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1.
Clin Infect Dis ; 75(1): e1000-e1010, 2022 Aug 24.
Article in English | MEDLINE | ID: covidwho-1816032

ABSTRACT

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic caused severe disruptions to healthcare in many areas of the world, but data remain scarce for sub-Saharan Africa. METHODS: We evaluated trends in hospital admissions and outpatient emergency department (ED) and general practitioner (GP) visits to South Africa's largest private healthcare system during 2016-2021. We fit time series models to historical data and, for March 2020-September 2021, quantified changes in encounters relative to baseline. RESULTS: The nationwide lockdown on 27 March 2020 led to sharp reductions in care-seeking behavior that persisted for 18 months after initial declines. For example, total admissions dropped 59.6% (95% confidence interval [CI], 52.4-66.8) during home confinement and were 33.2% (95% CI, 29-37.4) below baseline in September 2021. We identified 3 waves of all-cause respiratory encounters consistent with COVID-19 activity. Intestinal infections and non-COVID-19 respiratory illnesses experienced the most pronounced declines, with some diagnoses reduced 80%, even as nonpharmaceutical interventions (NPIs) relaxed. Non-respiratory hospitalizations, including injuries and acute illnesses, were 20%-60% below baseline throughout the pandemic and exhibited strong temporal associations with NPIs and mobility. ED attendances exhibited trends similar to those for hospitalizations, while GP visits were less impacted and have returned to pre-pandemic levels. CONCLUSIONS: We found substantially reduced use of health services during the pandemic for a range of conditions unrelated to COVID-19. Persistent declines in hospitalizations and ED visits indicate that high-risk patients are still delaying seeking care, which could lead to morbidity or mortality increases in the future.


Subject(s)
COVID-19 , Pandemics , COVID-19/epidemiology , Communicable Disease Control , Delivery of Health Care , Emergency Service, Hospital , Humans , Patient Acceptance of Health Care , Retrospective Studies , SARS-CoV-2 , South Africa/epidemiology
2.
Science ; 376(6593): eabn4947, 2022 05 06.
Article in English | MEDLINE | ID: covidwho-1741547

ABSTRACT

We provide two methods for monitoring reinfection trends in routine surveillance data to identify signatures of changes in reinfection risk and apply these approaches to data from South Africa's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic to date. Although we found no evidence of increased reinfection risk associated with circulation of the Beta (B.1.351) or Delta (B.1.617.2) variants, we did find clear, population-level evidence to suggest immune evasion by the Omicron (B.1.1.529) variant in previously infected individuals in South Africa. Reinfections occurring between 1 November 2021 and 31 January 2022 were detected in individuals infected in all three previous waves, and there has been an increase in the risk of having a third infection since mid-November 2021.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Humans , Reinfection/epidemiology , SARS-CoV-2/genetics , South Africa/epidemiology
3.
medRxiv; 2021.
Preprint in English | MedRxiv | ID: ppcovidwho-293547

