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1. Full Text Effects of Vaccination on Invasive Pneumococcal Disease in South Africa
by von Gottberg, Anne and de Gouveia, Linda and Tempia, Stefano and Quan, Vanessa and Meiring, Susan and von Mollendorf, Claire and Madhi, Shabir A and Zell, Elizabeth R and Verani, Jennifer R and O’Brien, Katherine L and Whitney, Cynthia G and Klugman, Keith P and Cohen, Cheryl and GERMS-SA Investigators
The New England Journal of Medicine, ISSN 0028-4793, 11/2014, Volume 371, Issue 20, pp. 1889 - 1899
Invasive pneumococcal disease is an important cause of severe illness. In South Africa, a national program to vaccinate children with the conjugated... 
IMMUNIZATION | MEDICINE, GENERAL & INTERNAL | STREPTOCOCCUS-PNEUMONIAE | CONJUGATE VACCINE | EFFICACY | ERA | SURVEILLANCE | PREVENTION | HIV-INFECTED ADULTS | EPIDEMIOLOGY | CHILDREN | Streptococcus pneumoniae - classification | Humans | South Africa - epidemiology | Serogroup | Heptavalent Pneumococcal Conjugate Vaccine | Infant | Pneumococcal Vaccines - administration & dosage | Incidence | Pneumococcal Infections - epidemiology | Penicillin Resistance | HIV Infections - complications | Pneumococcal Infections - prevention & control | Adult | Pneumococcal Infections - microbiology | Vaccines, Conjugate | Population Surveillance | Pneumonia | Immunization | Risk groups | Vaccination | Human immunodeficiency virus--HIV | Serotypes | Infants | Vaccines | Children | Age | Children & youth
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2. Full Text Estimates of global seasonal influenza-associated respiratory mortality: a modelling study
by Iuliano, A Danielle and Roguski, Katherine M and Chang, Howard H and Muscatello, David J and Palekar, Rakhee and Tempia, Stefano and Cohen, Adam L and Cohen, Cheryl and Gran, Jon Michael and Schanzer, Dena and Cowling, Benjamin J and Wu, Peng and Kyncl, Jan and Ang, Li Wei and Park, Minah and Redlberger-Fritz, Monika and Yu, Hongjie and Espenhain, Laura and Krishnan, Anand and Emukule, Gideon and van Asten, Liselotte and Pereira da Silva, Susana and Aungkulanon, Suchunya and Buchholz, Udo and Widdowson, Marc-Alain and Bresee, Joseph S and Azziz-Baumgartner, Eduardo and Cheng, Po-Yung and Dawood, Fatimah and Foppa, Ivo and Olsen, Sonja and Haber, Michael and Jeffers, Caprichia and MacIntyre, C Raina and Newall, Anthony T and Wood, James G and Kundi, Michael and Popow-Kraupp, Therese and Ahmed, Makhdum and Rahman, Mahmudur and Marinho, Fatima and Sotomayor Proschle, C Viviana and Vergara Mallegas, Natalia and Luzhao, Feng and Sa, Li and Barbosa-Ramírez, Juliana and Sanchez, Diana Malo and Gomez, Leandra Abarca and Vargas, Xiomara Badilla and Acosta Herrera, aBetsy and Llanés, María Josefa and Fischer, Thea Kølsen and Krause, Tyra Grove and Mølbak, Kåre and Nielsen, Jens and Trebbien, Ramona and Bruno, Alfredo and Ojeda, Jenny and Ramos, Hector and an der Heiden, Matthias and del Carmen Castillo Signor, Leticia and Serrano, Carlos Enrique and Bhardwaj, Rohit and Chadha, Mandeep and Narayan, Venkatesh and Kosen, Soewarta and Bromberg, Michal and Glatman-Freedman, Aharona and Kaufman, Zalman and Arima, Yuzo and Oishi, Kazunori and Chaves, Sandra and Nyawanda, Bryan and Al-Jarallah, Reem Abdullah and Kuri-Morales, Pablo A and Matus, Cuitláhuac Ruiz and Corona, Maria Eugenia Jimenez and Burmaa, Alexander and Darmaa, Oyungerel and Obtel, Majdouline and Cherkaoui, Imad and van den Wijngaard, Cees C and van der Hoek, Wim and Baker, Michael and Bandaranayake, Don and Bissielo, Ange and Huang, Sue and Huang, Wan-Ting and Lopez, Liza and Newbern, Claire and Flem, Elmira and Grøneng, Gry M and Hauge, Siri and de Cosío, Federico G and de Moltó, Yadira and Castillo, Lourdes Moreno and Cabello, Maria Agueda and von Horoch, Marta and Medina Osis, Jose and Machado, Ausenda and ... and Global Seasonal Influenza-Associat and Global Seasonal Influenza-associated Mortality Collaborator Network
The Lancet, ISSN 0140-6736, 03/2018, Volume 391, Issue 10127, pp. 1285 - 1300
Estimates of influenza-associated mortality are important for national and international decision making on public health priorities. Previous estimates of 250... 
