Detection and quantification of sars-cov-2 wastewater treatment plants from different cities in chile, towards to a permanent sentinel surveillance.

Background: The quantification of SARS-CoV-2 in wastewater is a tool that allows determining the trend of viral circulation in a particular geographical area. Aim(s): To quantify the SARS-CoV-2 virus in 15 wastewater treatment plants in different Chilean cities to establish a comparison with the variables of: I) Active cases per 100,000 inhabitants;ii) daily positivity (novel cases);and iii) phases of the lockdown strategy. Method(s): SARS-CoV-2 was concentrated from wastewater samples. To obtain the number of virus genomes per liter, absolute quantification was performed using qRT-PCR. Result(s): Between January and June 2021, 253 samples were processed, all of which were positive for the presence of the virus. Likewise, it will be determined that the rate of active cases per 100,000 inhabitants is the variable that best fits the trends obtained with the quantification of the viral load in wastewater. Conclusion(s): The quantification of SARS- CoV-2 in wastewater as a continuous strategy is an efficient tool to determine the trend of the viral circulation in a delimited geographical area and, combined with genomic surveillance, it can constitute an ideal sentinel surveillance alert on future outbreaks.Copyright © 2022, Sociedad Chilena de Infectologia. All rights reserved.

Respiratory syncytial virus surge in 2022 caused by lineages already present before the COVID-19 pandemic.

In 2022, Austria experienced a severe respiratory syncytial virus (RSV) epidemic with an earlier-than-usual start (Weeks 35/2021-45/2022) and increased numbers of pediatric patients in emergency departments. This surge came 2 years after a season with no cases detected as a result of coronavirus disease 2019 nonpharmaceutical interventions. We analyzed epidemiologic patterns and the phylodynamics of RSV based on approximately 30 800 respiratory specimens collected year-round over 10 years from ambulatory and hospitalized patients from 248 locations in Austria. Genomic surveillance and phylogenetic analysis of 186 RSV-A and 187 RSV-B partial glycoprotein sequences collected from 2018 to 2022 revealed that the 2022/2023 surge was driven by RSV-B in contrast to the surge in the 2021/2022 season that was driven by RSV-A. Whole-genome sequencing and phylodynamic analysis indicated that the RSV-B strain GB5.0.6a was the predominant genotype in the 2022/2023 season and emerged in late 2019. The results provide insight into RSV evolution and epidemiology that will be applicable to future monitoring efforts with the advent of novel vaccines and therapeutics.

Pan-Respiratory Disease Surveillance in Southeast Asia: Past, Present and Future

The Global Influenza Surveillance and Response System (GISRS) was established by WHO in 1952 to conduct surveillance for influenza to inform strain selection for seasonal vaccines and to monitor for influenza pandemics. In 2016 WHO initiated a pilot project to add RSV to influenza surveillance platforms;this was disrupted by the SARS CoV-2 pandemic, and SARS CoV-2 was the first pathogen to be incorporated into influenza sentinel surveillance on a wide scale. This resulted in a "GISRS-plus" surveillance network for influenza and SARS CoV-2 that is now being standardized by WHO. In the wake of the SARS CoV-2 pandemic, there is global interest and funding to support pan-respiratory disease surveillance, which could result in expanding influenza/SARS CoV-2 surveillance platforms to include other pathogens and enhancing event- and indicator-based surveillance. Challenges with expanding sentinel surveillance include overburdening sentinel surveillance systems, reduced number of samples collected and loss of data quality for influenza and SARS CoV-2;thus, other types of surveillance for respiratory diseases might also be considered. This talk describes CDC-supported influenza surveillance platforms in Southeast Asia and recent successes and challenges in adding SARS CoV-2 to this surveillance. It discusses potential risks and benefits to GISRS-plus surveillance created by including other pathogens. Finally, it discusses decision-making steps on which methods to use for collecting data on respiratory viruses.Copyright © 2023

COVID-19 impact on EuroTravNet infectious diseases sentinel surveillance in Europe.

