however, precise effects of urban growth on dengue are not well understood because of a lack of sufficiently fine-scaled data. We analyzed nine years of address-level dengue case data in Medellin, Colombia during a period of public transit expansion. We correlate changes in the spread and magnitude of localized outbreaks to changes in accessibility and usage of public transit. Locations closer to and with a greater utilization of public transit had greater dengue incidence. This relationship was modulated by socioeconomic status; lower socioeconomic status locations experienced stronger effects of public transit accessibility and usage on dengue incidence. Public transit is a vital urban resource, particularly among low socioeconomic populations. These results highlight the importance of public health services concurrent with urban growth.

Risk-Factors for Exposure Associated With SARS-CoV-2 Detection After Recent Known or Potential COVID-19 Exposures Among Patients Seeking Medical Care at a Large Urban, Public Hospital in Fulton County, Georgia - A Cross-Sectional Investigation.

We aimed to describe frequency of COVID-19 exposure risk factors among patients presenting for medical care at an urban, public hospital serving mostly uninsured/Medicare/Medicaid clients and risk factors associated with SARS-CoV-2 infection. Consenting, adult patients seeking care at a public hospital from August to November 2020 were enrolled in this cross-sectional investigation. Saliva, anterior nasal and nasopharyngeal swabs were collected and tested for SARS-CoV-2 using RT-PCR. Participant demographics, close contact, and activities ≤14 days prior to enrollment were collected through interview. Logistic regression was used to identify risk factors associated with testing positive for SARS-CoV-2. Among 1,078 participants, 51.8% were male, 57.0% were aged ≥50 years, 81.3% were non-Hispanic Black, and 7.6% had positive SARS-CoV-2 tests. Only 2.7% reported COVID-19 close contact ≤14 days before enrollment; this group had 6.79 adjusted odds of testing positive (95%CI = 2.78-16.62) than those without a reported exposure. Among participants who did not report COVID-19 close contact, working in proximity to ≥10 people (adjusted OR = 2.17; 95%CI = 1.03-4.55), choir practice (adjusted OR = 11.85; 95%CI = 1.44-97.91), traveling on a plane (adjusted OR = 5.78; 95%CI = 1.70-19.68), and not participating in an essential indoor activity (i.e., grocery shopping, public transit use, or visiting a healthcare facility; adjusted OR = 2.15; 95%CI = 1.07-4.30) were associated with increased odds of testing positive. Among this population of mostly Black, non-Hispanic participants seeking care at a public hospital, we found several activities associated with testing positive for SARS-CoV-2 infection in addition to close contact with a case. Understanding high-risk activities for SARS-CoV-2 infection among different communities is important for issuing awareness and prevention strategies.

Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA.

The Asian tiger mosquito (Aedes albopictus) arrived in the USA in the 1980's and rapidly spread throughout eastern USA within a decade. The predicted northern edge of its overwintering distribution on the East Coast of the USA roughly falls across New York, Connecticut, and Massachusetts, where the species has been recorded as early as 2000. It is unclear whether Ae. albopictus populations have become established and survive the cold winters in these areas or are recolonized every year. We genotyped and analyzed populations of Ae. albopictus from the northeast USA using 15 microsatellite markers and compared them with other populations across the country and to representatives of the major global genetic clades to investigate their connectivity and stability. Founder effects or bottlenecks were rare at the northern range of the Ae. albopictus distribution in the northeastern USA, with populations displaying high levels of genetic diversity and connectivity along the East Coast. There is no evidence of population turnover in Connecticut during the course of three consecutive years, with consistent genetic structure throughout this period. Overall, these results support the presence of established populations of Ae. albopictus in New York, Connecticut, and Massachusetts, successfully overwintering and migrating in large numbers. Given the stability and interconnectedness of these populations, Ae. albopictus has the potential to continue to proliferate and expand its range northward under mean warming conditions of climate change. Efforts to control Ae. albopictus in these areas should thus focus on vector suppression rather than eradication strategies, as local populations have become firmly established and are expected to reemerge every summer.

