Science Focus Issue 1 — November 2013 A bi-monthly newsletter that acknowledges NICD staffers who have published in peer reviewed journals.The Science Focus is a quarterly compilation of the scientific publications included in the quarterly report submitted to the National Department of Health and includes only publications where an NICD staff member is either the first or the last author. A DIMORPHIC FUNGUS CAUSING DISSEMINATED INFECTION IN SOUTH AFRICA Kenyon C, Bonorchis K, Corcocan C, Meintjes G, Locketz M, Lehloenya R, Vismer HF, Naicker P, Prozesky H, van Wyk M, Bamford C, du Plooy M, Imrie G, Dlamini S, Borman AM, Colebunders R, Yansouni CP, Mendelson M, Govender NP Govender NP The genus Emmonsia contains three species that are associated with human disease. Emmonsia crescens and Emmonsia parva are the agents that cause adiaspiromycosis, and one human case of Emmonsia pasteuriana infection has been described. We report a fungal pathogen within the genus Emmonsia that is most closely related to E. pasteuriana in human immunodeficiency virus (HIV)-infected adults in South Africa. Between July 2008 and July 2011, we conducted enhanced surveillance to identify the cause of systemic, dimorphic fungal infections in patients presenting to Groote Schuur Hospital and other hospitals affiliated with the University of Cape Town, Cape Town, South Africa. DNA sequencing was used to identify pathogenic fungi. A total of 24 cases of dimorphic fungal infection were diagnosed, 13 of which were caused by an Emmonsia species. All 13 patients were HIV-infected, with a median CD4+ T-cell count of 16 cells per cubic millimeter (interquartile range, 10 to 44), and all had evidence of disseminated fungal disease. Three patients died soon after presentation, but the others had a good response to a variety of antifungal agents and antiretroviral therapy. Phylogenetic analysis of five genes (LSU, ITS1-2, and the genes encoding actin, β-tubulin, and intein PRP8) revealed that this fungus belongs in the genus Emmonsia and is most closely related to E. pasteuriana. The findings suggest that these isolates of an Emmonsia species represent a new species of dimorphic fungus that is pathogenic to humans. The species appears to be an important cause of infections in Cape Town. Impact factor: 51.658 VIRAL ESCAPE FROM HIV-1 NEUTRALIZING ANTIBODIES DRIVES INCREASED PLASMA NEUTRALIZING BREADTH THROUGH SEQUENTIAL RECOGNITION OF MULTIPLE EPITOPES AND IMMUNOTYPES Wibmer CK, Bhiman JN, Gray ES, Tumba N, Abdool Karim SS, Williamson C, Morris L, Moore PL Identifying the targets of broadly neutralizing antibodies to HIV-1 and understanding how these antibodies develop remain important goals in the quest to rationally develop an HIV-1 vaccine. We previously identified a participant in Wibmer CK the CAPRISA Acute Infection Cohort (CAP257) whose plasma neutralized 84% of heterologous viruses. In this study we showed that breadth in CAP257 was largely due to the sequential, transient appearance of three distinct broadly neutralizing antibody specificities spanning the first 4.5 years of infection. The first specificity targeted an epitope in the V2 region of gp120 that was also recognized by strain-specific antibodies 7 weeks earlier. Specificity for the autologous virus was determined largely by a rare N167 antigenic variant of V2, with viral escape to the more common D167 immunotype coinciding with the development of the first wave of broadly neutralizing antibodies. Escape from these broadly neutralizing V2 antibodies through deletion of the glycan at N160 was associated with exposure of an epitope in the CD4 binding site that became the target for a second wave of broadly neutralizing antibodies. Neutralization by these CD4 binding site antibodies was almost entirely dependent on the glycan at position N276. Early viral escape mutations