BACKGROUND: The COVID-19 pandemic resulted in a sharp decline of post-travel patient encounters at the European sentinel surveillance network (EuroTravNet) of travellers' health. We report on the impact of COVID-19 on travel-related infectious diseases as recorded by EuroTravNet clinics. METHODS: Travelers who presented between January 1, 2019 and September 30, 2021 were included. Comparisons were made between the pre-pandemic period (14 months from January 1, 2019 to February 29, 2020); and the pandemic period (19 months from March 1, 2020 to September 30, 2021). RESULTS: Of the 15,124 visits to the network during the 33-month observation period, 10,941 (72%) were during the pre-pandemic period, and 4183 (28%) during the pandemic period. Average monthly visits declined from 782/month (pre-COVID-19 era) to 220/month (COVID-19 pandemic era). Among non-migrants, the top-10 countries of exposure changed after onset of the COVID-19 pandemic; destinations such as Italy and Austria, where COVID-19 exposure peaked in the first months, replaced typical travel destinations in Asia (Thailand, Indonesia, India). There was a small decline in migrant patients reported, with little change in the top countries of exposure (Bolivia, Mali). The three top diagnoses with the largest overall decreases in relative frequency were acute gastroenteritis (-5.3%), rabies post-exposure prophylaxis (-2.8%), and dengue (-2.6%). Apart from COVID-19 (which rose from 0.1% to 12.7%), the three top diagnoses with the largest overall relative frequency increase were schistosomiasis (+4.9%), strongyloidiasis (+2.7%), and latent tuberculosis (+2.4%). CONCLUSIONS: A marked COVID-19 pandemic-induced decline in global travel activities is reflected in reduced travel-related infectious diseases sentinel surveillance reporting.

A Novel Ontological Approach to Track Social Determinants of Health in Primary Care

The associated morbidity and mortality from COVID-19 and the public health response to prevent the spread of the virus has repeatedly demonstrated the significant impact of social determinants of health (SDoH) and social inequities on health outcomes. Social prescriptions are interventions aimed at tackling SDoH. In 2019, NHS-England committed to support the use of social prescribing across England. NHS-England commissioned the Oxford-Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) sentinel network to monitor the distribution of social prescribing services within English primary care and, within that, monitor the impact of the COVID-19 pandemic response on SDoH. To track incidence of people presenting to primary care with SDoH-related issues, we implemented an ontological approach to curate SDoH indicators in computerised medical records (CMR) using the Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT). These indicators were then extracted from the RCGP-RSC sentinel network database to present weekly incidence rates per 10,000 people to assess the impact of the pandemic on these SDoH. Pre- versus peri-pandemic, we observed an increase in the recording of several of our SDoH indicators;namely issues related to homelessness, unemployment, mental health, harmful substance use and financial difficulties. As far as we are aware, this is the first time that routinely collected primary care CMR data has been utilised for the monitoring and surveillance of SDoH and demonstrates the feasibility of this approach for future surveillance. © 2022, Springer Nature Switzerland AG.

Community Health Nurses' Role in Genetic Sequencing: A Prospect for Health Team Preparedness Against Covid-19

Genetic sequencing is a scientific process of reading genetic material using advanced technology. Through genetic sequencing, we can better comprehend super-spreader events and outbreaks, and strengthen national public health responses. A better understanding of the transmission of viruses, the severity of patient illness, and mortality rates can be gained by combining this information with that from the IDSP and patient reports. Connecting the dots between the data and the host's genetics, immunology, clinical outcomes, and risk factors is also possible. Many roadblocks must be overcome before raw sequence data can be put to direct clinical application. Since DNA sequencing has so many potential applications in the field of nursing, it ought to be a required topic for students in the profession. Group wellness Preparing patients for procedures, identifying those most at risk, doing sentinel surveillance, and conducting in-depth studies are all areas in which nurses can be of assistance. The goals of this paper are twofold: (1) to present the notion of genetic sequencing and (2) to highlight the role of Community health nurses. To reduce the impact of pandemics and endemics and improve nursing care, Western countries are seeing an uptick in the participation of nurse scientists in genetic sequencing;the case of newborn screening provides a particularly apt example.Copyright © 2023, Institute of Medico-legal Publication. All rights reserved.

