Enterovirus D68 and other enterovirus serotypes identified in South African patients with severe acute respiratory illness, 2009-2011

BACKGROUND : Human enteroviruses (EV) have been associated with severe acute respiratory illness (SARI) in South Africa. OBJECTIVES : We aimed to describe the molecular epidemiology of EV serotypes among patients hospitalized with SARI during 2009-2011. PATIENTS/METHODS : Study samples from patients were tested for the presence of enterovirus using a polymerase chain reaction assay. RESULTS : 8.2% (842/10 260) of SARI cases tested positive for enterovirus; 16% (7/45) were species EV-A, 44% (20/45) EV-B, 18% (8/45) EV-C and 22% (10/45) EV-D. Seventeen different EV serotypes were identified within EV-A to EV-D, of which EV-D68 (22%; 10/45) and Echovirus 3 (11%; 5/45) were the most prevalent. CONCLUSIONS : EV-D68 should be monitored in South Africa to assess the emergence of highly pathogenic strains.The United States Centers for Disease Control and Prevention, Atlanta, Georgia, USA (co-operative agreement number: 5U51IP000155).http://www.wileyonlinelibrary.com/journal/irvhttp://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1750-2659am2018Medical Virolog

Genetic diversity and molecular epidemiology of human rhinoviruses in South Africa

BACKGROUND Rhinoviruses (RV) are a well-established cause of respiratory illness. RV-C has been associated with more severe illness. We aimed to characterize and compare the clinical presentations and disease severity of different RV type circulating in South Africa. METHOD We performed two analyses of RV-positive specimens identified through surveillance in South Africa across all age groups. First, RV-positive specimens identified through severe acute respiratory illness (SARI) surveillance in four provinces was randomly selected from 2009 to 2010 for molecular characterization. Second, RV-positive specimens identified through SARI, influenzalike illness (ILI) and control surveillance at hospitals and outpatient clinics in during 2012–2013 were used to determine the association of RV type with severe disease. Selected specimens were sequenced, and phylogenetic analysis was performed. RESULTS Among the 599 sequenced specimens from 2009 to 2010 and 2012 to 2013, RV-A (285, 48%) and RV-C (247, 41%) were more commonly identified than RV-B (67, 11%), with no seasonality and a high genetic diversity. A higher prevalence of RV infection was identified in cases with SARI [515/962 (26%); aRRR = 1 6; 95% CI 1 21; 2 2] and ILI [356/962 (28%); aRRR = 1 9; 95% CI 1 37; 2 6] compared with asymptomatic controls (91/962, 22%). There was no difference in disease severity between the different type when comparing SARI, ILI and controls. CONCLUSION All three type of RV were identified in South Africa, although RV-A and RV-C were more common than RV-B. RV was associated with symptomatic respiratory illness; however, there was no association between RV type and disease severity.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1750-2659http://www.influenzajournal.comam201

Epidemiology of acute lower respiratory tract infection in HIV exposed uninfected infants