ABSTRACT

Objective To examine whether SARS-CoV-2 reinfection risk has changed through time in South Africa, in the context of the emergence of the Beta, Delta, and Omicron variantsDesign Retrospective analysis of routine epidemiological surveillance dataSetting Line list data on SARS-CoV-2 with specimen receipt dates between 04 March 2020 and 27 November 2021, collected through South Africa’s National Notifiable Medical Conditions Surveillance SystemParticipants 2,796,982 individuals with laboratory-confirmed SARS-CoV-2 who had a positive test result at least 90 days prior to 27 November 2021. Individuals having sequential positive tests at least 90 days apart were considered to have suspected reinfections.Main outcome measures Incidence of suspected reinfections through time;comparison of reinfection rates to the expectation under a null model (approach 1);empirical estimates of the time-varying hazards of infection and reinfection throughout the epidemic (approach 2)Results 35,670 suspected reinfections were identified among 2,796,982 individuals with laboratory-confirmed SARS-CoV-2 who had a positive test result at least 90 days prior to 27 November 2021. The number of reinfections observed through the end of the third wave was consistent with the null model of no change in reinfection risk (approach 1). Although increases in the hazard of primary infection were observed following the introduction of both the Beta and Delta variants, no corresponding increase was observed in the reinfection hazard (approach 2). Contrary to expectation, the estimated hazard ratio for reinfection versus primary infection was lower during waves driven by the Beta and Delta variants than for the first wave (relative hazard ratio for wave 2 versus wave 1: 0.75 (CI95: 0.59–0.97);for wave 3 versus wave 1: 0.71 (CI95: 0.56–0.92)). In contrast, the recent spread of the Omicron variant has been associated with a decrease in the hazard coefficient for primary infection and an increase in reinfection hazard coefficient. The estimated hazard ratio for reinfection versus primary infection for the period from 1 November 2021 to 27 November 2021 versus wave 1 was 2.39 (CI95: 1.88–3.11).Conclusion Population-level evidence suggests that the Omicron variant is associated with substantial ability to evade immunity from prior infection. In contrast, there is no population-wide epidemiological evidence of immune escape associated with the Beta or Delta variants. This finding has important implications for public health planning, particularly in countries like South Africa with high rates of immunity from prior infection. Urgent questions remain regarding whether Omicron is also able to evade vaccine-induced immunity and the potential implications of reduced immunity to infection on protection against severe disease and death.Box 1What is already known on this topicWhat is already known on this topicPrior infection with SARS-CoV-2 is estimated to provide at least an 80% reduction in infection risk (1,2).Laboratory-based studies indicate reduced neutralization by convalescent serum for the Beta and Delta variants relative to wild type virus (3–6);however, the impact of these reductions on risk of reinfection is not known, and laboratory assessments of Omicron are still underway.What this study addsWhat this study addsWe provide two methods for monitoring reinfection trends to identify signatures of changes in reinfection risk.We find no evidence of increased reinfection risk associated with circulation of Beta or Delta variants compared to the ancestral strain in routine epidemiological data from South Africa.In contrast, we find clear, population-level evidence to suggest substantial immune evasion by the Omicron variant.One sentence summary Analysis of routine surveillance data from South Africa suggests that, in contrast to the Beta and Delta, the Omicron variant of SARS-CoV-2 demonstrates substantial population-level evidence for evasion of immunity from prior infection.Competing Interest StatementAll authors have completed the ICMJE uniform isclosure form. CC and AvG have received funding from Sanofi Pasteur in the past 36 months. JRCP and KM serve on the Ministerial Advisory Committee on COVID-19 of the South African National Department of Health. The authors have declared no other relationships or activities that could appear to have influenced the submitted work.Funding StatementThis work was supported by the South African Department of Science and Innovation and the National Research Foundation and the Wellcome Trust (grant number 221003/Z/20/Z) in collaboration with the Foreign, Commonwealth and Development Office, United Kingdom.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:This study has received ethical clearance from University of the Witwatersrand (Clearance certificate number M210752, formerly M160667) and approval under reciprocal review from Stellenbosch University (Project ID 19330, Ethics Reference Number N20/11/074_RECIP_WITS_M160667_COVID-19).I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesData and code will be made available at https://github.com/jrcpulliam/reinfections. The following data are included in the repository: - Counts of reinfections and primary infections by province, age group (5-year bands), and sex (M, F, U) - Daily time series of primary infections and suspected reinfections by specimen receipt date (national) - Model output: posterior samples from the MCMC fitting procedure and simulation results Requests for additional data must be made in writing to the National Institute for Communicable Diseases, South Africa. https://github.com/jrcpulliam/reinfections

4.
PLoS Biol ; 19(6): e3001307, 2021 06.
Article in English | MEDLINE | ID: covidwho-1278163

ABSTRACT

More than 1.6 million Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) tests were administered daily in the United States at the peak of the epidemic, with a significant focus on individual treatment. Here, we show that objective-driven, strategic sampling designs and analyses can maximize information gain at the population level, which is necessary to increase situational awareness and predict, prepare for, and respond to a pandemic, while also continuing to inform individual treatment. By focusing on specific objectives such as individual treatment or disease prediction and control (e.g., via the collection of population-level statistics to inform lockdown measures or vaccine rollout) and drawing from the literature on capture-recapture methods to deal with nonrandom sampling and testing errors, we illustrate how public health objectives can be achieved even with limited test availability when testing programs are designed a priori to meet those objectives.


Subject(s)
Epidemiological Monitoring , Pandemics , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Testing , Humans , Pandemics/prevention & control , Public Health , Resource Allocation , SARS-CoV-2/isolation & purification , Sentinel Surveillance , United States/epidemiology
5.
Clin Infect Dis ; 72(9): 1642-1644, 2021 05 04.
Article in English | MEDLINE | ID: covidwho-1216617

ABSTRACT

Countries such as South Africa have limited intensive care unit (ICU) capacity to handle the expected number of patients with COVID-19 requiring ICU care. Remdesivir can prevent deaths in countries such as South Africa by decreasing the number of days people spend in ICU, therefore freeing up ICU bed capacity.


