Quantifying How Different Clinical Presentations, Levels of Severity, and Healthcare Attendance Shape the Burden of Influenza-associated Illness: A Modeling Study From South Africa

Comparing adults with severe SARS-CoV-2 or influenza infection: South Africa, 2016-2021

Background

Comparisons of the characteristics of individuals hospitalised with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or seasonal influenza in low-to middle-income countries with high human immunodeficiency virus (HIV) prevalence are limited.

Objectives

Determine the epidemiological differences with those hospitalised with influenza or SARS-CoV-2 infection.

Method

We investigated hospitalised individuals ≥18 years of age testing positive for seasonal influenza (2016-2019) or SARS-CoV-2 (2020-2021). We used random effects multivariable logistic regression, controlling for clustering by site, to evaluate differences among adults hospitalised with influenza or SARS-CoV-2 infection.

Results

Compared to individuals with influenza, individuals with SARS-CoV-2 infection were more likely to be diabetic (adjusted odds ratio [aOR]: 1.70, 95% confidence interval [CI]: 1.11-2.61) or die in hospital (aOR: 2.57, 95% CI: 1.61-4.12). Additionally, those with SARS-CoV-2 infection were less likely to be living with HIV (not immunosuppressed) (aOR: 0.50, 95% CI: 0.34-0.73) or living with HIV (immunosuppressed) (aOR: 0.27, 95% CI: 0.18-0.39) compared to not living with HIV and less likely to be asthmatic (aOR: 0.21, 95% CI: 0.13-0.33) rather than those living with influenza.

Conclusion

Individuals hospitalised with SARS-CoV-2 had different characteristics to individuals hospitalised with influenza before the coronavirus disease 2019 (COVID-19) pandemic. Risk factors should be considered in health management especially as we move into an era of co-circulation of SARS-CoV-2 and influenza pathogens.

Contribution

Identifying groups at high risk of severe disease could help to better monitor, prevent and control SARS-CoV-2 or influenza severe disease.

Healthcare utilization during the first two waves of the COVID-19 epidemic in South Africa: A cross-sectional household survey

Healthcare utilization surveys contextualize facility-based surveillance data for burden estimates. We describe healthcare utilization in the catchment areas for sentinel site healthcare facilities during the first year of the COVID-19 pandemic. We conducted a cross-sectional healthcare utilization survey in households in three communities from three provinces (KwaZulu-Natal, Western Cape and North West). Field workers administered structured questionnaires electronically with the household members reporting influenza-like illness (ILI) in the past 30 days or severe respiratory illness (SRI) since March 2020. Multivariable logistic regression was used to identify factors associated with healthcare utilization among individuals that reported illness. From November 2020 through April 2021, we enrolled 5804 households and 23,003 individuals. Any respiratory illness was reported by 1.6% of individuals; 0.7% reported ILI only, 0.8% reported SRI only, and 0.1% reported both ILI and SRI. Any form of medical care was sought by 40.8% (95% CI 32.9% - 49.6%) and 71.3% (95% CI 63.2% - 78.6%) of individuals with ILI and SRI, respectively. On multivariable analysis, respiratory illness was more likely to be medically attended for individuals at the Pietermaritzburg site (aOR 3.2, 95% CI 1.1-9.5, compared to Klerksdorp), that were underweight (aOR 11.5, 95% CI 1.5-90.2, compared to normal weight), with underlying illness (aOR 3.2, 95%CI 1.2-8.5), that experienced severe illness (aOR 4.8, 95% CI 1.6-14.3) and those with symptom duration of ≥10 days (aOR 7.9, 95% CI 2.1-30.2, compared to <5 days). Less than half of ILI episodes and only 71% of SRI episodes were medically attended during the first two COVID-19 waves in South Africa. Facility-based data may underestimate disease burden during the COVID-19 pandemic.

Estimation of influenza incidence and analysis of epidemic characteristics from 2009 to 2022 in Zhejiang Province, China

Background

Influenza infection causes a huge burden every year, affecting approximately 8% of adults and approximately 25% of children and resulting in approximately 400,000 respiratory deaths worldwide. However, based on the number of reported influenza cases, the actual prevalence of influenza may be greatly underestimated. The purpose of this study was to estimate the incidence rate of influenza and determine the true epidemiological characteristics of this virus.

Methods

The number of influenza cases and the prevalence of ILIs among outpatients in Zhejiang Province were obtained from the China Disease Control and Prevention Information System. Specimens were sampled from some cases and sent to laboratories for influenza nucleic acid testing. Random forest was used to establish an influenza estimation model based on the influenza-positive rate and the percentage of ILIs among outpatients. Furthermore, the moving epidemic method (MEM) was applied to calculate the epidemic threshold for different intensity levels. Joinpoint regression analysis was used to identify the annual change in influenza incidence. The seasonal trends of influenza were detected by wavelet analysis.