in the CD4 binding site drove an increase in wave two neutralization breadth, as this second wave of heterologous neutralization matured to recognize multiple immunotypes within this site. Altogether this study showed that the human immune system is capable of generating multiple broadly neutralizing antibodies in response to a constantly evolving viral population that exposes new targets as a consequence of escape from earlier neutralizing antibodies. Impact factor: 8.14 1 HIV AND INFLUENZA INFECTION ARE ASSOCIATED WITH INCREASED BLOOD PNEUMOCOCCAL LOAD,SOUTH AFRICA,2009-2011 Wolter N, Cohen C, Tempia S, Madhi SA, Venter M, Moyes J, Walaza S, Kgokong BM, Groome M, du Plessis M, Pretorius M, Dawood H, Kahn K, Variava E, Klugman KP, von Gottberg A 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. Wolter N Impact factor: 5.848 GENETIC CHARACTERIZATION OF HERPES SIMPLEX VIRUS TYPE 2 UL23 THYMIDINE KINASE IN JOHANNESBURG,SOUTH AFRICA Müller EE, Magooa MP, Lewis DA Müller EE Herpes simplex virus type 2 (HSV-2) is currently the leading cause of Genital Ulcer Disease (GUD) both globally and within South Africa. HSV-2 infections are most often treated with acyclovir (ACV), a guanosine nucleoside analogue that requires phosphorylation by virus -encoded thymidine kinase (TK). Resistance to ACV is mainly due to mutations in the viral UL23 gene that codes for TK. ACV was added as part of the first-line syndromic management treatment algorithm for GUD in South Africa in late 2008. In order to assess the prevalence of TK-associated ACV resistance among HSV-2 virions detected in genital ulcer specimens, pre- and post-introduction of ACV, we amplified and fully sequenced the UL23 gene of 254 HSV-2 positive specimens obtained from participants in GUD aetiological surveys conducted between 2007 and 2011 in Johannesburg, South Africa. We identified 63 nucleotide mutations in the UL23 genes analysed, that resulted in 30 silent mutations and 32 amino acid changes. A large proportion (41%) of these amino acid changes were due to previously described natural polymorphisms that occur in both sensitive and resistant HSV strains. In addition, we identified 19 unknown amino acid changes in 30 samples that have not been described before. All mutations detected were outside the recognised TK conserved domains where ACV resistance mutations typically occur. No frameshift mutations or mutations causing stop codons were identified in those UL23 genes analysed. Importantly, no evidence was found of known ACV resistance mutations in HSV-2 following the addition of ACV as first-line therapy for GUD. Impact factor: 3.685 2 PROSPECTIVE COHORT STUDY COMPARING SEASONAL AND H1N1 (2009) PANDEMIC INFLUENZA VIRUS ILLNESSES IN HIV INFECTED CHILDREN DURING 2009 Madhi SA, Kuwanda L,Venter M, Violari A Madhi SA A cohort of 410 young HIV-infected children was prospectively investigated for seasonal and A (H1N1p)2009 influenza virus illness during 2009. The incidence of confirmed illness due to seasonal influenza was three-fold greater than A(H1N1p)2009 (0.7 vs. 0.2 per 100 child-weeks, respectively; p=0.0001) and the clinical presentations were similar. Illnesses due to seasonal and A(H1N1p)2009 influenza were self-limiting without neuraminidase inhibitor therapy. Impact factor: 3.569 EPIDEMIOLOGY OF INVASIVE PNEUMOCOCCAL DISEASE IN THE PRE-CONJUGATE VACCINE-ERA: SOUTH AFRICA,2003-2008 von Gottberg A, Cohen C, de Gouveia L, Meiring S, Quan V, Whitelaw A, Crowther-Gibson P, Madhi SA, Whitney CG, Klugman KP von Gottberg A Dynamics of pneumococcal disease incidence and serotype distribution prior to introduction of pneumococcal conjugate vaccines (PCV) will assist in understanding effects of the vaccine over time and will be important in choosing the optimal PCV formulation.We conducted active, laboratory-based, national surveillance for