The impact of influenza viruses and influenza vaccination coverage in Italy in the 2021-2022 season: the InfluNet integrated surveillance system and the introduced news

Introduction: In Italy, the InfluNet integrated influenza surveillance system, during the 2021-2022 season, in the middle of the SARS-CoV-2 pandemic, was adequately modified and strengthened to support the monitoring of the spread of the SARS-CoV-2 virus. The present work aims to describe the impact of the 2021-2022 flu season on the Italian population, also in the light of the changes introduced in the InfluNet surveillance system. For a complete assessment of the impact of influenza viruses, the influenza vaccination coverage achieved during the season was also evaluated. Materials and methods: InfluNet is based on a network of sentinel physicians made up of general practitioners and pediatricians, recruited by the Italian Regions, who report cases of Influenza Like Illness (ILI) observed among their patients. Sentinel physicians (sentinel flow) and other doctors working in hospitals (hospital flow) also collaborate in the collection of biological samples for the identification of circulating viruses. To evaluate the impact of ILI on the Italian population, overall incidence (per 1,000 assisted) was calculated, as well as stratified by age group. Furthermore, vaccination coverage (%) in the total Italian population and by age group were also calculated. Results: The 2021-2022 season was characterized by limited circulation of flu viruses. At the end of December 2021, the incidence of ILI reached an initial peak of 5.16 cases per 1,000 assisted. A second peak was identified, also very contained, at the end of March 2022, equal to 5.25 cases per 1,000 assisted. Virological surveillance made it possible to characterize the two waves: the first was mainly supported by the circulation of respiratory syncytial virus, especially in children under five years of age, while the second wave was characterized by the circulation of influenza viruses. 14.4% of clinical samples analyzed by InfluNet network laboratories were found to be positive for influenza viruses. Among the positive samples, 82.9% belonged to the A(H3N2) virus and 29.3% tested positive for SARS-CoV-2. Vaccination coverage in the 2021-2022 season, which decreased in all age groups, was 20.5% in the general population and 58.1% in the elderly population. Discussion and conclusions: In Italy, the 2021-2022 season marked the return of the circulation of influenza viruses after the start of the COVID-19 pandemic, though in a moderate intensity. The InfluNet surveillance system is turning into a respiratory virus monitoring system and has made it possible, this season, to characterize the trend of ILI and to attribute the increase in cases to the various respiratory viruses. Vaccination coverage decreased compared to the previous season. The adoption of preventive measures in recent seasons has profoundly changed the epidemiology of ILI and respiratory viruses in terms of intensity and seasonality. The accumulation of susceptible population, especially in the pediatric age groups, has partly allowed a greater circulation of respiratory viruses in the 2021-2022 season and will also presumably allow it in future seasons. It is therefore increasingly important to vaccinate against flu to reduce serious complications and deaths, especially in the fragile population.

Analysis of epidemic characteristics and related factors of norovirus in diarrhea patients in Guangxi, 2015-2020

To analyze the epidemiological characteristics and related factors of norovirus in Guangxi from 2015 to 2020, and to provide scientific recommendations for norovirus prevention and control. Methods The foodborne diseases surveillance data were collected from 11 sentinel hospitals through the National Foodborne Disease Monitoring and Reporting System from 2015 to 2020. R software with version 4.0.3 was used for descriptive and statistical analysis, including epidemic curve, chi-square test, and trend chi-square and so on. Logistic regression was used to analyze norovirus-related factors, OR values and 95% confidence intervals were calculated respectively with the statistical test level of P < 0.05. Results There were 1 008 norovirus cases detected, with a detection rate of 12.75% (1 008/7 903). Children with age less than 5 years (OR=1.43, 95%CI: 1.13-1.82) and patients at age 20-45 (OR=1.45, 95%CI: 1.13-1.87) were high risk population. The detection rate was higher in autumn (OR=1.29, 95%CI: 1.08-1.53) but lower in summer (OR=0.67, 95%CI: 0.55-0.80). In addition, the tourist area (Guilin City) presented a higher detection rate than other areas (OR=1.41, 95%CI: 1.10-1.80). Aquatic products (OR=1.40, 95%CI: 1.03-1.91), meat and dairy products (OR=1.31, 95%CI: 1.06-1.61) were high-risk foods for norovirus infection. The prevention and control policies of COVID-19 can reduce the possibility of norovirus by 61% (OR=0.39, 95%CI: 0.31-0.49) showed a declining trend (Trend X2=85.33, P < 0.001). In addition, prolonged visit time can lead to 19%-23% decrease in the detection rate of norovirus (OR24-48 hours=0.81, 95%CI: 0.70-0.95;OR>48 hours=0.77, 95%CI: 0.63-0.93). Conclusions The epidemic of norovirus presented seasonal and regional distribution in Guangxi with a declining detection rate trend in diarrhea patients during recent 6 years. Young children were high-risk population in infection norovirus. The intake of seafood can increase the risk of norovirus infection. The prevention and control policies of COVID-19 can sharply decrease the possibility of infection norovirus. The monitoring of key foods such as seafood should be strengthened, and the early screening of suspected cases should be taken. The norovirus monitoring should be improved to ensure the health of the population.