UNITED-STATES | CAPACITY | AFRICA | MEDICINE, GENERAL & INTERNAL | EXCESS MORTALITY | VIRUS | NUMBERS | PANDEMIC INFLUENZA | DEATHS | BURDEN | EPIDEMIOLOGY | Humans | Middle Aged | Child, Preschool | Infant | Linear Models | Male | Influenza, Human - complications | Socioeconomic Factors | Young Adult | Adolescent | Global Health - statistics & numerical data | Influenza, Human - mortality | Adult | Female | Aged | Seasons | Child | Infant, Newborn | Models | Health aspects | Mortality | Analysis | Influenza | Low income groups | Global health | Pneumonia | Pandemics | Decision making | Viruses | Infections | Regression analysis | Estimates | Regression models | Surveillance | Population | Death | Fatalities | Division | Children | Public health | Age | Viral infections | Age groups
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3. Full Text Comparison of quantitative real-time PCR and direct immunofluorescence for the detection of Pneumocystis jirovecii
by Moodley, Bhavani and Tempia, Stefano and Frean, John Andrew
PLoS ONE, ISSN 1932-6203, 07/2017, Volume 12, Issue 7, p. e0180589
Background Pneumocystis pneumonia (PCP) is a serious risk for HIV-positive patients. Asymptomatic infection or colonisation with P. jirovecii has been shown to... 
CARINII-PNEUMONIA | DIAGNOSIS | ASSAY | IMMUNOCOMPROMISED PATIENTS | DNA | MULTIDISCIPLINARY SCIENCES | COLONIZATION | HIV-INFECTED PATIENTS | Pneumonia, Pneumocystis - diagnosis | Humans | Real-Time Polymerase Chain Reaction - methods | Adult | Female | Male | Fluorescent Antibody Technique, Direct - methods | Pneumonia, Pneumocystis - microbiology | Pneumocystis carinii - isolation & purification | Pneumocystis carinii - genetics | Fluorescent antibody technique | Pneumonia | Immunofluorescence | Health aspects | Bacterial pneumonia | Analysis | Gold | Laboratories | Cut-off | Copy number | Health risks | Asymptomatic infection | Infections | Assaying | Real time | Patients | Disease control | Zoonoses | Polymerase chain reaction | Sensitivity | Cysts | Parasitic diseases | Influenza | Human immunodeficiency virus--HIV | Sputum | Diagnosis | Colonization | Deoxyribonucleic acid--DNA | Deoxyribonucleic acid | HIV | Human immunodeficiency virus
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4. Full Text Replacement and Positive Evolution of Subtype A and B Respiratory Syncytial Virus G-Protein Genotypes From 1997-2012 in South Africa
by Marthi A. Pretorius and Stephanie van Niekerk and Stefano Tempia and Jocelyn Moyes and Cheryl Cohen and Shabir A. Madhi and Marietjie Venter and SARI Surveillance Grp and SARI Surveillance Group
The Journal of Infectious Diseases, ISSN 0022-1899, 12/2013, Volume 208, Issue 3, pp. S227 - S237
Background. Of the respiratory syncytial virus (RSV) genotypes previously described in South Africa during 1997-2002, only GA2 and GA5 persisted until 2006,... 