Epidemiologic, Immunologic, and Virus Characteristics in Patients With Paired Severe Acute Respiratory Syndrome Coronavirus 2 Serology and Reverse-Transcription Polymerase Chain Reaction Testing.

BACKGROUND: The natural history and clinical progression of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections can be better understood using combined serological and reverse-transcription polymerase chain reaction (RT-PCR) testing. METHODS: Nasopharyngeal swabs and serum were collected at a single time-point from patients at an urban, public hospital during August-November 2020 and tested for SARS-CoV-2 using RT-PCR, viral culture, and anti-spike pan-immunoglobulin antibody testing. Participant demographics and symptoms were collected through interview. The χ 2 and Fisher exact tests were used to identify associations between RT-PCR and serology results with presence of viable virus and frequency of symptoms. RESULTS: Among 592 participants, 129 (21.8%) had evidence of SARS-CoV-2 infection by RT-PCR or serology. Presence of SARS-CoV-2 antibodies was strongly associated with lack of viable virus (P = .016). COVID-19 symptom frequency was similar for patients testing RT-PCR positive/seronegative and patients testing RT-PCR positive/seropositive. Patients testing RT-PCR positive/seronegative reported headaches, fatigue, diarrhea, and vomiting at rates not statistically significantly different from those testing RT-PCR negative/seropositive. CONCLUSIONS: While patients testing SARS-CoV-2 seropositive were unlikely to test positive for viable virus and were therefore at low risk for forward transmission, coronavirus disease 2019 (COVID-19) symptoms were common. Paired SARS-CoV-2 RT-PCR and antibody testing provides more nuanced understanding of patients' COVID-19 status.

Entomovirological Surveillance in Schools: Are They a Source for Arboviral Diseases Transmission?

Surveillance and control activities for virus-transmitting mosquitoes have primarily focused on dwellings. There is little information about viral circulation in heavily trafficked places such as schools. We collected and analyzed data to assess the presence and prevalence of dengue, chikungunya, and Zika viruses in mosquitoes, and measured Aedes indices in schools in Medellín (Colombia) between 2016-2018. In 43.27% of 2632 visits we collected Aedes adults, creating 883 pools analyzed by RT-PCR. 14.27% of pools yielded positive for dengue or Zika (infection rates of 1.75-296.29 for Aedes aegypti). Ae. aegypti was more abundant and had a higher infection rate for all studied diseases. Aedes indices varied over time. There was no association between Aedes abundance and mosquito infection rates, but the latter did correlate with cases of arboviral disease and climate. Results suggest schools are important sources of arbovirus and health agencies should include these sites in surveillance programs; it is essential to know the source for arboviral diseases transmission and the identification of the most population groups exposed to these diseases to research and developing new strategies.

Effects of Patient Characteristics on Diagnostic Performance of Self-Collected Samples for SARS-CoV-2 Testing.

We evaluated the performance of self-collected anterior nasal swab (ANS) and saliva samples compared with healthcare worker-collected nasopharyngeal swab specimens used to test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We used the same PCR diagnostic panel to test all self-collected and healthcare worker-collected samples from participants at a public hospital in Atlanta, Georgia, USA. Among 1,076 participants, 51.9% were men, 57.1% were >50 years of age, 81.2% were Black (non-Hispanic), and 74.9% reported >1 chronic medical condition. In total, 8.0% tested positive for SARS-CoV-2. Compared with nasopharyngeal swab samples, ANS samples had a sensitivity of 59% and saliva samples a sensitivity of 68%. Among participants tested 3-7 days after symptom onset, ANS samples had a sensitivity of 80% and saliva samples a sensitivity of 85%. Sensitivity varied by specimen type and patient characteristics. These findings can help physicians interpret PCR results for SARS-CoV-2.

Impact of Policy and Funding Decisions on COVID-19 Surveillance Operations and Case Reports - South Sudan, April 2020-February 2021.

