Excess Invasive Meningococcal Disease Associated With Seasonal Influenza, South Africa, 2003-2018.

BACKGROUND: Invasive meningococcal disease (IMD) is a devastating illness with high mortality rates. Like influenza, endemic IMD is seasonal, peaking in winter. Studies suggest that circulation of influenza virus may influence the timing and magnitude of IMD winter peaks. METHODS: This ecological study used weekly data from 2 nationwide surveillance programs: Viral Watch (proportion of outpatient influenza-positive cases from throat or nasal swab samples) and GERMS-SA (laboratory-confirmed cases of IMD), occurring across South Africa from 2003 through 2018 in all age bands. A bivariate time series analysis using wavelet transform was conducted to determine cocirculation of the diseases and the time lag between the peak seasons. We modeled excess meningococcal disease cases attributable to influenza cocirculation, using univariate regression spline models. Stata and R statistical software packages were used for the analysis. RESULTS: A total of 5256 laboratory-confirmed IMD cases were reported, with an average annual incidence of 0.23 episodes per 100 000 population and a mean seasonal peak during week 32 (±3 weeks). Forty-two percent of swab samples (10 421 of 24 741) were positive for influenza during the study period. The mean peak for all influenza occurred at week 26 (±4 weeks). There was an average lag time of 5 weeks between annual influenza and IMD seasons. Overall, 5% (1%-9%) of IMD cases can be attributable to influenza cocirculation, with, on average, 17 excess IMD cases per year attributable to influenza. CONCLUSIONS: A quantifiable proportion of IMD in South Africa is associated with influenza cocirculation; therefore, seasonal influenza vaccination may have an effect on preventing a small portion of IMD in addition to preventing influenza.

Elevated influenza-related excess mortality in South African elderly individuals, 1998-2005.

BACKGROUND: Although essential to guide control measures, published estimates of influenza-related seasonal mortality for low- and middle-income countries are few. We aimed to compare influenza-related mortality among individuals aged ≥65 years in South Africa and the United States. METHODS: We estimated influenza-related excess mortality due to all causes, pneumonia and influenza, and other influenza-associated diagnoses from monthly age-specific mortality data for 1998-2005 using a Serfling regression model. We controlled for between-country differences in population age structure and nondemographic factors (baseline mortality and coding practices) by generating age-standardized estimates and by estimating the percentage excess mortality attributable to influenza. RESULTS: Age-standardized excess mortality rates were higher in South Africa than in the United States: 545 versus 133 deaths per 100,000 population for all causes (P<.001) and 63 vs 21 deaths per 100,000 population for pneumonia and influenza (P=.03). Standardization for nondemographic factors decreased but did not eliminate between-country differences; for example, the mean percentage of winter deaths attributable to influenza was 16% in South Africa and 6% in the United States (P<.001). For all respiratory causes, cerebrovascular disease, and diabetes, age-standardized excess death rates were 4-8-fold greater in South Africa than in the United States, and the percentage increase in winter deaths attributable to influenza was 2-4-fold higher. CONCLUSIONS: These data suggest that the impact of seasonal influenza on mortality among elderly individuals may be substantially higher in an African setting, compared with in the United States, and highlight the potential for influenza vaccination programs to decrease mortality.

Evaluation of two influenza surveillance systems in South Africa.

BACKGROUND: The World Health Organisation recommends outpatient influenza-like illness (ILI) and inpatient severe acute respiratory illness (SARI) surveillance. We evaluated two influenza surveillance systems in South Africa: one for ILI and another for SARI. METHODOLOGY: The Viral Watch (VW) programme has collected virological influenza surveillance data voluntarily from patients with ILI since 1984 in private and public clinics in all 9 South African provinces. The SARI surveillance programme has collected epidemiological and virological influenza surveillance data since 2009 in public hospitals in 4 provinces by dedicated personnel. We compared nine surveillance system attributes from 2009-2012. RESULTS: We analysed data from 18,293 SARI patients and 9,104 ILI patients. The annual proportion of samples testing positive for influenza was higher for VW (mean 41%) than SARI (mean 8%) and generally exceeded the seasonal threshold from May to September (VW: weeks 21-40; SARI: weeks 23-39). Data quality was a major strength of SARI (most data completion measures >90%; adherence to definitions: 88-89%) and a relative weakness of the VW programme (62% of forms complete, with limited epidemiologic data collected; adherence to definitions: 65-82%). Timeliness was a relative strength of both systems (e.g. both collected >93% of all respiratory specimens within 7 days of symptom onset). ILI surveillance was more nationally representative, financially sustainable and expandable than the SARI system. Though the SARI programme is not nationally representative, the high quality and detail of SARI data collection sheds light on the local burden and epidemiology of severe influenza-associated disease. CONCLUSIONS: To best monitor influenza in South Africa, we propose that both ILI and SARI should be under surveillance. Improving ILI surveillance will require better quality and more systematic data collection, and SARI surveillance should be expanded to be more nationally representative, even if this requires scaling back on information gathered.