Varying numbers of acute wheezing cases presenting to paediatric emergency during the COVID-19 pandemic

Acute wheezing in children due to underlying asthma or airways hypersensitivity (including allergic rhinitis) can be exacerbated by infectious and non-infectious causes. Of the infectious causes, seasonal rhinoviruses are the most common. Particulate airborne pollutants (PM2.5, PM10) can also play a role. During the COVID-19 pandemic, we observed changes in the pattern of paediatric emergency department (PED) presentations for acute wheezing. In this retrospective observational cohort study, data was extracted for children (0-18 years) presenting to the PED during 2018-2021, whose illness episodes were coded as 'asthma' or 'viral induced wheeze', along with their age, ethnicity, gender, and clinical outcomes, from hospital databases. The Figure shows the number of PED presentations for acute wheezing during 2018-2021, with annotations to explain the changing patterns. The number of cases presenting during the pandemic years 2020-2021 were similar to those in 2018-2019 in the same months, except for April-June 2020, July-August 2020, November 2020 and January-March 2021. Decreases in PED presentations coincided with periods of enforced national and local lockdowns, likely due to parental reluctance to expose their children to SARS-CoV-2 in a hospital setting. In addition, fluctuations in the incidence of rhinovirus infections, as shown by national sentinel surveillance data, likely contributed to changes in case numbers. Higher and lower incidence of rhinovirus infections tended to increase and decrease the number of presentations, respectively. Surprisingly, the level of airborne particulates (PM2.5, PM10) showed no correlation with these PED presentations for acute wheezing.

A Novel Ontological Approach to Estimate Inequalities and Underuse of Social Prescriptions for Mental Health in Primary Care in England

Mental health conditions are a significant contributor to morbidity and mortality and cost an estimated £1.6 trillion per year globally. The COVID-19 pandemic and its associated lockdowns have contributed to increases in common mental health problems (CMHP) like depression. Bodies in the UK recommend the use of non-medical interventions like social prescriptions to support individuals suffering from CMHP. In 2019, NHS-England committed to support the use of social prescribing across England. Despite this commitment, the proportion of eligible individuals with a CMHP that actually receive a social prescription remains unknown. To overcome this knowledge gap, a novel ontological approach was used to estimate the proportion of individuals with a CMHP that received a social prescription, disaggregated by different attributes (region, ethnicity, socio-economic status, sex, age) across a four-year period from 2017–2020. We discovered two general trends. First, there was a 1.4-fold increase in the presentation of individuals, across all attributes, to primary care with a CMHP across the four-year period analysed. There was also marked variation in the presentation to primary care with a CMHP based on different attributes (2020 variation figures - regions: 2.8-fold;ethnicity: 1.8-fold;socio-economic status: 1.4-fold;sex: 1.7-fold;age: 3.9-fold). Second, despite an increase in the use of social prescribing for mental health, there was still substantial underuse of it across all attributes in England (the highest percentage seen across all attributes in 2020 was 14%). The general trends revealed through our analyses provide valuable insights that can help to inform both policy and practice to address variation, health inequalities as well as to proactively design and implement appropriate services. © 2022, Springer Nature Switzerland AG.