Results

From 2009 to 2021, a total of 990,016 influenza cases and 8 deaths were reported in Zhejiang Province. The numbers of estimated influenza cases from 2009 to 2018 were 743,449, 47,635, 89,026, 132,647, 69,218, 190,099, 204,606, 190,763, 267,168 and 364,809, respectively. The total number of estimated influenza cases is 12.11 times the number of reported cases. The APC of the estimated annual incidence rate was 23.33 (95% CI: 13.2 to 34.4) from 2011 to 2019, indicating a constant increasing trend. The intensity levels of the estimated incidence from the epidemic threshold to the very high-intensity threshold were 18.94 cases per 100,000, 24.14 cases per 100,000, 141.55 cases per 100,000, and 309.34 cases per 100,000, respectively. From the first week of 2009 to the 39th week of 2022, there were a total of 81 weeks of epidemics: the epidemic period reached a high intensity in 2 weeks, the epidemic period was at a moderate intensity in 75 weeks, and the epidemic period was at a low intensity in 2 weeks. The average power was significant on the 1-year scale, semiannual scale, and 115-week scale, and the average power of the first two cycles was significantly higher than that of the other cycles. In the period from the 20th week to the 35th week, the Pearson correlation coefficients between the time series of influenza onset and the positive rate of pathogens, including A(H3N2), A (H1N1)pdm2009, B(Victoria) and B(Yamagata), were - 0.089 (p = 0.021), 0.497 (p < 0.001), -0.062 (p = 0.109) and - 0.084 (p = 0.029), respectively. In the period from the 36th week of the first year to the 19th week of the next year, the Pearson correlation coefficients between the time series of influenza onset and the positive rate of pathogens, including A(H3N2), A (H1N1)pdm2009, B(Victoria) and B(Yamagata), were 0.516 (p < 0.001), 0.148 (p < 0.001), 0.292 (p < 0.001) and 0.271 (p < 0.001), respectively.

Conclusion

The disease burden of influenza has been seriously underestimated in the past. An appropriate method for estimating the incidence rate of influenza may be to comprehensively consider the influenza-positive rate as well as the percentage of ILIs among outpatients. The intensity level of the estimated incidence from the epidemic threshold to the very high-intensity threshold was calculated, thus yielding a quantitative standard for judging the influenza prevalence level in the future. The incidence of influenza showed semi-annual peaks in Zhejiang Province, including a main peak from December to January of the next year followed by a peak in summer. Furthermore, the driving factors of the influenza peaks were preliminarily explored. While the peak in summer was mainly driven by pathogens of A(H3N2), the peak in winter was alternately driven by various pathogens. Our research suggests that the government urgently needs to address barriers to vaccination and actively promote vaccines through primary care providers.

The National COVID-19 Epi Model (NCEM): Estimating cases, admissions and deaths for the first wave of COVID-19 in South Africa

In March 2020 the South African COVID-19 Modelling Consortium was formed to support government planning for COVID-19 cases and related healthcare. Models were developed jointly by local disease modelling groups to estimate cases, resource needs and deaths due to COVID-19. The National COVID-19 Epi Model (NCEM) while initially developed as a deterministic compartmental model of SARS-Cov-2 transmission in the nine provinces of South Africa, was adapted several times over the course of the first wave of infection in response to emerging local data and changing needs of government. By the end of the first wave, the NCEM had developed into a stochastic, spatially-explicit compartmental transmission model to estimate the total and reported incidence of COVID-19 across the 52 districts of South Africa. The model adopted a generalised Susceptible-Exposed-Infectious-Removed structure that accounted for the clinical profile of SARS-COV-2 (asymptomatic, mild, severe and critical cases) and avenues of treatment access (outpatient, and hospitalisation in non-ICU and ICU wards). Between end-March and early September 2020, the model was updated 11 times with four key releases to generate new sets of projections and scenario analyses to be shared with planners in the national and provincial Departments of Health, the National Treasury and other partners. Updates to model structure included finer spatial granularity, limited access to treatment, and the inclusion of behavioural heterogeneity in relation to the adoption of Public Health and Social Measures. These updates were made in response to local data and knowledge and the changing needs of the planners. The NCEM attempted to incorporate a high level of local data to contextualise the model appropriately to address South Africa's population and health system characteristics that played a vital role in producing and updating estimates of resource needs, demonstrating the importance of harnessing and developing local modelling capacity.

The burden of RSV-associated illness in children aged < 5 years, South Africa, 2011 to 2016

BACKGROUND

Vaccines and monoclonal antibodies to protect the very young infant against the respiratory syncytial virus (RSV)-associated illness are effective for limited time periods. We aimed to estimate age-specific burden to guide implementation strategies and cost-effectiveness analyses.

