Introduction: we investigated an outbreak of influenza-like illness (ILI) at a boarding school in Eastern Cape Province, South Africa. We aimed to confirm the etiological agent, estimate attack rates and identify risk factors for illness.
Abstract Background South Africa bears the highest HIV burden globally, marked by a substantial expansion of antiretroviral therapy (ART) that curbs HIV and AIDS cases, morbidity, and mortality. As a result, it faces potential challenges from HIV drug resistance (HIVDR), which could undermine these advancements and prevent the attainment of UNAIDS 95-95-95 targets. This study investigated the national prevalence, geospatial trends, and predictors of HIVDR in people 15 years and older in South Africa in 2017 before the introduction of dolutegravir containing ART regimens. Methods This study used the 2017 secondary data of 1,974 virally unsuppressed adults aged ≥ 15 years old and were tested for HIVDR from a nationally representative cross-sectional multi-stage stratified cluster random sample survey, the South African National HIV Prevalence, Incidence, Behaviour and Communication Survey (SABSSM V). Univariate and multivariable logistic regression models were used to determine predictors for HIVDR. Geospatial analyses were applied to estimate HIVDR prevalence in all nine provinces and three locality types. Survey weights were used across all analyses to adjust for unequal sampling probabilities and non-responses. Results Of 1,253 participants of PLHIV aged ≥ 15 years, a large portion constituted the 25–34 years age group (33.6%) and females (55.7%). The virally unsuppressed rate was estimated at 37.8% (95%CI: 35.2 to 40.2) for viral non-suppression (≥ 1,000 copies/mL) and 26.3% (95%CI: 22.5 to 30.5) for national HIVDR prevalence (n = 369). Eastern Cape province had the highest HIVDR prevalence at 36.6%, while North-West had the lowest at 21.6%. Multivariable logistic regression model established that exposure to ART (adjusted odds ratio [aOR] 4.44, 95%CI: 2.78 to 7.10, p < 0.001), HIV stigmatisation (aOR 1.66, 95%CI: 1.06 to 2.59, p = 0.025), and secondary schooling as highest education level (aOR 1.71, 95%CI: 1.05 to 2.81, p = 0.032) were risk factors for HIVDR. However, being aged 25–34 years (aOR 0.50, 95%CI: 0.25 to 0.99, p = 0.047) and ≥ 45 years old (aOR 0.45, 95%CI: 0.21 to 0.94, p = 0.033) were identified as protective factors against HIVDR compared to the younger age group of 15–24 years. Conclusion High HIVDR prevalence estimates among the virally unsuppressed PLHIV on ART emphasize the importance of increasing viral load testing, enhancing adherence counselling, and prompt switching to the appropriate ART regimens. The analysis revealed that exposure to ART, HIV stigmatisation, and secondary education level were identified as risk factors associated with HIVDR, while older age groups, specifically 25–34 and ≥ 45 years old, exhibited a protective effect against HIVDR.
Data on the susceptibility of influenza viruses from South Africa to neuraminidase inhibitors (NAIs) are scarce, and no extensive analysis was done.We aimed to determine oseltamivir and zanamivir susceptibility of influenza A and B virus neuraminidases (NAs), 2007-2013, South Africa.We enrolled participants through national influenza-like illness surveillance, 2007-2013. Influenza diagnosis was by virus isolation and quantitative polymerase chain reaction (qPCR). Drug susceptibility was determined by chemiluminescence-based NA-STAR/NA-XTD assay. Sanger sequencing was used to determine molecular markers of NAI resistance.Forty percent (6341/15 985) of participants were positive for influenza viruses using virus isolation (2007-2009) and qPCR (2009-2013) methods. A total of 1236/6341 (19.5%) virus isolates were generated of which 307/1236 (25%) were tested for drug susceptibility. During 2007-2008, the median 50% inhibitory concentration (IC50 ) of oseltamivir for seasonal influenza A(H1N1) increased from of 0.08 nmol/L (range 0.01-3.60) in 2007 to 73 nmol/L (range 1.56-305 nmol/L) in 2008. Influenza A isolates from 2009 to 2013 were susceptible to oseltamivir [A(H3N2) median IC50 = 0.05 nmol/L (range 0.01-0.08); A(H1N1)pdm09 = 0.11 nmol/L (range 0.01-0.78)] and zanamivir [A(H3N2) median IC50 = 0.56 nmol/L (range 0.47-0.66); A(H1N1)pdm09 = 0.35 nmol/L (range 0.27-0.533)]. Influenza B viruses were susceptible to both NAIs. NAI resistance-associated substitutions H275Y, E119V, and R150K (N1 numbering) were not detected in influenza A viruses that circulated in 2009-2013.We confirm replacement of NAI susceptible by resistant phenotype influenza A(H1N1) in 2008. Influenza A and B viruses (2009-2013) remained susceptible to NAIs; therefore, these drugs are useful for treating influenza-infected patients.