invasive pneumococcal disease (IPD) through the Group for Enteric, Respiratory and Meningeal Disease Surveillance in South Africa (GERMS-SA) from 2003 through 2008. Over 130 laboratories report to this system. Pneumococci were serotyped using Quellung and isolates screened for resistance by disk diffusion; minimum inhibitory concentrations were determined on potentially resistant isolates. We used univariate and multivariable multinomial regression models to assess differences between serotypes.GERMS-SA identified 8674 cases among children <5 years. Overall, 58% (3849/6668), 65% (4314/6668), and 85% (5669/6668) of cases and 61% (455/751), 64% (482/751), 82% (616/751) of deaths were due to serotypes included in 7-valent PCV, 10-valent PCV and 13-valent PCV, respectively. Serotypes 6A and 19A accounted for 16% (527/3252) of penicillin non-susceptible disease. In 2008, reported incidence of IPD was 6-fold higher in children <1 compared to children 1-4 years of age: 87 per 100,000 population and 14/100,000, respectively. The relative risk of IPD was 21-fold (95% CI, 19-24) and 34-fold (29-41) greater in HIV-infected compared to HIV-uninfected children in the <1 year and 1-4-year-old age groups respectively. On multivariable analysis serotypes 6B (relative risk ratio (RRR) 0.7; confidence interval (CI) 0.5-0.9), 18C (RRR 0.3; CI 0.1-0.5), 1 (RRR 0.2; CI 0.1-0.4) and 8 (RRR 0.2; CI 0.1-0.4) were significantly less common in HIV-infected individuals than serotype 14. All vaccine formulations have the potential to prevent most cases and deaths from IPD in children in South Africa. Vaccines with protection against 19A would be advantageous in South Africa. Impact factor: 3.492 3 INACTIVATED WEST NILE VIRUS (WNV) VACCINE, DUVAXYN WNV, PROTECTS AGAINST A HIGHLY NEUROINVASIVE LINEAGE 2 WNV STRAIN IN MICE Venter M, van Vuren PJ, Mentoor J, Paweska J, Williams J Lineage 2 West Nile Virus (WNV) is endemic to southern Africa and Madagascar, and has recently been associated with encephalitis outbreaks in humans and horses in South Africa, central Europe, Italy Venter M and Greece. Commercial vaccines have mostly been evaluated against WNV lineage 1 strains and their efficacy against lineage 2 strains rarely reported. To evaluate protection of Duvaxyn WNV vaccine against lineage 2 strains associated with encephalitis in South Africa, mice were vaccinated twice intramuscularly three weeks apart, and challenged four weeks later with highly neuroinvasive lineage 1 strain NY385/99 or lineage 2 strain SPU93/01. Neutralising antibody titres were measured at the time of challenge and three weeks later. Immunohistochemistry and reverse transcription polymerase chain reaction (RT-PCR) were conducted on brains of mice that succumbed during the trial, on controls and on vaccinated mice that survived. Serum neutralising antibodies in vaccinated mice were detected but low three weeks after primovaccination. Three weeks post-challenge, vaccinated mice had significantly higher serum neutralising antibody titres against both lineages than unvaccinated controls. After challenge, all vaccinated mice remained healthy but all unvaccinated mice demonstrated severe neurological signs with 75% mortality rate. WNV was not detected in brains of vaccinated mice whereas virus replicated in most unvaccinated mice challenged with either lineage. Gross and microscopic lesions were found only in unvaccinated mice challenged with both lineages. Duvaxyn WNV vaccine provided complete protection against challenge with lineage 2 WNV and stimulated significant cross protective neutralising antibodies in mice against lineage 2. Impact factor: 3.492 MECHANISMS OF HIV-1 SUBTYPE C RESISTANCE TO GRFT,CV-N AND SVN Alexandre K, Moore PL,Nonyane M, Gray ES,Ranchobe R, Chakauya E, McMahon J, O’Keefe B, Chikwamba R, Morris L Alexandre K We examined the ability