BACKGROUND : Increased morbidity and mortality from lower respiratory tract infection (LRTI) abstract has been suggested in HIV-exposed uninfected (HEU) children; however, the contribution of respiratory viruses is unclear. We studied the epidemiology of LRTI hospitalization in HIVunexposed uninfected (HUU) and HEU infants aged <6 months in South Africa. METHODS : We prospectively enrolled hospitalized infants with LRTI from 4 provinces from 2010 to 2013. Using polymerase chain reaction, nasopharyngeal aspirates were tested for 10 viruses and blood for pneumococcal DNA. Incidence for 2010–2011 was estimated at 1 site with population denominators. RESULTS : We enrolled 3537 children aged <6 months. HIV infection and exposure status were determined for 2507 (71%), of whom 211 (8%) were HIV infected, 850 (34%) were HEU, and 1446 (58%) were HUU. The annual incidence of LRTI was elevated in HEU (incidence rate ratio [IRR] 1.4; 95% confidence interval [CI] 1.3–1.5) and HIV infected (IRR 3.8; 95% CI 3.3–4.5), compared with HUU infants. Relative incidence estimates were greater in HEU than HUU, for respiratory syncytial virus (RSV; IRR 1.4; 95% CI 1.3–1.6) and human metapneumovirus–associated (IRR 1.4; 95% CI 1.1–2.0) LRTI, with a similar trend observed for influenza (IRR 1.2; 95% CI 0.8–1.8). HEU infants overall, and those with RSV-associated LRTI had greater odds (odds ratio 2.1, 95% CI 1.1–3.8, and 12.2, 95% CI 1.7–infinity, respectively) of death than HUU. CONCLUSIONS : HEU infants were more likely to be hospitalized and to die in-hospital than HUU, including specifically due to RSV. This group should be considered a high-risk group for LRTI.http://pediatrics.aappublications.orgam2017Medical Virolog

HIV and influenza infection are associated with increased blood pneumococcal load : a prospective, hospital-based observational study in South Africa, 2009–2011

BACKGROUND : Increased pneumococcal loads are associated with severe outcomes. We determined the prevalence of pneumococcal DNA in blood specimens from patients hospitalized with acute lower respiratory tract infection and identified factors associated with invasive pneumococcal pneumonia, bacterial loads, and death. METHODS : A total of 8523 patients were enrolled as part of prospective hospital-based surveillance. Blood was collected for quantitative pneumococcal (lytA) detection, and nasopharyngeal specimens were collected for detection of influenza virus and other respiratory viruses by real-time polymerase chain reaction. RESULTS : Of 6396 cases (75%) with lytA results, 422 (7%) were positive for pneumococcal DNA. The prevalences of human immunodeficiency virus (HIV) and influenza virus were 51% (2965/5855) and 8% (485/6358), respectively. On multivariable analysis, HIV infection (adjusted odds ratio [aOR], 2.4; 95% confidence interval [CI], 1.6–3.6), influenza virus coinfection (aOR, 1.4; 95% CI, 1.2–2.1), oxygen therapy during admission (aOR, 1.6; 95% CI, 1.1– 2.3) and in-hospital death (aOR, 2.1; 95% CI, 1.1–4.0) were significantly associated with increased pneumococcal load. Among lytA-positive patients, after adjustment for length of hospitalization, duration of symptoms, and oxygen therapy during admission, pneumococcal loads ≥10,000 DNA copies/mL (aOR, 3.6; 95% CI, 1.8–7.2) were associated with increased risk of death. CONCLUSIONS : HIV and influenza virus infections were associated with elevated pneumococcal loads, which, in turn, were associated with increased risk of death.http://jid.oxfordjournals.orghb201

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

Human metapneumovirus-associated severe acute respiratory illness hospitalisation in HIV-infected and HIV-uninfected South African children and adults