Subject(s)
COVID-19 , Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , COVID-19/drug therapy , Humans , Intensive Care Units , SARS-CoV-2 , South Africa/epidemiology
6.
Open Forum Infect Dis ; 8(3): ofab040, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1057871

ABSTRACT

BACKGROUND: Dexamethasone and remdesivir have the potential to reduce coronavirus disease 2019 (COVID)-related mortality or recovery time, but their cost-effectiveness in countries with limited intensive care resources is unknown. METHODS: We projected intensive care unit (ICU) needs and capacity from August 2020 to January 2021 using the South African National COVID-19 Epi Model. We assessed the cost-effectiveness of (1) administration of dexamethasone to ventilated patients and remdesivir to nonventilated patients, (2) dexamethasone alone to both nonventilated and ventilated patients, (3) remdesivir to nonventilated patients only, and (4) dexamethasone to ventilated patients only, all relative to a scenario of standard care. We estimated costs from the health care system perspective in 2020 US dollars, deaths averted, and the incremental cost-effectiveness ratios of each scenario. RESULTS: Remdesivir for nonventilated patients and dexamethasone for ventilated patients was estimated to result in 408 (uncertainty range, 229-1891) deaths averted (assuming no efficacy [uncertainty range, 0%-70%] of remdesivir) compared with standard care and to save $15 million. This result was driven by the efficacy of dexamethasone and the reduction of ICU-time required for patients treated with remdesivir. The scenario of dexamethasone alone for nonventilated and ventilated patients requires an additional $159 000 and averts 689 [uncertainty range, 330-1118] deaths, resulting in $231 per death averted, relative to standard care. CONCLUSIONS: The use of remdesivir for nonventilated patients and dexamethasone for ventilated patients is likely to be cost-saving compared with standard care by reducing ICU days. Further efforts to improve recovery time with remdesivir and dexamethasone in ICUs could save lives and costs in South Africa.

7.
medRxiv ; 2020 Sep 27.
Article in English | MEDLINE | ID: covidwho-807378

ABSTRACT

Background South Africa recently experienced a first peak in COVID-19 cases and mortality. Dexamethasone and remdesivir both have the potential to reduce COVID-related mortality, but their cost-effectiveness in a resource-limited setting with scant intensive care resources is unknown. Methods We projected intensive care unit (ICU) needs and capacity from August 2020 to January 2021 using the South African National COVID-19 Epi Model. We assessed cost-effectiveness of 1) administration of dexamethasone to ventilated patients and remdesivir to non-ventilated patients, 2) dexamethasone alone to both non-ventilated and ventilated patients, 3) remdesivir to non-ventilated patients only, and 4) dexamethasone to ventilated patients only; all relative to a scenario of standard care. We estimated costs from the healthcare system perspective in 2020 USD, deaths averted, and the incremental cost effectiveness ratios of each scenario. Results Remdesivir for non-ventilated patients and dexamethasone for ventilated patients was estimated to result in 1,111 deaths averted (assuming a 0-30% efficacy of remdesivir) compared to standard care, and save $11.5 million. The result was driven by the efficacy of the drugs, and the reduction of ICU-time required for patients treated with remdesivir. The scenario of dexamethasone alone to ventilated and non-ventilated patients requires additional $159,000 and averts 1,146 deaths, resulting in $139 per death averted, relative to standard care. Conclusions The use of dexamethasone for ventilated and remdesivir for non-ventilated patients is likely to be cost-saving compared to standard care. Given the economic and health benefits of both drugs, efforts to ensure access to these medications is paramount.

8.
Proc Biol Sci ; 287(1932): 20201405, 2020 08 12.
Article in English | MEDLINE | ID: covidwho-711780

ABSTRACT

Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.


Subject(s)
Coronavirus Infections/epidemiology , Coronavirus Infections/transmission , Immunity, Herd , Models, Theoretical , Pneumonia, Viral/epidemiology , Pneumonia, Viral/transmission , COVID-19 , Child , Coronavirus Infections/immunology , Coronavirus Infections/prevention & control , Disease Eradication , Family Characteristics , Humans , Pandemics/prevention & control , Pneumonia, Viral/immunology , Pneumonia, Viral/prevention & control , Schools , Seroepidemiologic Studies
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