Influenza During the 2010-2020 Decade in the United States: Seasonal Outbreaks and Vaccine Interventions.

The 10 years between the last influenza pandemic and start of the severe acute respiratory syndrome coronavirus 2 pandemic have been marked by great advances in our ability to follow influenza occurrence and determine vaccine effectiveness (VE), largely based on widespread use of the polymerase chain reaction assay. We examine the results, focusing mainly on data from the United States and inactivated vaccines. Surveillance has expanded, resulting in increased ability to characterize circulating viruses and their impact. The surveillance has often confirmed previous observations on timing of outbreaks and age groups affected, which can now be examined in greater detail. Selection of strains for vaccines is now based on enhanced viral characterization using immunologic, virologic, and computational techniques not previously available. Vaccine coverage has been largely stable, but VE has remained modest and, in some years, very low. We discuss ways to improve VE based on existing technology while we work toward supraseasonal vaccines.

Increased cases of influenza C virus in children and adults in Austria, 2022.

Sentinel surveillance of influenza-like illnesses revealed an increase in the cases of influenza C virus in children and adults in Austria, 2022, compared to previous years, following one season (2020/2021), wherein no influenza C virus was detected. Whole-genome sequencing revealed no obvious genetic basis for the increase. We propose that the reemergence is explained by waning immunity from lack of community exposure due to restrictions intended to limit severe acute respiratory syndrome coronavirus 2 spread in prior seasons, pending further investigation.

Adverse events following first and second dose COVID-19 vaccination in England, October 2020 to September 2021: a national vaccine surveillance platform self-controlled case series study.

BackgroundPost-authorisation vaccine safety surveillance is well established for reporting common adverse events of interest (AEIs) following influenza vaccines, but not for COVID-19 vaccines.AimTo estimate the incidence of AEIs presenting to primary care following COVID-19 vaccination in England, and report safety profile differences between vaccine brands.MethodsWe used a self-controlled case series design to estimate relative incidence (RI) of AEIs reported to the national sentinel network, the Oxford-Royal College of General Practitioners Clinical Informatics Digital Hub. We compared AEIs (overall and by clinical category) 7 days pre- and post-vaccination to background levels between 1 October 2020 and 12 September 2021.ResultsWithin 7,952,861 records, 781,200 individuals (9.82%) presented to general practice with 1,482,273 AEIs, 4.85% within 7 days post-vaccination. Overall, medically attended AEIs decreased post-vaccination against background levels. There was a 3-7% decrease in incidence within 7 days after both doses of Comirnaty (RI: 0.93; 95% CI: 0.91-0.94 and RI: 0.96; 95% CI: 0.94-0.98, respectively) and Vaxzevria (RI: 0.97; 95% CI: 0.95-0.98). A 20% increase was observed after one dose of Spikevax (RI: 1.20; 95% CI: 1.00-1.44). Fewer AEIs were reported as age increased. Types of AEIs, e.g. increased neurological and psychiatric conditions, varied between brands following two doses of Comirnaty (RI: 1.41; 95% CI: 1.28-1.56) and Vaxzevria (RI: 1.07; 95% CI: 0.97-1.78).ConclusionCOVID-19 vaccines are associated with a small decrease in medically attended AEI incidence. Sentinel networks could routinely report common AEI rates, contributing to reporting vaccine safety.

Adapting an integrated acute respiratory infections sentinel surveillance to the COVID-19 pandemic requirements, Egypt, 2020-2022.