Abstract Background In June 2017, an outbreak of the highly pathogenic avian influenza A(H5N8) was detected in commercial poultry farms in South Africa, which rapidly spread to all nine South African provinces. Objectives We conducted active surveillance for the transmission of influenza A(H5N8) to humans working with infected birds during the South African outbreak. Methods Influenza A(H5N8)‐positive veterinary specimens were used to evaluate the ability of real‐time PCR‐based assays to detect contemporary avian influenza A(H5N8) strains. Whole genome sequences were generated from these specimens by next‐generation sequencing for phylogenetic characterization and screening for mammalian‐adaptive mutations. Results Human respiratory samples from 74 individuals meeting our case definition, all tested negative for avian influenza A(H5) by real‐time PCR, but 2 (3%) were positive for human influenza A(H3N2). 54% (40/74) reported wearing personal protective equipment including overalls, boots, gloves, masks, and goggles. 94% (59/63) of veterinary specimens positive for H5N8 were detected on an influenza A(H5) assay for human diagnostics. A commercial H5N8 assay detected H5 in only 6% (3/48) and N8 in 92% (44/48). Thirteen (13/25; 52%) A(H5N8) genomes generated from veterinary specimens clustered in a single monophyletic clade. These sequences contained the NS (P42S) and PB2 (L89V) mutations noted as markers of mammalian adaptation. Conclusions Diagnostic assays were able to detect and characterize influenza A(H5N8) viruses, but poor performance is reported for a commercial assay. Absence of influenza A(H5N8) in humans with occupational exposure and no clear impression of molecular adaptation for mammalian infection suggest that this avian pathogen continues to be low‐risk human pathogen.
Data on risk factors for influenza-associated hospitalizations in low- and middle-income countries are limited.We conducted active syndromic surveillance for hospitalized severe acute respiratory illness (SARI) and outpatient influenza-like illness (ILI) in 2 provinces of South Africa during 2012-2015. We compared the characteristics of influenza-positive patients with SARI to those with ILI to identify factors associated with severe disease requiring hospitalization, using unconditional logistic regression.During the study period, influenza virus was detected in 5.9% (110 of 1861) and 15.8% (577 of 3652) of SARI and ILI cases, respectively. On multivariable analysis factors significantly associated with increased risk of influenza-associated SARI hospitalization were as follows: younger and older age (<6 months [adjusted odds ratio {aOR}, 37.6], 6-11 months [aOR, 31.9], 12-23 months [aOR, 22.1], 24-59 months [aOR, 7.1], and ≥65 years [aOR, 40.7] compared with 5-24 years of age), underlying medical conditions (aOR, 4.5), human immunodeficiency virus infection (aOR, 4.3), and Streptococcus pneumoniae colonization density ≥1000 deoxyribonucleic acid copies/mL (aOR, 4.8). Underlying medical conditions in children aged <5 years included asthma (aOR, 22.7), malnutrition (aOR, 2.4), and prematurity (aOR, 4.8); in persons aged ≥5 years, conditions included asthma (aOR, 3.6), diabetes (aOR, 7.1), chronic lung diseases (aOR, 10.7), chronic heart diseases (aOR, 9.6), and obesity (aOR, 21.3). Mine workers (aOR, 13.8) and pregnant women (aOR, 12.5) were also at increased risk for influenza-associated hospitalization.The risk groups identified in this study may benefit most from annual influenza immunization, and children <6 months of age may be protected through vaccination of their mothers during pregnancy.
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