Phylogenetic studies of influenza B viruses isolated in southern Africa: 1998-2001.

Influenza B viruses isolated in southern Africa during the period from 1998 to 2001 were analysed by sequence analysis of the viral haemagglutinin HA1 subunit and the phylogenetic relationships were determined. Influenza B activity varied considerably in South Africa during the 4-year study period with no activity detected in 2000. Phylogenetic analysis revealed that viruses isolated in 1998 from a localised outbreak in Durban belonged to two distinct sub-lineages. Some of the influenza B viruses isolated throughout South Africa in 1999 as well as several viruses obtained from Mozambique in the same year were closely related to the B/Yamanashi/166/98-like viruses. In contrast, the majority of the 1999 isolates, represented by B/Johannesburg/5/99, exhibited considerable drift from the B/Yamanashi/166/98 stain. The viruses isolated during the 2001 season fell into two sub-lineages, one of which had evolved from the B/Johannesburg/5/99-like viruses and the other which had evolved from the group of viruses that included one of the 1998 Durban isolates. These molecular epidemiological studies reveal a diverse and complex pattern of influenza B virus strains circulating in southern Africa.

Epidemiologic and virologic assessment of the 2009 influenza A (H1N1) pandemic on selected temperate countries in the Southern Hemisphere: Argentina, Australia, Chile, New Zealand and South Africa.

UNLABELLED: INTRODUCTION AND SETTING: Our analysis compares the most comprehensive epidemiologic and virologic surveillance data compiled to date for laboratory-confirmed H1N1pdm patients between 1 April 2009 - 31 January 2010 from five temperate countries in the Southern Hemisphere-Argentina, Australia, Chile, New Zealand, and South Africa. OBJECTIVE: We evaluate transmission dynamics, indicators of severity, and describe the co-circulation of H1N1pdm with seasonal influenza viruses. RESULTS: In the five countries, H1N1pdm became the predominant influenza strain within weeks of initial detection. South Africa was unique, first experiencing a seasonal H3N2 wave, followed by a distinct H1N1pdm wave. Compared with the 2007 and 2008 influenza seasons, the peak of influenza-like illness (ILI) activity in four of the five countries was 3-6 times higher with peak ILI consultation rates ranging from 35/1,000 consultations/week in Australia to 275/100,000 population/week in New Zealand. Transmission was similar in all countries with the reproductive rate ranging from 1.2-1.6. The median age of patients in all countries increased with increasing severity of disease, 4-14% of all hospitalized cases required critical care, and 26-68% of fatal patients were reported to have ≥1 chronic medical condition. Compared with seasonal influenza, there was a notable downward shift in age among severe cases with the highest population-based hospitalization rates among children <5 years old. National population-based mortality rates ranged from 0.8-1.5/100,000. CONCLUSIONS: The difficulty experienced in tracking the progress of the pandemic globally, estimating its severity early on, and comparing information across countries argues for improved routine surveillance and standardization of investigative approaches and data reporting methods.

Antigenic and molecular analysis of influenza A (H3N2) virus strains isolated from a localised influenza outbreak in South Africa in 2003.

A severe acute institutional influenza outbreak occurred in a police residential college in Pretoria amongst new recruits and staff members at the end of May 2003. The outbreak was characterised by marked illness which affected a total of 648 students, 26 of whom were admitted to hospital. Symptoms included pyrexia, severe headache, and myalgia. The attack rate per dormitory building ranged from 20 to 47%, with an overall attack rate of 34%. Throat swabs and bronchoalveolar lavage specimens were sent to the National Institute for Communicable Diseases (NICD) from 20 patients. All were positive for influenza A by multiplex PCR and/or indirect immunofluorescence, and were further identified as subtype H3N2. Additional specimens from sporadic influenza cases in Johannesburg and surrounding areas were collected through the NICD active viral surveillance programme for respiratory viral testing and were also positive for influenza A H3N2 viruses. Viruses isolated from patients from both the institutional outbreak as well as from sporadic cases were analysed both antigenically and at the molecular level to determine the characteristics of the influenza strain responsible for the epidemic. The results showed clearly that the outbreak was caused by the introduction in 2003 into South Africa of the novel A/Fujian/411/02-like H3N2 influenza strain, which is antigenically distinct from the A/Panama/2007/99 vaccine strain. The rapid spread of these variant viruses to the southern hemisphere indicates that the H3N2 component of the influenza vaccine needs to be updated for the 2004 southern hemisphere winter.