of HIV-1 subtype C to develop resistance to the inhibitory lectins, griffithsin (GRFT), cyanovirin-N (CV-N) and scytovirin (SVN), which bind multiple mannose-rich glycans on gp120. Four primary HIV-1 strains cultured under escalating concentrations of these lectins became increasingly resistant tolerating 2 to 12 times their 50% inhibitory concentrations. Sequence analysis of gp120 showed that most had deletions of 1 to 5 mannose-rich glycans. Glycosylation sites at positions 230, 234, 241, 289 located in the C2 region and 339, 392 and 448 in the C3-C4 region were affected. Furthermore, deletions and insertions of up to 5 amino acids in the V4 region were observed in 3 of the 4 isolates. These data suggest that loss of glycosylation sites on gp120 as well as rearrangement of glycans in V4 are mechanisms involved in HIV-1 subtype C escape from GRFT, CV-N and SVN. Impact factor:3.367 4 TRENDS AND ASSOCIATIONS OF TRICHOMONAS VAGINALIS INFECTION IN MEN AND WOMEN WITH GENITAL DISCHARGE SYNDROMES IN JOHANNESBURG,SOUTH AFRICA Lewis DA, Marsh K, Radebe F, Maseko V, Hughes G Lewis DA To better understand the epidemiology of Trichomonas vaginalis infection, we investigated the association between T vaginalis and demographic, clinical, microbiological and behavioural characteristics of patients presenting with genital discharges to a primary healthcare clinic in Johannesburg, South Africa. During six annual surveys (2007-2012), 1218 cases of male urethral discharge syndrome and 1232 cases of vaginal discharge syndrome were consecutively recruited. Diagnostic methods included nucleic acid amplification (Neisseria gonorrhoeae, Chlamydia trachomatis, T vaginalis and Mycoplasma genitalium), microscopy (bacterial vaginosis and Candida) and serology (Treponema pallidum, herpes simplex virus type 2 (HSV-2) and HIV). Logistic regression analyses and χ2 tests were used to identify predictors of T vaginalis infection. The prevalence of T vaginalis decreased from 2007 to 2012 (men from 13.4% to 4.8%; women from 33.8 to 23.1%). Overall, 74 (6.1%) men and 291 (23.6%) women were T vaginalis positive, with the highest prevalence in those aged ≥40 years (men 13.6%; women 30.9%). T vaginalis infection occurred more often in pregnant women (adjusted OR (aOR) 2.67; 95% CI 1.29 to 5.54) and in women with serological evidence of T pallidum (aOR 1.63; 95% CI 1.08 to 2.45) or HSV-2 infections (aOR 1.75; 95% CI 1.16 to 2.64). T vaginalis infection occurred less often in men with coexistent gonorrhoea (aOR 0.35; 95% CI 0.21 to 0.57) and in women with either bacterial vaginosis (aOR 0.60; 95% CI 0.44 to 0.82) or Candida morphotypes (OR 0.61; 95% CI 0.43 to 0.86). Although the prevalence of T vaginalis infection has decreased over time, it remains an important cause of genital discharge in South Africa, particularly in older patients and pregnant women. Impact factor: 2.611 5 FIRST INSIGHTS INTO SPECIES AND GENOTYPES OF ECHINOCOCCUS IN SOUTH AFRICA Mogoye BK, Menezes CN, Wong ML, Stacey S, von Delft D, Wahlers K, Wassermann M, Romig T, Kern P, Grobusch MP, Frean J Frean J Cystic echinococcosis is a serious and neglected parasitic zoonosis that is regarded as an emerging disease world-wide. Effective control of the disease is based on understanding the variability of Echinococcus granulosus (sensu lato), as genotypic characteristics may influence lifecycle patterns, development rate, and transmission. No molecular epidemiological research has previously been conducted to shed light on genotypes responsible for the disease in South Africa. To identify strains circulating in the country, parasite material was collected from patients between August 2010 and September 2012 and analyzed by PCR/RFLP methods. A total of 32 samples was characterized as E. granulosus sensu stricto (G1-G3) (81%), E. canadensis (G6/7) (16%) and E. ortleppi (G5) (3%). Furthermore, two co-amplifying G6/7 genotypes were confirmed as G7 by sequencing. This is the first report on genotyping of Echinococcus species in South Africa, and, to the best of our knowledge, the first report of the G5 and G7 genotypes from humans in Africa. Impact factor: 2.381 DEVELOPMENT OF A RIFT VALLEY FEVER REAL-TIME RT-PCR ASSAY THAT CAN DETECT ALL THREE GENOME SEGMENTS Wilson WC, Romito M, Jasperson DC, Weingartl H, Binepal YS, Maluleke MR, Wallace DB, van Vuren PJ, Paweska JT Paweska JT Outbreaks of Rift Valley fever in Kenya, Madagascar, Mauritania, and South Africa had devastating effects on livestock and human health. In addition, this disease is a food security issue for endemic countries. There is growing concern for the potential introduction of RVF into non-endemic countries. A number of single-gene target amplification assays have been developed for the rapid detection of RVF viral RNA. This paper describes the development of an improved amplification assay that includes two confirmatory target RNA segments (L and M) and a third target gene, NSs, which is deleted in the Clone 13 commercial vaccine and other candidate vaccines. The assay also contains an exogenous RNA control added during the PCR setup for detection of amplification inhibitors. The assay was evaluated initially with samples from experimentally infected animals, after which clinical veterinary and human samples from endemic countries were tested for further evaluation. The assay has a sensitivity range of 66.7-100% and a specificity of 92.0-100% depending on the comparison. The assay has an overall sensitivity of 92.5%, specificity of 95% and a positive predictive value of 98.7%. The single-tube assay provides confirmation of the presence of RVFV RNA for improved confidence in diagnostic results and a "differentiate infected from vaccinated animals" (DIVA)--compatible marker for RVFV NSs --deleted vaccines, which is useful for RVF endemic countries, but especially important in non-endemic countries. Impact factor: 2.065 6 MALARIA: CONTROL TO ELIMINATION (SAMJ SUPPLEMENT) Blumberg L, D Moonasar South Africa (SA) is one of 34 malaria-endemic countries that are currently targeting elimination of the disease. This supplement of the SAMJ documents SA’s remarkable public health achievement in moving from malaria control to the threshold of elimination (zero local transmission in a defined geographical area). Nevertheless, SA’s malaria programme still needs to travel some distance before it attains its goal of elimination by 2018. The articles in this supplement pay tribute to sterling efforts by dedicated persons who contributed and guided policies and interventions, not only in SA, but also elsewhere on the African continent and globally. These pioneering efforts deserve high-level recognition. The key lesson from early malaria control is that hard-won gains are rapidly lost when important control measures are curtailed, especially in low-transmission settings. Progress on every front, and at every level, is fragile. Malaria is a disease that can take full advantage of any lapse in investment, vigilance or control. SA has come a long way in fighting malaria. This supplement is a useful reference for those keen to learn lessons from the past, and key issues that need to be addressed to move from malaria control to elimination in SA. These are: targeted approaches to vector control; strong programmes for detection of parasite and vector resistance; active surveillance; ensuring that the chain of transmission is broken; regional and cross-border malaria control initiatives; and maintaining advocacy and political commitment for the malaria programme. The benefits of elimination of the disease in SA lie in demonstrating the country’s ability to tackle a significant public health problem, the positive impact on