METHODS

We combined case-based surveillance and ecological data to generate a national estimate of the burden of RSV-associated acute respiratory illness (ARI) and severe acute respiratory illness (SARI) in South African children aged < 5 years (2011-2016), including adjustment for attributable fraction. We estimated the RSV burden by month of life in the < 1-year age group, by 3-month intervals until 2 years, and then 12 monthly intervals to < 5 years for medically and non-medically attended illness.

RESULTS

We estimated a mean annual total (medically and non-medically attended) of 264,112 (95% confidence interval (CI) 134,357-437,187) cases of RSV-associated ARI and 96,220 (95% CI 66,470-132,844) cases of RSV-associated SARI (4.7% and 1.7% of the population aged < 5 years, respectively). RSV-associated ARI incidence was highest in 2-month-old infants (18,361/100,000 population, 95% CI 9336-28,466). The highest incidence of RSV-associated SARI was in the < 1-month age group 14,674/100,000 (95% CI 11,175-19,645). RSV-associated deaths were highest in the first and second month of life (110.8 (95% CI 74.8-144.5) and 111.3 (86.0-135.8), respectively).

CONCLUSIONS

Due to the high burden of RSV-associated illness, specifically SARI cases in young infants, maternal vaccination and monoclonal antibody products delivered at birth could prevent significant RSV-associated disease burden.

Estimating the cost-effectiveness of maternal vaccination and monoclonal antibodies for respiratory syncytial virus in Kenya and South Africa

BACKGROUND

Respiratory syncytial virus (RSV) causes a substantial burden of acute lower respiratory infection in children under 5 years, particularly in low- and middle-income countries (LMICs). Maternal vaccine (MV) and next-generation monoclonal antibody (mAb) candidates have been shown to reduce RSV disease in infants in phase 3 clinical trials. The cost-effectiveness of these biologics has been estimated using disease burden data from global meta-analyses, but these are sensitive to the detailed age breakdown of paediatric RSV disease, for which there have previously been limited data.

METHODS

We use original hospital-based incidence data from South Africa (ZAF) and Kenya (KEN) collected between 2010 and 2018 of RSV-associated acute respiratory infection (ARI), influenza-like illness (ILI), and severe acute respiratory infection (SARI) as well as deaths with monthly age-stratification, supplemented with data on healthcare-seeking behaviour and costs to the healthcare system and households. We estimated the incremental cost per DALY averted (incremental cost-effectiveness ratio or ICER) of public health interventions by MV or mAb for a plausible range of prices (5-50 USD for MV, 10-125 USD for mAb), using an adjusted version of a previously published health economic model of RSV immunisation.

RESULTS

Our data show higher disease incidence for infants younger than 6 months of age in the case of Kenya and South Africa than suggested by earlier projections from community incidence-based meta-analyses of LMIC data. Since MV and mAb provide protection for these youngest age groups, this leads to a substantially larger reduction of disease burden and, therefore, more favourable cost-effectiveness of both interventions in both countries. Using the latest efficacy data and inferred coverage levels based on antenatal care (ANC-3) coverage (KEN: 61.7%, ZAF: 75.2%), our median estimate of the reduction in RSV-associated deaths in children under 5 years in Kenya is 10.5% (95% CI: 7.9, 13.3) for MV and 13.5% (10.7, 16.4) for mAb, while in South Africa, it is 27.4% (21.6, 32.3) and 37.9% (32.3, 43.0), respectively. Starting from a dose price of 5 USD, in Kenya, net cost (for the healthcare system) per (undiscounted) DALY averted for MV is 179 (126, 267) USD, rising to 1512 (1166, 2070) USD at 30 USD per dose; for mAb, it is 684 (543, 895) USD at 20 USD per dose and 1496 (1203, 1934) USD at 40 USD per dose. In South Africa, a MV at 5 USD per dose would be net cost-saving for the healthcare system and net cost per DALY averted is still below the ZAF's GDP per capita at 40 USD dose price (median: 2350, 95% CI: 1720, 3346). For mAb in ZAF, net cost per DALY averted is 247 (46, 510) USD at 20 USD per dose, rising to 2028 (1565, 2638) USD at 50 USD per dose and to 6481 (5364, 7959) USD at 125 USD per dose.

CONCLUSIONS

Incorporation of new data indicating the disease burden is highly concentrated in the first 6 months of life in two African settings suggests that interventions against RSV disease may be more cost-effective than previously estimated.