Objectives: In Egypt, an integrated surveillance for acute respiratory infections (ARIs) was established in 2016 to identify the causes of ARIs. The surveillance system includes 19 governmental hospitals. In response to the coronavirus disease 2019 (COVID-19) pandemic, the World Health Organisation (WHO) requested surveillance adaptation to address the emerging challenges. This study aims to describe the experience in Egypt of adapting ARI surveillance to the COVID-19 pandemic. Methods: WHO case definitions were used to identify patients with ARIs. Nasopharyngeal/oropharyngeal swabs were collected for SARS-CoV-2 and influenza testing. Demographic and clinical information were obtained by interviewing patients at the hospitals. During the COVID-19 pandemic, the first two outpatients daily and every fifth admitted patient were enrolled in the study. To determine the status of ARIs in Egypt during the pandemic, patient demographic, clinical and laboratory data from 2020 to 2022 were obtained and descriptive analyses were performed. Results: Overall, 18,160 patients were enrolled in the study, including 7923 (43.6%) seen at outpatient clinics and 10,237 (56.4%) inpatients. Of the study participants, 6453 (35.5%) tested positive for ARIs, including 5620 (87.1%) for SARS-CoV-2, 781 (12.1%) for influenza and 52 (0.8%) for SARS-CoV-2/influenza coinfection. SARS-CoV-2 was the cause for 95.3% of admitted patients and 65.4% of outpatients. Influenza subtypes included A/H3 (55.7%), Influenza-B (29.1%) and H1/pdm09 (14.2%). Compared with influenza, SARS-CoV-2 tended to infect the elderly, in warm weather and in urban governorates, and resulted in more hospitalisations, longer hospital stays and higher case fatalities (16.3% vs 6.6%, p < 0.001). Conclusions: ARI surveillance in Egypt was successfully adapted to the COVID-19 pandemic and effectively described the clinical characteristics and severity of circulating viruses. Surveillance reported the re-emergence of influenza with a severe course and high fatality. Surveillance is essential for monitoring the activity of respiratory viruses with the aim of guiding clinical management, including preventative and control measures.

Representativeness, Vaccination Uptake, and COVID-19 Clinical Outcomes 2020-2021 in the UK Oxford-Royal College of General Practitioners Research and Surveillance Network: Cohort Profile Summary.

BACKGROUND: The Oxford-Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) is one of Europe's oldest sentinel systems, working with the UK Health Security Agency (UKHSA) and its predecessor bodies for 55 years. Its surveillance report now runs twice weekly, supplemented by online observatories. In addition to conducting sentinel surveillance from a nationally representative group of practices, the RSC is now also providing data for syndromic surveillance. OBJECTIVE: The aim of this study was to describe the cohort profile at the start of the 2021-2022 surveillance season and recent changes to our surveillance practice. METHODS: The RSC's pseudonymized primary care data, linked to hospital and other data, are held in the Oxford-RCGP Clinical Informatics Digital Hub, a Trusted Research Environment. We describe the RSC's cohort profile as of September 2021, divided into a Primary Care Sentinel Cohort (PCSC)-collecting virological and serological specimens-and a larger group of syndromic surveillance general practices (SSGPs). We report changes to our sampling strategy that brings the RSC into alignment with European Centre for Disease Control guidance and then compare our cohort's sociodemographic characteristics with Office for National Statistics data. We further describe influenza and COVID-19 vaccine coverage for the 2020-2021 season (week 40 of 2020 to week 39 of 2021), with the latter differentiated by vaccine brand. Finally, we report COVID-19-related outcomes in terms of hospitalization, intensive care unit (ICU) admission, and death. RESULTS: As a response to COVID-19, the RSC grew from just over 500 PCSC practices in 2019 to 1879 practices in 2021 (PCSC, n=938; SSGP, n=1203). This represents 28.6% of English general practices and 30.59% (17,299,780/56,550,136) of the population. In the reporting period, the PCSC collected >8000 virology and >23,000 serology samples. The RSC population was broadly representative of the national population in terms of age, gender, ethnicity, National Health Service Region, socioeconomic status, obesity, and smoking habit. The RSC captured vaccine coverage data for influenza (n=5.4 million) and COVID-19, reporting dose one (n=11.9 million), two (n=11 million), and three (n=0.4 million) for the latter as well as brand-specific uptake data (AstraZeneca vaccine, n=11.6 million; Pfizer, n=10.8 million; and Moderna, n=0.7 million). The median (IQR) number of COVID-19 hospitalizations and ICU admissions was 1181 (559-1559) and 115 (50-174) per week, respectively. CONCLUSIONS: The RSC is broadly representative of the national population; its PCSC is geographically representative and its SSGPs are newly supporting UKHSA syndromic surveillance efforts. The network captures vaccine coverage and has expanded from reporting primary care attendances to providing data on onward hospital outcomes and deaths. The challenge remains to increase virological and serological sampling to monitor the effectiveness and waning of all vaccines available in a timely manner.