socioeconomic conditions and health of persons living in affected areas, and increasing the tourism potential of the country. Blumberg L NICD Contributing authors to SAMJ Malaria supplement: Frean J Poonsamy B Coetzee M Mayet NT Koekemoer L Impact factor: 1.676 7 Brooke B Kenyon C, Bonorchis K, Corcocan C, Meintjes G, Locketz M, Lehloenya R, Vismer HF, Naicker P, Prozesky H, van Wyk M, Bamford C, du Plooy M, Imrie G, Dlamini S, Borman AM, Colebunders R, Yansouni CP, Mendelson M, Govender NP. A dimorphic fungus causing disseminated infection in South Africa. The New England Journal of Medicine. 2013 Oct 10;369(15):1416-24. doi: 10.1056/NEJMoa1215460. Wibmer CK, Bhiman JN, Gray ES, Tumba N, Abdool Karim SS, Williamson C, Morris L, Moore PL. Viral escape from HIV-1 neutralizing antibodies drives increased plasma neutralization breadth through sequential recognition of multiple epitopes and immunotypes. PLoS Pathog 9(10):e1003738.doi:10.1371/journal.ppat.1003738 Wolter N, Cohen C, Tempia S, Madhi SA, Venter M, Moyes J, Walaza S, Kgokong BM, Groome M, du Plessis M, Pretorius M, Dawood H, Kahn K, Variava E, Klugman KP, von Gottberg A. HIV and influenza infection are associated with increased blood pneumococcal load,South Africa,2009-2011. The Journal of Infectious Diseases. 2013 August: doi 10.1093/ infdis/jit427 Müller EE, Magooa MP, Lewis DA. Genetic characterization of herpes simplex virus type 2 UL23 thymidine kinase in Johanneburg , South Africa. Journal of Antivirals & Antiretrovirals 5:080-084. doi: 10.4172/jaa.1000068 Madhi SA, Kuwanda L, Venter M, Violari A. Prospective cohort study comparing seasonal and H1N1(2009)pandemic influenza virus illnesses in HIV-infected children during 2009. The Pediatric Infectious Disease Journal. 2013 July 21; doi: 10.1097/INF 0.b013e3182a73ebb von Gottberg A, Cohen C, de Gouveia L, Meiring S, Quan V, Whitelaw A, Crowther-Gibson P, Madhi SA, Whitney CG, Klugman KP. Epidemiology of invasive pneumococcal disease in the pre-conjugate vaccine era: South Africa, 2003-2008.Vaccine. 2013 August 28;31(38): 4200-8 doi: 10.1016/jvaccine.2013.04.077 Venter M, van Vuren PJ, Mentoor J, Paweska J, Williams J. Vaccine. Inactivated West Nile virus (WNV) vaccine, Duvaxyn WNV, protects against a highly neuroinvasive lineage 2 WNV strain in mice. Vaccine. 2013 Aug 20;31 (37):3856-62. doi: 10.1016/j.vaccine.2013.06.059 Alexandre K, Moore PL, Nonyane M, Gray ES, Ranchobe R, Chakauya E, McMahon J, O’Keefe B, Chikwamba R, Morris L. Mechanisms of HIV-1 subtypes resistance to GRFT,CV-N and SVN. Virology. 2013 Nov;446(1-2):66-76. doi: 10.1016/j.virol.2013.07.019 Lewis DA, Marsh K, Radebe F, Maseko V, Hughes G. Trends and associations of Trichomonas vaginalis infection in men and women with genital discharge syndromes in Johannesburg, South Africa. Sexually Transmitted Infections. 2013 Sep;89(6):523-7. doi: 10.1136/sextrans-2013-051049 Mogoye BK, Menezes CN, Wong ML, Stacey S, von Delft D, Wahlers K, Wassermann M, Romig T, Kern P, Grobusch MP, Frean J . First Insights into species and genotypes of Echinococcus in South Africa. Veterinary Parasitology.2013. Sep 23;196(3-4):427-32. doi: 10.1016/j.vetpar.2013.03.033. Wilson WC, Romito M, Jasperson DC, Weingartl H, Binepal YS, Maluleke MR, Wallace DB, van Vuren PJ, Paweska JT. Developments of Rift Valley fever real time PCR-assay that can detect all three genome segments. Journal of Virological Methods. 2013 Nov;193(2):426-31. doi: 10.1016/j.jviromet.2013.07.006. Blumberg L, Moonasar D. Malaria: control to elimination. South African Medical Journal 2013;103(10):769. doi:10.7196/samj.7401 This issue of Science Focus includes publications in the report covering the period July 2013 – September 2013. The abstracts are extracted directly from the publications. Published by NICD Communications. For comments and queries please email: nombusos@nicd.ac.za