Low influenza vaccine uptake by healthcare workers caring for the elderly in South African old age homes and primary healthcare facilities

BACKGROUND

The elderly bear the highest burden of South Africa's estimated annual > 10 million influenza cases and > 11,000 influenza-related deaths. Unvaccinated healthcare workers (HCWs) are at high occupational risk of contracting influenza, and may transmit influenza to elderly patients in their care. Thus, the South African National Department of Health recommends that HCWs receive annual influenza vaccination. This study aimed to determine influenza vaccination coverage among HCWs; identify reasons for their vaccination status; and investigate if HCWs recommend vaccination to their elderly patients.

METHODS

A descriptive study was conducted in 18 community health centres and 44 private sector and non-governmental organisation managed old age homes across South Africa, using a self-administered structured questionnaire, which was distributed to 360 HCWs present on the day of data collection. Data were captured using Microsoft Excel® and imported to Epi Info™ 7 (Centers for Disease Control and Prevention, USA) for descriptive statistical analysis. Ethics approval (SMUREC/P/36/2018: PG) and permission to conduct the study at the facilities were obtained. All participants provided informed consent.

RESULTS

The response rate was 76.7% (276/360). Most participants were female (90.9% [251/276]), nursing professionals (81.2% [224/276]) with a mean age of 41.1 ± 11.7 years. Although 62.7% of participants indicated having ever received at least one dose of the influenza vaccine, influenza vaccine uptake for 2017 and 2018 was 24.36% (41/276) and 33.3% (92/276) respectively. The main reasons given for never being vaccinated against influenza were related to the unavailability of the vaccine (70.9%) and vaccine hesitancy (27.2%). Most participants (67.8% [187/276]) recommended vaccines to elderly patients in their care.

CONCLUSION

The main reasons behind low influenza vaccine uptake by HCWs in South Africa who care for the elderly were related to unavailability of the vaccine and vaccine hesitancy. Strategies to educate HCWs on the importance of influenza vaccination, while concurrently increasing sustained and easy access to the vaccine by HCWs are needed to preserve public health.

Influenza Vaccination Results in Differential Hemagglutinin Stalk-Specific Fc-Mediated Functions in Individuals Living With or Without HIV

Influenza virus hemagglutinin (HA) stalk-specific antibodies have been shown to potently induce Fc-mediated effector functions which are important in protection from disease. In placebo-controlled maternal influenza (MatFlu) vaccination trials of pregnant women living with or without HIV, reduced risk of influenza illness was associated with high HA stalk antibody titers following trivalent inactivated vaccination (TIV). However, the mechanisms of immunity conferred by the HA stalk antibodies were not well understood. Here, we investigated HA stalk-specific Fc effector functions including antibody-dependent cellular phagocytosis (ADCP), antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent complement deposition (ADCD), and FcγRIIa and FcγRIIIa binding in response to seasonal influenza vaccination. These were measured pre- and 1-month post-vaccination in 141 HIV-uninfected women (67 TIV and 74 placebo recipients) and 119 women living with HIV (WLWH; 66 TIV and 53 placebo recipients). In contrast to HIV-uninfected women, where HA stalk-specific ADCP and FcγRIIa binding were significantly boosted, WLWH showed no increase in response to vaccination. HA stalk-specific ADCC potential and FcγRIIIa binding were not boosted regardless of HIV status but were higher in WLWH compared with HIV-uninfected women prior to vaccination. HA stalk-specific ADCD was significantly increased by vaccination in all women, but was significantly lower in the WLWH both pre- and post- vaccination. Co-ordination between HA stalk-specific ADCP and ADCD in WLWH was improved by vaccination. Fc polyfunctionality was enhanced by vaccination in HIV-uninfected women and driven by the HA stalk antibody titers. However, in the WLWH, higher pre-vaccination Fc polyfunctionality was maintained post-vaccination but was decoupled from titer. Overall, we showed differential regulation of Fc effector HA stalk responses, suggesting that HIV infection results in unique humoral immunity in response to influenza vaccination, with relevance for future strategies that aim to target the HA stalk in this population.

The national burden of influenza-like illness and severe respiratory illness overall and associated with nine respiratory viruses in South Africa, 2013-2015

BACKGROUND

Estimates of the disease burden associated with different respiratory viruses are severely limited in low- and middle-income countries, especially in Africa.

METHODS

We estimated age-specific numbers and rates of medically and non-medically attended influenza-like illness (ILI) and severe respiratory illness (SRI) that were associated with influenza, respiratory syncytial virus (RSV), rhinovirus, human metapneumovirus, adenovirus, enterovirus and parainfluenza virus types 1-3 after adjusting for the attributable fraction (AF) of virus detection to illness in South Africa during 2013-2015. The base rates were estimated from five surveillance sites and extrapolated nationally.