BACKGROUND : Data on human metapneumovirus (HMPV)-associated severe acute respiratory illness (SARI) are limited in settings with high human immunodeficiency virus (HIV) infection prevalence. OBJECTIVES : To describe clinical characteristics and seasonality (all sites), and incidence (Soweto only) of HMPV-associated SARI among children and adults. STUDY DESIGN : Active, prospective, hospital-based, sentinel surveillance for patients hospitalised with SARI was conducted at four sites in South Africa from February 2009−December 2013. Upper respiratory tract samples were tested by multiplex real-time polymerase chain reaction assays for HMPV and other respiratory viruses. Incidence of hospitalisation, stratified by age and HIV-infection status, was calculated for one hospital with population denominators. RESULTS : HMPV was identified in 4.1% of patients enrolled, including 5.6% (593/10503) in children and 1.7% in adults (≥18 years; 119/6934). The majority of adults (84.0%) had an underlying medical condition, including HIV infection in 87/110 (79.1%). HMPV detection occurred perennially with periods of increased detection, which varied from year to year. The incidence of HMPV-associated hospitalisation in Soweto was highest in infants (653.3 per 100 000 person-years; 95% confidence interval (CI) 602.2−707.6). The incidence was higher in HIV-infected persons compared to HIV-uninfected persons in age-groups 5−17 years (RR 6.0; 1.1−20.4), 18−44 years (RR 67.6; 38.0−132.6) and 45−64 years (RR 5.3; 3.4−8.3), while not differing in other age-groups. CONCLUSIONS : The burden of HMPV-associated SARI hospitalisation among adults occurred predominantly in HIV-infected persons. Among children, infants were at highest risk, with similar burden of hospitalisation in HIV-infected and HIV-uninfected children.The National Institute for Communicable Diseases of the National Health Laboratory Service and was supported in part by funds from the United States Centers for Disease Control and Prevention (CDC), Atlanta, Georgia Preparedness and Response to Avian and Pandemic Influenza in South Africa (Cooperative Agreement Number: U51/IP000155-04).http://www.elsevier.com/locate/jcvhb2017Mathematics and Applied Mathematic

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

Epidemiology of viral-associated acute lower respiratory tract infection among children < 5 years of age in a high HIV prevalence setting, South Africa, 2009-2012

BACKGROUND : Data on the epidemiology of viral-associated acute lower respiratory tract infection (LRTI) from high HIV prevalence settings are limited. We aimed to describe LRTI hospitalizations among South African children aged <5 years. METHODS : We prospectively enrolled hospitalized children with physiciandiagnosed LRTI from 5 sites in 4 provinces from 2009 to 2012. Using polymerase chain reaction (PCR), nasopharyngeal aspirates were tested for 10 viruses and blood for pneumococcal DNA. Incidence was estimated at 1 site with available population denominators. RESULTS : We enrolled 8723 children aged <5 years with LRTI, including 64% <12 months. The case-fatality ratio was 2% (150/8512). HIV prevalence among tested children was 12% (705/5964). The overall prevalence of respiratory viruses identified was 78% (6517/8393), including 37% rhinovirus, 26% respiratory syncytial virus (RSV), 7% influenza and 5% human metapneumovirus. Four percent (253/6612) tested positive for pneumococcus. The annual incidence of LRTI hospitalization ranged from 2530 to 3173/100,000 population and was highest in infants (8446–10532/100,000). LRTI incidence was 1.1 to 3.0-fold greater in HIV-infected than HIV-uninfected children. In multivariable analysis, compared to HIV-uninfected children, HIVinfected children were more likely to require supplemental-oxygen [odds ratio (OR): 1.3, 95% confidence interval (CI): 1.1–1.7)], be hospitalized >7 days (OR: 3.8, 95% CI: 2.8–5.0) and had a higher case-fatality ratio (OR: 4.2, 95% CI: 2.6–6.8). In multivariable analysis, HIV-infection (OR: 3.7, 95% CI: 2.2–6.1), pneumococcal coinfection (OR: 2.4, 95% CI: 1.1–5.6), mechanical ventilation (OR: 6.9, 95% CI: 2.7–17.6) and receipt of supplemental- oxygen (OR: 27.3, 95% CI: 13.2–55.9) were associated with death. CONCLUSIONS : HIV-infection was associated with an increased risk of LRTI hospitalization and death. A viral pathogen, commonly RSV, was identified in a high proportion of LRTI cases.http://journals.lww.com/pidjhb201

Investigation of the association of Rhinovirus and Respiratory Syncytial Virus with severe acute respiratory illness in South Africa