Early models predicted substantial COVID-19-associated morbidity and mortality across Africa (1-3). However, as of March 2021, countries in Africa are among those with the lowest reported incidence of COVID-19 worldwide (4). Whether this reflects effective mitigation, outbreak response, or demographic characteristics, (5) or indicates limitations in disease surveillance capacity is unclear (6). As countries implemented changes in funding, national policies, and testing strategies in response to the COVID-19 pandemic, surveillance capacity might have been adversely affected. This study assessed whether changes in surveillance operations affected reporting in South Sudan; testing and case numbers reported during April 6, 2020-February 21, 2021, were analyzed relative to the timing of funding, policy, and strategy changes.* South Sudan, with a population of approximately 11 million, began COVID-19 surveillance in February 2020 and reported 6,931 cases through February 21, 2021. Surveillance data analyzed were from point of entry screening, testing of symptomatic persons who contacted an alert hotline, contact tracing, sentinel surveillance, and outbound travel screening. After travel restrictions were relaxed in early May 2020, international land and air travel resumed and mandatory requirements for negative pretravel test results were initiated. The percentage of all testing accounted for by travel screening increased >300%, from 21.1% to 91.0% during the analysis period, despite yielding the lowest percentage of positive tests among all sources. Although testing of symptomatic persons and contact tracing yielded the highest percentage of COVID-19 cases, the percentage of all testing from these sources decreased 88%, from 52.6% to 6.3% after support for these activities was reduced. Collectively, testing increased over the project period, but shifted toward sources least likely to yield positive results, possibly resulting in underreporting of cases. Policy, funding, and strategy decisions related to the COVID-19 pandemic response, such as those implemented in South Sudan, are important issues to consider when interpreting the epidemiology of COVID-19 outbreaks.

Evaluation of Unmanned Aerial Vehicles and Neural Networks for Integrated Mosquito Management of Aedes albopictus (Diptera: Culicidae).

Aedes albopictus (Skuse), an invasive disease vector, poses a nuisance and public health threat to communities in the Northeastern United States. Climate change and ongoing adaptation are leading to range expansion of this mosquito into upstate New York and other northeastern states. Organized mosquito control can suppress populations, but it is time consuming, costly, and difficult as Ae. albopictus oviposits in small, artificial, water-holding containers. Unmanned aerial vehicles (UAVs), with centimeter-resolution imaging capabilities, can aid surveillance efforts. In this work, we show that a convolutional neural network trained on images from a UAV is able to detect Ae. albopictus habitat in suburban communities, and the number of containers successfully imaged by UAV predicted the number of containers positive for mosquito larvae per home. The neural network was able to identify some, but not all, potential habitat, with up to 67% precision and 40% recall, and can classify whole properties as positive or negative for larvae 80% of the time. This combined approach of UAV imaging and neutral network analysis has the potential to dramatically increase capacity for surveillance, increasing the reach and reducing the time necessary for conventional on-the-ground surveillance methods.

Oviposition site attraction of Aedes albopictus to sites with conspecific and heterospecific larvae during an ongoing invasion in Medellín, Colombia.

BACKGROUND: Aedes aegypti and Aedes albopictus are two globally invasive vectors with similar ecological niches. Encounters between them can result in either competitive exclusion or stable co-existence, but it is unclear what drives these variable outcomes. Larval competition in favor of Ae. albopictus is a main hypothesis for the competitive exclusion of Ae. aegypti observed in some regions. However, the role of oviposition preference in determining the degree of competitive larval interactions in the field is not well understood. In this study, we used a combination of mark-release-recapture methods with ovitraps in the open-field and a semi-field cage to test whether gravid Ae. albopictus seek oviposition sites in response to the presence, species, and density of either conspecific or heterospecific Ae. aegypti larvae in the aquatic habitat. We conducted our study in Medellín, Colombia, where Ae. aegypti is a long-term resident and Ae. albopictus is a recent invader. RESULTS: In the open-field and semi-field cage experiments, gravid Ae. albopictus showed strong preference for ovitraps with larvae over those without. They consistently preferred ovitraps with higher density of conspecific (Ae. albopictus) larvae and low density of heterospecific (Ae. aegypti) larvae over traps with no larvae or high density of heterospecific (Ae. aegypti) larvae. In the semi-field cage experiment, traps with low density of Ae. albopictus were not preferred more or less than any other trap, but in the open-field experiment they were preferred over traps without larvae. CONCLUSIONS: We demonstrate, through open-field and semi-field cage experiments, that Ae. albopictus are more attracted to oviposition sites with larvae and that the combination of species and density of larvae influence attraction. This demonstrated preference could increase interspecific larval competition as Ae. albopictus actively seek containers with conspecific and heterospecific larvae. Any resulting competition with Ae. aegypti may favor one species over the other and alter the distribution or abundance of both. Because these species vary in vectorial capacity and insecticide resistance, effects of interspecific competition could ultimately impact arbovirus transmission rates and the success of vector control efforts .