RESULTS

The mean annual rates per 100,000 population were 51,383 and 4196 for ILI and SRI, respectively. Of these, 26% (for ILI) and 46% (for SRI) were medically attended. Among outpatients with ILI, rhinovirus had the highest AF-adjusted rate (7221), followed by influenza (6443) and adenovirus (1364); whereas, among inpatients with SRI, rhinovirus had the highest AF-adjusted rate (400), followed by RSV (247) and influenza (130). Rhinovirus (9424) and RSV (2026) had the highest AF-adjusted rates among children aged <5 years with ILI or SRI, respectively, whereas rhinovirus (757) and influenza (306) had the highest AF-adjusted rates among individuals aged ≥65 years with ILI or SRI, respectively.

CONCLUSIONS

There was a substantial burden of ILI and SRI in South Africa during 2013-2015. Rhinovirus and influenza had a prominent disease burden among patients with ILI. RSV and influenza were the most prominent causes of SRI in children and the elderly, respectively.

Development of influenza-associated disease burden pyramid in Shanghai, China, 2010-2017: a Bayesian modelling study

OBJECTIVES

Negative estimates can be produced when statistical modelling techniques are applied to estimate morbidity and mortality attributable to influenza. Based on the prior knowledge that influenza viruses are hazardous pathogens and have adverse health outcomes of respiratory and circulatory disease (R&C), we developed an improved model incorporating Bayes' theorem to estimate the disease burden of influenza in Shanghai, China, from 2010 to 2017.

DESIGN

A modelling study using aggregated data from administrative systems on weekly R&C mortality and hospitalisation, influenza surveillance and meteorological data. We constrained the regression coefficients for influenza activity to be positive by truncating the prior distributions at zero.

SETTING

Shanghai, China.

PARTICIPANTS

People registered with R&C deaths (450 298) and hospitalisations (2621 787, from 1 July 2013), and with influenza-like illness (ILI) outpatient visits (342 149) between 4 January 2010 and 31 December 2017.

PRIMARY OUTCOME MEASURES

Influenza-associated disease burden (mortality, hospitalisation and outpatient visit rates) and clinical severity (outpatient-mortality, outpatient-hospitalisation and hospitalisation-mortality risks).

RESULTS

Influenza was associated with an annual average of 15.49 (95% credibility interval (CrI) 9.06-22.06) excess R&C deaths, 100.65 (95% CrI 48.79-156.78) excess R&C hospitalisations and 914.95 (95% CrI 798.51-1023.66) excess ILI outpatient visits per 100 000 population in Shanghai. 97.23% and 80.24% excess R&C deaths and hospitalisations occurred in people aged ≥65 years. More than half of excess morbidity and mortality were associated with influenza A(H3N2) virus, and its severities were 1.65-fold to 3.54-fold and 1.47-fold to 2.16-fold higher than that for influenza A(H1N1) and B viruses, respectively.

CONCLUSIONS

The proposed Bayesian approach with reasonable prior information improved estimates of influenza-associated disease burden. Influenza A(H3N2) virus was generally associated with higher morbidity and mortality, and was relatively more severe compared with influenza A(H1N1) and B viruses. Targeted influenza prevention and control strategies for the elderly in Shanghai may substantially reduce the disease burden.

The importation and establishment of community transmission of SARS-CoV-2 during the first eight weeks of the South African COVID-19 epidemic

BACKGROUND

We describe the epidemiology of COVID-19 in South Africa following importation and during implementation of stringent lockdown measures.

METHODS

Using national surveillance data including demographics, laboratory test data, clinical presentation, risk exposures (travel history, contacts and occupation) and outcomes of persons undergoing COVID-19 testing or hospitalised with COVID-19 at sentinel surveillance sites, we generated and interpreted descriptive statistics, epidemic curves, and initial reproductive numbers (Rt).

FINDINGS

From 4 March to 30 April 2020, 271,670 SARS-CoV-2 PCR tests were performed (462 tests/100,000 persons). Of these, 7,892 (2.9%) persons tested positive (median age 37 years (interquartile range 28-49 years), 4,568 (58%) male, cumulative incidence of 13.4 cases/100,000 persons). Hospitalization records were found for 1,271 patients (692 females (54%)) of whom 186 (14.6%) died. Amongst 2,819 cases with data, 489/2819 (17.3%) travelled internationally within 14 days prior to diagnosis, mostly during March 2020 (466 (95%)). Cases diagnosed in April compared with March were younger (median age, 37 vs. 40 years), less likely female (38% vs. 53%) and resident in a more populous province (98% vs. 91%). The national initial Rt was 2.08 (95% confidence interval (CI): 1.71-2.51).

INTERPRETATION

The first eight weeks following COVID-19 importation were characterised by early predominance of imported cases and relatively low mortality and transmission rates. Despite stringent lockdown measures, the second month following importation was characterised by community transmission and increasing disease burden in more populous provinces.

Variability in published rates of influenza-associated hospitalizations: A systematic review, 2007-2018

Background

Influenza burden estimates help provide evidence to support influenza prevention and control programs at local and international levels.