Incorporating COVID-19 into Acute Febrile Illness Surveillance Systems, Belize, Kenya, Ethiopia, Peru, and Liberia, 2020-2021.

Existing acute febrile illness (AFI) surveillance systems can be leveraged to identify and characterize emerging pathogens, such as SARS-CoV-2, which causes COVID-19. The US Centers for Disease Control and Prevention collaborated with ministries of health and implementing partners in Belize, Ethiopia, Kenya, Liberia, and Peru to adapt AFI surveillance systems to generate COVID-19 response information. Staff at sentinel sites collected epidemiologic data from persons meeting AFI criteria and specimens for SARS-CoV-2 testing. A total of 5,501 patients with AFI were enrolled during March 2020-October 2021; >69% underwent SARS-CoV-2 testing. Percentage positivity for SARS-CoV-2 ranged from 4% (87/2,151, Kenya) to 19% (22/115, Ethiopia). We show SARS-CoV-2 testing was successfully integrated into AFI surveillance in 5 low- to middle-income countries to detect COVID-19 within AFI care-seeking populations. AFI surveillance systems can be used to build capacity to detect and respond to both emerging and endemic infectious disease threats.

Interdisciplinary Informatics to Support Primary Care Sentinel Surveillance of Respiratory Infectious Disease Including COVID-19: Donabedian Evaluation.

The Oxford-Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) is one of Europe's oldest sentinel systems, providing sentinel surveillance since 1967. We report the interdisciplinary informatics required to run such a system. We used the Donabedian framework to describe the interdisciplinary informatics roles that support the structures, processes and outcomes of the RSC. Over the course of the COVID-19 pandemic University, RCGP, information technology specialists, SQL developers, analysts, practice liaison team, network member primary care providers, and their registered patients have nearly quadrupled the size of the RSC from working with 5 million to 19 million peoples pseudonymised health data. We have produced outputs used by the UK Health Security Agency to describe the epidemiology of COVID-19 and report vaccine effectiveness. We have also supported a trial of community-based therapies for COVID-19 and other observational studies. The home of the primary care sentinel surveillance network is with a clinical informatics research group. Interdisciplinary informatics teamwork was required to support primary care sentinel surveillance; such teams can accelerate the scale, scope and digital maturity of surveillance systems as demonstrated by the RSC across the COVID-19 pandemic.

Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in three Kenyan referral hospitals

Introduction/ Background: The high proportion of SARS-CoV-2 infections that remain undetected presents a challenge to tracking the progress of the pandemic and implementing control measures in Kenya. Pregnant women represent a sentinel sero-surveillance population as they routinely supply blood samples at their first antenatal care visit. Methods: We determined the prevalence of IgG to SARS-CoV-2 in residual blood samples from mothers attending antenatal care services at 3 referral hospitals in Kenya (Kilifi County Hospital, Kenyatta National Hospital and Busia County Referral Hospital). We used a validated IgG ELISA for SARS-Cov-2 spike protein and adjusted the results for assay sensitivity and specificity. We then used mixture models to estimate true cumulative exposure in the context of waning IgG titres over time. Results: In Kenyatta National Hospital, Nairobi, adjusted seroprevalence in August 2020 was 50% (95% CI 42.7- 58.0) but had decreased to 32% (26.2-38.4) in February 2021. In Kilifi County Hospital, seroprevalence increased from 1% (95% CI 0.04-4.7) in September 2020 to 23% in March 2021. Only 7% of women reported past symptoms. Further results from Nairobi, Busia and Kilifi up until October 2021 and the results of the mixture modelling will be available by the 30th November 2021. Impact: Residual blood samples from antenatal care visits represent an efficient sentinel surveillance population for sero-surveillance activities. The sero-surveillance estimates from this group can be compared with those from blood donors and other sentinel populations to identify high-risk groups. Conclusion: There has been substantial, unobserved transmission of SARS-CoV-2 in parts of Nairobi, Busia and Kilifi Counties. Due to the length of time since the beginning of the pandemic, repeated cross-sectional surveys are now difficult to interpret without the use of models to account for sero-reversion.