Aedes albopictus (Diptera: Culicidae) on an Invasive Edge: Abundance, Spatial Distribution, and Habitat Usage of Larvae and Pupae Across Urban and Socioeconomic Environmental Gradients.

The Asian tiger mosquito [Aedes albopictus (Skuse)] is an invasive species of public health importance that is currently expanding its range in the Northeast United States. Effective Ae. albopictus control depends on a thorough understanding of factors influencing their abundance, spatial distribution, and habitat preference. We conducted a series of container surveys for Ae. albopictus larvae/pupae over 2 yr across nine sites in neighborhoods along its invasive range in southern New York. Selected sites represented a gradient of percent impervious surface and median household income. Two hypotheses were tested: 1) Ae. albopictus larval/pupal abundance increases and spatial distribution becomes less clustered as site-level median income decreases and percent impervious surface increases because of increased larval habitat quality and availability; and 2) container-level characteristics are predictive of Ae. albopictus larval/pupal infestation across a range of sites. In 2016, neither median household income nor impervious surface predicted Ae. albopictus abundance. In 2017, sites with greater impervious surface were more heavily infested by some measures. In both years, Ae. albopictus larval/pupal spatial distribution as measured by K-function was more clustered in with greater median household income. Most container characteristics were either not predictive of Ae. albopictus or varied between years. Based on the variability of predictive container characteristics, we conclude that identification of key containers is not useful in this region. However, Ae. albopictus can be nonhomogenously distributed or abundant based on income level and impervious surface. Improved control of immatures should consider these regional predictors of Ae. albopictus populations.

Hermit crab response to a visual threat is sensitive to looming cues.

Prior work in our lab has shown that an expanding image on a computer screen elicits a hiding response in the Caribbean terrestrial hermit crab (Coenobita clypeatus). We conducted two experiments to identify what properties of the expanding stimulus contribute to its effectiveness as a visual threat. First we found that an expanding geometric star evoked a strong hiding response while a contracting or full-sized stationary star did not. A second experiment revealed that the more quickly the stimulus expanded the shorter the latency to hide. These findings suggest that the anti-predator response to looming stimulus relies heavily on visual cues relating to the manner of approach. The simulated visual threat on a computer screen captures key features of a real looming object that elicits hiding behavior in crabs in the wild.

Zika and chikungunya: mosquito-borne viruses in a changing world.

The reemergence and growing burden of mosquito-borne virus infections have incited public fear and growing research efforts to understand the mechanisms of infection-associated health outcomes and to provide better approaches for mosquito vector control. While efforts to develop therapeutics, vaccines, and novel genetic mosquito-control technologies are underway, many important underlying ecological questions remain that could significantly enhance our understanding and ability to predict and prevent transmission. Here, we review the current knowledge about the transmission ecology of two recent arbovirus invaders, the chikungunya and Zika viruses. We introduce the viruses and mosquito vectors, highlighting viral biology, historical routes of transmission, and viral mechanisms facilitating rapid global invasion. In addition, we review factors contributing to vector global invasiveness and transmission efficiency. We conclude with a discussion of how human-induced biotic and abiotic environmental changes facilitate mosquito-borne virus transmission, emphasizing critical gaps in understanding. These knowledge gaps are tremendous; much of our data on basic mosquito ecology in the field predate 1960, and the mosquitoes themselves, as well as the world they live in, have substantially changed. A concerted investment in understanding the basic ecology of these vectors, which serve as the main drivers of pathogen transmission in both wildlife and human populations, is now more important than ever.