Methods

Through a systematic review, we aimed to identify all published articles estimating rates of influenza-associated hospitalizations, describe methods and data sources used, and identify regions of the world where estimates are still lacking. We evaluated study heterogeneity to determine if we could pool published rates to generate global estimates of influenza-associated hospitalization.

Results

We identified 98 published articles estimating influenza-associated hospitalization rates from 2007-2018. Most articles (65%) identified were from high-income countries, with 34 of those (53%) presenting estimates from the United States. While we identified fewer publications (18%) from low- and lower-middle-income countries, 50% of those were published from 2015-2018, suggesting an increase in publications from lower-income countries in recent years. Eighty percent (n = 78) used a multiplier approach. Regression modelling techniques were only used with data from upper-middle or high-income countries where hospital administrative data was available. We identified variability in the methods, case definitions, and data sources used, including 91 different age groups and 11 different categories of case definitions. Due to the high observed heterogeneity across articles (I²>99%), we were unable to pool published estimates.

Conclusions

The variety of methods, data sources, and case definitions adapted locally suggests that the current literature cannot be synthesized to generate global estimates of influenza-associated hospitalization burden.

Asymptomatic transmission and high community burden of seasonal influenza in an urban and a rural community in South Africa, 2017-18 (PHIRST): a population cohort study

BACKGROUND

Data on influenza community burden and transmission are important to plan interventions especially in resource-limited settings. However, data are limited, particularly from low-income and middle-income countries. We aimed to evaluate the community burden and transmission of influenza in a rural and an urban setting in South Africa.

METHODS

In this prospective cohort study approximately 50 households were selected sequentially from both a rural setting (Agincourt, Mpumalanga Province, South Africa; with a health and sociodemographic surveillance system) and an urban setting (Klerksdorp, Northwest Province, South Africa; using global positioning system data), enrolled, and followed up for 10 months in 2017 and 2018. Different households were enrolled in each year. Households of more than two individuals in which 80% or more of the occupants agreed to participate were included in the study. Nasopharyngeal swabs were collected twice per week from participating household members irrespective of symptoms and tested for influenza using real-time RT-PCR. The primary outcome was the incidence of influenza infection, defined as the number of real-time RT-PCR-positive episodes divided by the person-time under observation. Household cumulative infection risk (HCIR) was defined as the number of subsequent infections within a household following influenza introduction.

FINDINGS

81 430 nasopharyngeal samples were collected from 1116 participants in 225 households (follow-up rate 88%). 917 (1%) tested positive for influenza; 178 (79%) of 225 households had one or more influenza-positive individual. The incidence of influenza infection was 43·6 (95% CI 39·8-47·7) per 100 person-seasons. 69 (17%) of 408 individuals who had one influenza infection had a repeat influenza infection during the same season. The incidence (67·4 per 100 person-seasons) and proportion with repeat infections (22 [23%] of 97 children) were highest in children younger than 5 years and decreased with increasing age (p<0·0001). Overall, 268 (56%) of 478 infections were symptomatic and 66 (14%) of 478 infections were medically attended. The overall HCIR was 10% (109 of 1088 exposed household members infected [95% CI 9-13%). Transmission (HCIR) from index cases was highest in participants aged 1-4 years (16%; 40 of 252 exposed household members) and individuals with two or more symptoms (17%; 68 of 396 exposed household members). Individuals with asymptomatic influenza transmitted infection to 29 (6%) of 509 household contacts. HIV infection, affecting 167 (16%) of 1075 individuals, was not associated with increased incidence or HCIR.

INTERPRETATION

Approximately half of influenza infections were symptomatic, with asymptomatic individuals transmitting influenza to 6% of household contacts. This suggests that strategies, such as quarantine and isolation, might be ineffective to control influenza. Vaccination of children, with the aim of reducing influenza transmission might be effective in African settings given the young population and high influenza burden.

FUNDING

US Centers for Disease Control and Prevention.

Promoting Healthy Ageing in South Africa Through Vaccination of the Elderly

The World Health Organization estimates that globally, the proportion of people aged ≥60 years will more than double by the year 2050, with the majority of elderly people living in low- and middle-income countries such as South Africa. Population ageing is an impending public health concern, potentially negatively impacting on South Africa's economy and health system if the government does not adequately prepare for this change. Globally, many potential solutions to ensure healthy ageing are being discussed and implemented, including adopting a “life-course” approach to vaccination which includes vaccination of the elderly, since they are at considerable risk of severe morbidity and mortality from vaccine-preventable diseases. While vaccines are considered as one of the greatest tools for preventing childhood infectious disease morbidity and mortality, they are under-utilised in strategies for promoting healthy ageing in South Africa, where only influenza vaccination is available free of charge to the elderly accessing public sector healthcare. Population ageing coupled with the high incidence of vaccine-preventable diseases amongst elderly South Africans, necessitates establishing a comprehensive national policy and guidelines for vaccination of the elderly.

