Evaluation of influenza vaccine effectiveness and description of circulating strains in outpatient settings in South Africa, 2014

The effectiveness of the trivalent seasonal influenza vaccine during the 2014 season in South Africa was assessed using a test-negative case–control study design including 472 cases and 362 controls. Influenza A(H3N2) was the dominant strain circulating. The overall vaccine effectiveness estimate, adjusted for age and underlying conditions, was43.1% (95% CI: 26.8-74.5). 2014 H3N2 viruses from South Africa were mainly in sublineage 3C.3 with accumulation of amino acid changes that differentiate them from the vaccine strain in 3C.1

Evaluation of influenza vaccine effectiveness and description of circulating strains in outpatient settings in South Africa, 2014

The effectiveness of the trivalent seasonal influenza vaccine during the 2014 season in South Africa was assessed using a test-negative case–control study design including 472 cases and 362 controls. Influenza A(H3N2) was the dominant strain circulating. The overall vaccine effectiveness estimate, adjusted for age and underlying conditions, was43.1% (95% CI: 26.8-74.5). 2014 H3N2 viruses from South Africa were mainly in sublineage 3C.3 with accumulation of amino acid changes that differentiate them from the vaccine strain in 3C.1

Effectiveness and knowledge, attitudes and practices of seasonal influenza vaccine in primary healthcare settings in South Africa, 2010-2013

OBJECTIVES : Influenza vaccine effectiveness (VE) and coverage data for sub-Saharan Africa are scarce. Using a test-negative case–control design, we estimated influenza VE annually among individuals with influenza-like illness presenting to an outpatient sentinel surveillance programme in South Africa from 2010 to 2013. A knowledge, attitudes and practices (KAP) influenza vaccine survey of programme clinicians was conducted in 2013. SAMPLE : In total, 9420 patients were enrolled in surveillance of whom 5344 (56.7%) were included in the VE analysis: 2678 (50.1%) were classified as controls (influenza test-negative) and 2666 (49.9%) as cases (influenza test-positive). RESULTS : Mean annual influenza vaccine coverage among controls was 4.5% for the four years. Annual VE estimates adjusted for age, underlying medical conditions and seasonality for 2010-2013 were 54.2% (95% confidence interval (CI): 2.4–78.6%), 57.1% (95% CI: 15.5–78.2%), 38.4% (95% CI: 71.7–78.1%) and 87.2% (95% CI: 67.2–95.0%), respectively. The KAP survey showed that >90% of clinicians were familiar with the indications for and the benefits of influenza vaccination. CONCLUSIONS : Our study showed that the vaccine was significantly protective in 2010, 2011 and 2013, but not in 2012 when the circulating A(H3N2) strain showed genetic drift. Vaccine coverage was low despite good clinician knowledge of vaccination indications. Further studies are needed to investigate the reason for the low uptake of influenza vaccine.The programme forms part of the National Institute for Communicable Diseases core function and is not funded by external bodies.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1750-2659hb2016Medical Virolog

Epidemiology of influenza B/Yamagata and B/Victoria lineages in South Africa, 2005-2014

BACKGROUND : Studies describing the epidemiology of influenza B lineages in South Africa are lacking. METHODS : We conducted a prospective study to describe the circulation of influenza B/Victoria and B/ Yamagata lineages among patients of all ages enrolled in South Africa through three respiratory illness surveillance systems between 2005 and 2014: (i) the Viral Watch (VW) program enrolled outpatients with influenza-like illness (ILI) from private healthcare facilities during 2005±2014; (ii) the influenza-like illnesses program enrolled outpatients in public healthcare clinics (ILI/PHC) during 2012±2014; and (iii) the severe acute respiratory illnesses (SARI) program enrolled inpatients from public hospitals during 2009±2014. Influenza B viruses were detected by virus isolation during 2005 to 2009 and by real-time reverse transcription polymerase chain reaction from 2009±2014. Clinical and epidemiological characteristics of patients hospitalized with SARI and infected with different influenza B lineages were also compared using unconditional logistic regression. RESULTS : Influenza viruses were detected in 22% (8,706/39,804) of specimens from patients with ILI or SARI during 2005±2014, of which 24% (2,087) were positive for influenza B. Influenza B viruses predominated in all three surveillance systems in 2010. B/Victoria predominated prior to 2011 (except 2008) whereas B/Yamagata predominated thereafter (except 2012). B lineages co-circulated in all seasons, except in 2013 and 2014 for SARI and ILI/PHC surveillance. Among influenza B-positive SARI cases, the detection of influenza B/Yamagata compared to influenza B/Victoria was significantly higher in individuals aged 45±64 years (adjusted odds ratio [aOR]: 4.2; 95% confidence interval [CI]: 1.1±16.5) and 65 years (aOR: 12.2; 95% CI: 2.3±64.4) compared to children aged 0±4 years, but was significantly lower in HIV-infected patients (aOR: 0.4; 95% CI: 0.2±0.9). CONCLUSION : B lineages co-circulated in most seasons except in 2013 and 2014. Hospitalized SARI cases display differential susceptibility for the two influenza B lineages, with B/Victoria being more prevalent among children and HIV-infected persons.The National Institute for Communicable Diseases (NICD) (http://www.nicd.ac.za/) and the US Centers for Disease Control and Prevention (https://www.cdc. gov/) grant number 5U51/IP000155.http://www.plosone.orgam2017Medical Virolog