Pneumonia is a major cause of morbidity and mortality in children worldwide and causes 18% of all deaths in children less than 5 years of age. In order to best understand the full burden of acute respiratory infection in South Africa, it is important to conduct surveillance and measure the burden of mild, outpatient disease as well as more severe, inpatient disease. By comparing the prevalence of these respiratory viruses detected in patients with influenza-like illness (ILI) and severe acute respiratory illness (SARI) to control patients the contribution of these respiratory viruses to SARI maybe better understood. The aim of this study was to determine the contribution of the major respiratory viruses to severe acute respiratory illness in South Africa both during and after the pandemic and compare molecular epidemiology and host innate immune responses as factors that may influence the role of the two most frequently detected viruses, respiratory syncytial virus (RSV) and rhinovirus as pathogens in a population with a high HIV sero-prevalence. To facilitate the detection of these viruses, a multiplex reverse transcription real-time polymerase chain reaction (rRT-PCR) assay that can detect the ten major respiratory viruses influenza A and B, RSV, enterovirus, human metapneumovirus, adenovirus, rhinovirus and parainfluenza 1, 2 and 3, was developed. This assay allowed us to determine the prevalence of these respiratory viruses in patients with SARI, ILI and controls, as well as to determine the attributable fraction of each of these viruses in SARI and ILI relative to controls. We were also able to determine the seasonality of each of these viruses in South Africa. While RSV was detected most frequently in children, rhinovirus was by far the most prevalent virus detected over all age groups in the study. We described the molecular epidemiology of rhinovirus in SARI, ILI and control cases to determine whether a specific rhinovirus species could be linked to severe disease. All 3 species of rhinovirus was identified in South Africa, although RV-A and RV-C were more common than RV-B. While rhinovirus was associated with symptomatic respiratory illness; there was no association between RV species and disease severity. In order to determine if RSV genotypes could be identified in more severe cases and how the virus re-establish epidemics over time, we described the molecular epidemiology of RSV over 16 years in South Africa. Positive selection drove both RSV-A and B genotypes to evolve, resulting in replacement of all genotypes over the 16-year period in South Africa. We were unable to attribute more severe disease to either RSV-A or B; rather that it was linked to the predominant strain of the season, which was likely driven by herd immunity in previous seasons. In a previous study in South Africa RSV-B deletion mutants were identified in HIV-infected patients in South Africa. To determine the frequency of this phenomena and the possible role in disease in these patients the surveillance program was used to address these questions in a larger population group. Deletions in the G-protein of both RSV-A and RSV-B strains were identified in HIV-infected SARI patients. Whole genome analysis of the deletion mutants revealed that even though there were unique non-synonymous mutations for the deletions mutants and the cumulative effect of these substitutions might affect RSV fitness, no changes were observed that could result in altered virus-host attachment, changes in immune evasion strategies or distorted fusion abilities. The specimens obtained from the patients carrying the RSV strains containing the G-protein deletions contained significantly lower levels of pro-and anti-inflammatory cytokines, suggesting that the absence of the G-protein inhibited the virus s ability to activate the normal RSV anti-viral response. The inflammatory responses of children infected by RSV, rhinovirus or both showed that rhinovirus infection elicits a strong Th1 response, while RSV infection skews the balance towards a Th2 response. Co-infections did not result in more severe disease and the effect that these 2 viruses have on the innate immune response may results in a further Th1/Th2 imbalance. Understanding the contribution of RSV and RV to severe respiratory disease will allow for informed decision making when selecting and setting criteria for vaccine development and implementation as well as therapeutic interventions. To conclude, this study provided a useful tool for defining the major respiratory viruses in SARI and confirmed the importance of Influenza, RSV, rhinovirus, and human metapneumovirus as pathogens. Changes in the circulating strains of RSV may overcome herd immunity and re-establish infections. RSV G-protein deletion mutants appeared only in HIV-infected patients and had a much reduced immune-modulatory effect relative to wild type strains. Results suggest that a co-infection between RSV and rhinovirus will further imbalance the innate immune response and may affect the pathogenesis in HIV infected and young patients.Thesis (PhD)--University of Pretoria, 2016.Medical VirologyPhDUnrestricte