The epidemiology of seasonal influenza after the 2009 influenza pandemic in Africa: a systematic review

Background

Influenza infection is a serious public health problem that causes an estimated 3 to 5 million cases and 250,000 deaths worldwide every year. The epidemiology of influenza is well-documented in high- and middle-income countries, however minimal effort had been made to understand the epidemiology, burden and seasonality of influenza in Africa. This study aims to assess the state of knowledge of seasonal influenza epidemiology in Africa and identify potential data gaps for policy formulation following the 2009 pandemic.

Method

We reviewed articles from Africa published into four databases namely: MEDLINE (PubMed), Google Scholar, Cochrane Library and Scientific Research Publishing from 2010 to 2019.

Results

We screened titles and abstracts of 2070 studies of which 311 were selected for full content evaluation and 199 studies were considered. Selected articles varied substantially on the basis of the topics they addressed covering the field of influenza surveillance (n=80); influenza risk factors and co-morbidities (n=15); influenza burden (n=37); influenza vaccination (n=40); influenza and other respiratory pathogens (n=22) and influenza diagnosis (n=5).

Conclusion

Significant progress has been made since the last pandemic in understanding the influenza epidemiology in Africa. However, efforts still remain for most countries to have sufficient data to allow countries to prioritize strategies for influenza prevention and control.

A cost-effectiveness analysis of South Africa's seasonal influenza vaccination programme

BACKGROUND

Seasonal influenza imposes a significant health and economic burden in South Africa, particularly in populations vulnerable to severe consequences of influenza. This study assesses the cost-effectiveness of South Africa's seasonal influenza vaccination strategy, which involves vaccinating vulnerable populations with trivalent inactivated influenza vaccine (TIV) during routine facility visits. Vulnerable populations included in our analysis are persons aged ≥ 65 years; pregnant women; persons living with HIV/AIDS (PLWHA), persons of any age with underlying medical conditions (UMC) and children aged 6-59 months.

METHOD

We employed the World Health Organisation's (WHO) Cost Effectiveness Tool for Seasonal Influenza Vaccination (CETSIV), a decision tree model, to evaluate the 2018 seasonal influenza vaccination campaign from a public healthcare provider and societal perspective. CETSIV was populated with existing country-specific demographic, epidemiologic and coverage data to estimate incremental cost-effectiveness ratios (ICERs) by comparing costs and benefits of the influenza vaccination programme to no vaccination.

RESULTS

The highest number of clinical events (influenza cases, outpatient visits, hospitalisation and deaths) were averted in PLWHA and persons with other UMCs. Using a cost-effectiveness threshold of US$ 3400 per quality-adjusted life year (QALY), our findings suggest that the vaccination programme is cost-effective for all vulnerable populations except for children aged 6-59 months. ICERs ranged from ~US$ 1 750 /QALY in PLWHA to ~US$ 7500/QALY in children. In probabilistic sensitivity analyses, the vaccination programme was cost-effective in pregnant women, PLWHA, persons with UMCs and persons aged ≥65 years in >80% of simulations. These findings were robust to changes in many model inputs but were most sensitive to uncertainty in estimates of influenza-associated illness burden.

CONCLUSION

South Africa's seasonal influenza vaccination strategy of opportunistically targeting vulnerable populations during routine visits is cost-effective. A budget impact analysis will be useful for supporting future expansions of the programme.

Influenza economic burden among potential target risk groups for immunization in South Africa, 2013-2015

BACKGROUND

Data on influenza economic burden in risk groups for severe influenza are important to guide targeted influenza immunization, especially in resource-limited settings. However, this information is limited in low- and middle-income countries.

METHODS

We estimated the cost (from a health system and societal perspective) and years of life lost (YLL) for influenza-associated illness in South Africa during 2013-2015 among (i) children aged 6-59 months, (ii) individuals aged 5-64 years with HIV, pulmonary tuberculosis (PTB) and selected underlying medical conditions (UMC), separately, (iii) pregnant women and (iv) individuals aged ≥65 years, using publicly available data and data collected through laboratory-confirmed influenza surveillance and costing studies. All costs were expressed in 2015 prices using the South Africa all-items Consumer Price Index.

RESULTS

During 2013-2015, the mean annual cost of influenza-associated illness among the selected risk groups accounted for 52.1% ($140.9/$270.5 million) of the total influenza-associated illness cost (for the entire population of South Africa), 45.2% ($52.2/$115.5 million) of non-medically attended illness costs, 43.3% ($46.7/$107.9 million) of medically-attended mild illness costs and 89.3% ($42.0/$47.1 million) of medically-attended severe illness costs. The YLL among the selected risk groups accounted for 86.0% (262,069 /304,867 years) of the total YLL due to influenza-associated death.