Measles outbreak in South Africa: epidemiology of laboratory-confirmed measles cases and assessment of intervention, 2009-2011

BACKGROUND: Since 1995, measles vaccination at nine and 18 months has been routine in South Africa; however, coverage seldom reached .95%. We describe the epidemiology of laboratory-confirmed measles case-patients and assess the impact of the nationwide mass vaccination campaign during the 2009 to 2011 measles outbreak in South Africa. METHODS: Serum specimens collected from patients with suspected-measles were tested for measles-specific IgM antibodies using an enzyme-linked immunosorbent assay and genotypes of a subset were determined. To estimate the impact of the nationwide mass vaccination campaign, we compared incidence in the seven months pre- (1 September 2009–11 April 2010) and seven months post-vaccination campaign (24 May 2010–31 December 2010) periods in seven provinces of South Africa. RESULTS: A total of 18,431 laboratory-confirmed measles case-patients were reported from all nine provinces of South Africa (cumulative incidence 37 per 100,000 population). The highest cumulative incidence per 100,000 population was in children aged ,1 year (603), distributed as follows: ,6 months (302/100,000), 6 to 8 months (1083/100,000) and 9 to 11 months (724/100,000). Forty eight percent of case-patients were $5 years (cumulative incidence 54/100,000). Cumulative incidence decreased with increasing age to 2/100,000 in persons$40 years. A single strain of measles virus (genotype B3) circulated throughout the outbreak. Prior to the vaccination campaign, cumulative incidence in the targeted vs. non-targeted age group was 5.9-fold higher, decreasing to 1.7 fold following the campaign (P,0.001) and an estimated 1,380 laboratoryconfirmed measles case-patients were prevented. CONCLUSION: We observed a reduction in measles incidence following the nationwide mass vaccination campaign even though it was conducted approximately one year after the outbreak started. A booster dose at school entry may be of value given the high incidence in persons .5 years.Our acknowledgements go to the Department of Health South Africa, National, provincial and districts, the South African Field Epidemiology and Laboratory Training Programme (SAFELTP), for ongoing support in surveillance and outbreak activities; Division of Epidemiology (Tsakani Nkuna, Kelebogile Lebogang Motsepe) and Virology (Londiwe Mahlaba, Mduduzi Buthelezi, Nomfundo Radebe, Muzi Hlanzi, Wayne Howard) at the NICD-NHLS for data management and laboratory testing support respectively and Private Laboratories for their support and referring specimens to the NICD.www.plosone.orgam201

The role of human immunodeficiency virus in influenza- and respiratory syncytial virus-associated hospitalizations in South African children, 2011-2016

BACKGROUND : Data describing influenza– or respiratory syncytial virus (RSV)–associated hospitalized illness in children aged <5 years in Africa are limited. METHODS : During 2011–2016, we conducted surveillance for severe respiratory illness (SRI) in children aged <5 years in 3 South African hospitals. Nasopharyngeal aspirates were tested for influenza and RSV using real-time reverse transcription polymerase chain reaction. We estimated rates of influenza- and RSV-associated hospitalized SRI by human immunodeficiency virus (HIV) status and compared children who tested positive for influenza vs RSV using multivariable penalized logistic regression. RESULTS : Among 3650 hospitalized children, 203 (5.6%) tested positive for influenza viruses, 874 (23.9%) for RSV, and 19 (0.5%) for both. The median age of children hospitalized with influenza was 13.9 months vs 4.4 months for RSV (P < .01). Annual influenza-associated hospitalization rates per 100000 were highest among infants aged 6–11 months (545; 95% confidence interval [CI], 409–703), while RSV-associated hospitalization rates were highest in infants aged 0–2 months (6593; 95% CI, 5947–7217). HIV exposure was associated with increased incidence of influenza- and RSV-associated hospitalization in infants aged 0–5 months, with relative risk (RR) 2.2 (95% CI, 1.4–3.4) and 1.4 (95% CI, 1.3–1.6), respectively. HIV infection was associated with increased incidence of influenza- and RSV-associated hospitalization in all age groups; RR 2.7 (95% CI, 2.0–3.5) and 3.8 (95% CI, 3.1–4.8), respectively. CONCLUSIONS : Influenza- and RSV-associated hospitalizations are common among South African infants. HIV infection and HIV exposure in infants increase risk of influenza- and RSV-associated hospitalization.The CDC through a cooperative agreement with the National Institute for Communicable Diseases, South Africa (5U01IP001048).http://cid.oxfordjournals.orghj2019Medical Virolog