New networks in improving mortality surveillance beyond COVID-19, 2021

Introduction/ Background: Excess mortality reports suggest underreporting of COVID-19 related deaths, as routine surveillance utilizes mainly in-facility data. SARS-CoV-2 postmortem testing (PMT) for home deaths from natural causes has been implemented in South Africa. We provide information to highlight the critical role of morticians in improving mortality surveillance in South Africa. Methods: Sentinel surveillance was implemented in three Districts to support SARS-CoV-2 PMT and reporting in two provinces of South Africa. A repository of out of-facility natural deaths was compiled using mortuary registers from public and private sectors, with multiple stakeholder involvement. Deaths were linked to cumulative COVID-19 laboratory test data and case linelists. Data from August 2020 to October 2021 were analyzed to assess the contribution of community COVID-19 related deaths to the overall reported mortality. Results: A total of 8,254 COVID-19 related deaths were reported, comprising of 70% (n=5,751) hospital and 30% (n=2,503) community deaths. Most of the deaths were females (57.5%;n=4,742) and 60 years and older (61.5%;n=5,079). Of the 2,503 community deaths, 47% (n=1,184) were tested prior to death and 53% (n=1,319) post-mortem. Overall, reporting of COVID-19 related deaths markedly improved by 16% (1,319/8,254) with engagement and additional reporting of data from post-mortem testing. Impact: Morticians play a critical role in COVID-19 mortality surveillance, providing the much-needed sociodemographic information and vital to the handling and transport of corpses to health facilities for specimen collection. Conclusion: The number of reported COVID-19 related deaths was enhanced by linking mortuary registers with laboratory test data and case line lists. Expansion of this model to all mortuaries, across the districts in South Africa, could be a vital component of efforts to improve community-based surveillance.

SARS-CoV-2 cases reported from long-term residential facilities (care homes) in South Africa: A retrospective cohort study

Introduction/ Background: Long-term care facilities (LTCFs) experienced a large burden of SARS-CoV-2 due the COVID-19 pandemic. The purpose of this study was to describe the temporal trends as well as the characteristics and risk factors for mortality among residents and staff testing positive for SARS-CoV-2 in LTCFs across South Africa. Methods: We implemented a retrospective cohort analysis of SARS-CoV-2 positive cases in LTCFs across South Africa from 5 March 2020- 31 July 2021. We analysed 45 LTCFs from the DATCOV sentinel surveillance system in South Africa. Outbreaks in LTCFs were defined as large if more than one third of residents and staff had been infected or there were more than 20 cases that were epidemiologically linked. Multivariable logistic regression was used to assess risk factors for mortality amongst LTCF residents. Results: Total of 2,324 SARS-CoV-2 cases were reported;1,504 (65%) were residents and 820 (35%) staff. Ten (26%) reported one outbreak and 29 (74%) reported more than one outbreak, while 15 (38%) reported small outbreaks and 24 (62%) large outbreaks. There were 1,259 cases during the first COVID-19 wave, 362 during wave two, and 299 during wave three. Among residents, 9% died and among staff 0.5% died. Factors associated with mortality among residents were age 40-59 years, 60-79 years and ≥80 years compared to <40 years. Compared to pre-wave 1, there was a lower risk of mortality across waves. Impact: There is currently very little literature on the impact of COVID-19 in LTCFs in low- and middle-income countries (LMIC). This study will impact by adding knowledge to SARS-CoV-2 in LTCFs in a LMIC. Conclusion: Sentinel LTCFs in South Africa shows an encouraging trend of decreasing numbers of outbreaks, cases, and risk for mortality since the first wave. LTCFs have likely learnt from international experience and adopted national protocols, including improved measures to limit transmission and early and appropriate clinical care.