CONCLUSION

In South Africa, individuals in risk groups for severe influenza accounted for approximately half of the total influenza-associated illness cost but most of the cost of influenza-associated medically attended severe illness and YLL. This study provides the foundation for future studies on the cost-effectiveness of influenza immunization among risk groups.

Heterogeneity in influenza seasonality and vaccine effectiveness in Australia, Chile, New Zealand and South Africa: early estimates of the 2019 influenza season

We compared 2019 influenza seasonality and vaccine effectiveness (VE) in four southern hemisphere countries: Australia, Chile, New Zealand and South Africa. Influenza seasons differed in timing, duration, intensity and predominant circulating viruses. VE estimates were also heterogeneous, with all-ages point estimates ranging from 7-70% (I2: 33%) for A(H1N1)pdm09, 4-57% (I2: 49%) for A(H3N2) and 29-66% (I2: 0%) for B. Caution should be applied when attempting to use southern hemisphere data to predict the northern hemisphere influenza season.

Influenza disease burden among potential target risk groups for immunization in South Africa, 2013-2015

BACKGROUND

Data on influenza burden in risk groups for severe influenza are important to guide targeted influenza immunization, especially in resource limited settings. However, this information is limited overall and in particular in low- and middle-income countries. We sought to assess the mean annual national burden of medically and non-medically attended influenza-associated mild, severe-non-fatal and fatal illness among potential target groups for influenza immunization in South Africa during 2013-2015.

METHODS

We used published mean national annual estimates of mild, severe-non-fatal, and fatal influenza-associated illness in South Africa during 2013-2015 and estimated the number of such illnesses occurring among the following risk groups: (i) children aged 6-59 months; (ii) individuals aged 5-64 years with HIV, and/or pulmonary tuberculosis (PTB), and/or selected underlying medical conditions (UMC); (iii) pregnant women; and (iv) individuals aged ≥65 years. We also estimated the number of individuals among the same risk groups in the population.

RESULTS

During 2013-2015, individuals in the selected risk groups accounted for 45.3% (24,569,328/54,086,144) of the population and 43.5% (4,614,763/10,598,138), 86.8% (111,245/128,173) and 94.5% (10,903/11,536) of the mean annual estimated number of influenza-associated mild, severe-non-fatal and fatal illness episodes, respectively. The rates of influenza-associated illness were highest in children aged 6-59 months (23,983 per 100,000 population) for mild illness, in pregnant women (930 per 100,000 population) for severe-non-fatal illness and in individuals aged ≥65 years (138 per 100,000 population) for fatal illness.

CONCLUSION

Influenza immunization of the selected risk groups has the potential to prevent a substantial number of influenza-associated severe illness. Nonetheless, because of the high number of individuals at risk, South Africa, due to financial resources constrains, may need to further prioritize interventions among risk populations. Cost-burden and cost-effectiveness estimates may assist with further prioritization.

Health and economic burden of influenza-associated illness in South Africa, 2013-2015

Background

Economic burden estimates are essential to guide policy‐making for influenza vaccination, especially in resource‐limited settings.

Methods

We estimated the cost, absenteeism, and years of life lost (YLL) of medically and non‐medically attended influenza‐associated mild and severe respiratory, circulatory and non‐respiratory/non‐circulatory illness in South Africa during 2013‐2015 using a modified version of the World Health Organization (WHO) worksheet based tool for estimating the economic burden of seasonal influenza. Additionally, we restricted the analysis to influenza‐associated severe acute respiratory illness (SARI) and influenza‐like illness (ILI; subsets of all‐respiratory illnesses) as suggested in the WHO manual.

Results

The estimated mean annual cost of influenza‐associated illness was $270.5 million, of which $111.3 million (41%) were government‐incurred costs, 40.7 million (15%) were out‐of‐pocket expenses, and $118.4 million (44%) were indirect costs. The cost of influenza‐associated medically attended mild illness ($107.9 million) was 2.3 times higher than that of severe illness ($47.1 million). Influenza‐associated respiratory illness costs ($251.4 million) accounted for 93% of the total cost. Estimated absenteeism and YLL were 13.2 million days and 304 867 years, respectively. Among patients with influenza‐associated WHO‐defined ILI or SARI, the costs ($95.3 million), absenteeism (4.5 million days), and YLL (65 697) were 35%, 34%, and 21% of the total economic and health burden of influenza.

Conclusion

The economic burden of influenza‐associated illness was substantial from both a government and a societal perspective. Models that limit estimates to those obtained from patients with WHO‐defined ILI or SARI substantially underestimated the total economic and health burden of influenza‐associated illness.