Attributable fraction of influenza virus detection to mild and severe respiratory illnesses in HIV-Infected and HIV-uninfected patients, South Africa, 2012–2016

The attributable fraction (AF) of influenza virus detection to illness has not been described for patients in different age groups or with different HIV infection statuses. We compared the age group–specific prevalence of influenza virus infection among patients with influenza-like illness (ILI) or severe acute or chronic respiratory illness (SARI and SCRI, respectively) with that among controls, stratified by HIV serostatus. The overall AF for influenza virus detection to illness was 92.6% for ILI, 87.4% for SARI, and 86.2% for SCRI. Among HIV-uninfected patients, the AF for all syndromes was highest among persons 65 years of age and lowest among persons 25–44 years of age; this trend was not observed among HIV-infected patients. Overall, influenza viruses when detected in patients with ILI, SARI, or SCRI are likely attributable to illness. This finding is particularly likely among children and the elderly irrespective of HIV serostatus and among HIV-infected persons irrespective of age.The National Institute for Communicable Diseases of the National Health Laboratory Service and the Centers for Disease Control and Prevention (cooperative agreement no. 5U51IP000155).http://wwwnc.cdc.gov/eidam2017Medical Virolog

Rubella in South Africa : an impending Greek tragedy?

BACKGROUND: The incidence of congenital rubella syndrome (CRS) is unknown in South Africa. There is evidence that it may be significant and largely undetected, particularly in the upper socio-economic group. This may be due to incomplete routine administration of MMR vaccine in infancy and a build-up of susceptible females reaching the childbearing age group who could be exposed to the extensive reservoir of virus in the unimmunised public sector of the population. OBJECTIVE: To assess the extent of the immunity gap to rubella by testing for protective IgG antibodies and the incidence of rubella infection by testing for IgM antibodies in sera. The data obtained would also be used to model the extent of CRS. DESIGN: Residual laboratory serum specimens from public and private laboratories were serologically tested for rubella IgG antibodies to investigate the immunity gap in the population and IgM antibodies in sera collected from the measles rashlike illness surveillance programme. Modelling exercises calculated the force of infection and the predicted incidence of CRS in South Africa. RESULTS: The serological immunity gap was significantly greater in the private sector specimens compared with the public sector - 10.7% versus 5.4%, respectively. In most years rubella caused much more rash-like illness than measles, with a significant number (5.1 - 9.6%) of rubella-positive IgM specimens occurring in women of childbearing age. CONCLUSION: Modelling of the data suggests that the extent of CRS may be grossly underestimated in South Africa. Approximately 654 cases are calculated to occur every year. It is suggested that selective immunisation of girls before puberty should be instituted together with a routine rubella immunisation programme of infants to forestall a possible future outbreak of CRS, as occurred in Greece in 1993

Mortality associated with seasonal and pandemic influenza and respiratory syncytial virus among children <5 years of age in a high HIV prevalence setting - South Africa, 1998-2009

BACKGROUND. There are few published data describing the mortality burden associated with influenza and respiratory syncytial virus (RSV) infection in children in low- and middle-income countries and particularly from Africa and settings with high prevalence of human immunodeficiency virus (HIV). METHODS. We modeled the excess mortality attributable to influenza (seasonal and pandemic) and RSV infection by applying Poisson regression models to monthly all-respiratory and pneumonia and influenza deaths, using national influenza and RSV laboratory surveillance data as covariates. In addition, we estimated the seasonal influenza– and RSV-associated deaths among HIV-infected and -uninfected children using Poisson regression models that incorporated HIV prevalence and highly active antiretroviral therapy coverage as covariates. RESULTS. In children less than 5 years of age, the mean annual numbers of seasonal influenza– and RSV-associated allrespiratory deaths were 452 (8 per 100 000 person-years [PY]) and 546 (10 per 100 000 PY), respectively. Infants <1 year of age experienced higher mortality rates compared with children 1–4 years of age for both influenza (22 vs 5 per 100 000 PY) and RSV (35 vs 4 per 100 000 PY). HIV-infected compared with HIV-uninfected children <5 years of age were at increased risk of death associated with influenza (age-adjusted relative risk [aRR], 11.5; 95% confidence interval [CI], 9.6–12.6) and RSV (aRR, 8.1; 95% CI, 6.9–9.3) infection. In 2009, we estimated 549 (11 per 100 000 PY) all-respiratory influenza A(H1N1)pdm09-associated deaths among children aged <5 years. CONCLUSIONS. Our findings support increased research efforts to guide and prioritize interventions such as influenza vaccination and HIV prevention in low- and middle-income countries with high HIV prevalence such as South Africa.http://cid.oxfordjournals.orghb201