COUNTRY-SPECIFIC RSV SURVEILLANCE | Evolutionary rate | Respiratory syncytial virus | Positive selection | Genotypes | INFECTIOUS DISEASES | PHYLOGENETIC ANALYSIS | CONSECUTIVE SEASONS | genotypes | CIRCULATION PATTERNS | MICROBIOLOGY | G-GLYCOPROTEIN | SUBGROUP-B | 60-NUCLEOTIDE DUPLICATION | IMMUNOLOGY | MOLECULAR EPIDEMIOLOGIC ANALYSIS | GENETIC-VARIABILITY | ANALYSIS TOOLS | positive selection | GROUP-A | respiratory syncytial virus | evolutionary rate | Respiratory Syncytial Virus Infections - epidemiology | Viral Fusion Proteins - genetics | Humans | Middle Aged | Child, Preschool | Molecular Sequence Data | Infant | Male | Phylogeny | Respiratory Syncytial Virus, Human - classification | Respiratory Syncytial Virus, Human - genetics | Young Adult | Adult | Female | Respiratory Syncytial Virus Infections - virology | Child | South Africa - epidemiology | Selection, Genetic | Genotype | Sequence Analysis, DNA | Molecular Epidemiology | Adolescent | Respiratory Syncytial Virus, Human - isolation & purification | Aged | Evolution, Molecular
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5. Full Text Severe influenza-associated respiratory infection in high HIV prevalence setting, South Africa, 2009-2011
by Cohen, Cheryl and Moyes, Jocelyn and Tempia, Stefano and Groom, Michelle and Walaza, Sibongile and Pretorius, Marthi and Dawood, Halima and Chhagan, Meera and Haffejee, Summaya and Variava, Ebrahim and Kahn, Kathleen and Tshangela, Akhona and von Gottberg, Anne and Wolter, Nicole and Cohen, Adam L and Kgokong, Babatyi and Venter, Marietjie and Madhi, Shabir A and Medicinska fakulteten and Institutionen för folkhälsa och klinisk medicin and Epidemiologi och global hälsa and Umeå universitet
Emerging Infectious Diseases, ISSN 1080-6040, 11/2013, Volume 19, Issue 11, pp. 1766 - 1774
Data on influenza epidemiology in HIV-infected persons are limited, particularly for sub-Saharan Africa, where HIV infection is widespread. We tested... 
UNITED-STATES | INFECTIOUS DISEASES | STREPTOCOCCUS-PNEUMONIAE | PNEUMOCOCCAL DNA | EFFICACY | VACCINE | DOUBLE-BLIND | ADULTS | TIME | IMMUNOLOGY | TRACT INFECTIONS | CHILDREN | Coinfection | Prevalence | Prospective Studies | HIV Infections - epidemiology | Humans | Middle Aged | South Africa - epidemiology | Child, Preschool | Infant | Influenza, Human - epidemiology | Male | Hospitalization | Incidence | Young Adult | Public Health Surveillance | Adolescent | Aged, 80 and over | Adult | Female | Aged | Respiratory Tract Infections - epidemiology | Child | Infant, Newborn | Analysis | Influenza | Lung diseases | HIV testing | HIV (Viruses) | Health aspects | HIV infection | Prevalence studies (Epidemiology) | influenza | viruses | co-infection | bacteria | adults | AIDS | pneumoccocus | Research | pneumococcal | respiratory infections | HIV | pneumonia | children | lower respiratory tract infection | South Africa | vaccination | Clinical Medicine | Allmänmedicin | Medical and Health Sciences | Klinisk medicin | Medicin och hälsovetenskap | General Practice
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6. Full Text Mutations in the mitochondrial protease gene AFG3L2 cause dominant hereditary ataxia SCA28
by Di Bella, Daniela and Lazzaro, Federico and Brusco, Alfredo and Plumari, Massimo and Battaglia, Giorgio and Pastore, Annalisa and Finardi, Adele and Cagnoli, Claudia and Tempia, Filippo and Frontali, Marina and Veneziano, Liana and Sacco, Tiziana and Boda, Enrica and Brussino, Alessandro and Bonn, Florian and Castellotti, Barbara and Baratta, Silvia and Mariotti, Caterina and Gellera, Cinzia and Fracasso, Valentina and Magri, Stefania and Langer, Thomas and Plevani, Paolo and Di Donato, Stefano and Muzi-Falconi, Marco and Taroni, Franco
Nature Genetics, ISSN 1061-4036, 04/2010, Volume 42, Issue 4, pp. 313 - 321
Autosomal dominant spinocerebellar ataxias (SCAs) are genetically heterogeneous neurological disorders characterized by cerebellar dysfunction mostly due to... 
RESPIRATORY-CHAIN COMPLEXES | ATP HYDROLYSIS | FTSH | SPINOCEREBELLAR ATAXIA | SPASTIC PARAPLEGIA | GENETICS & HEREDITY | SUBUNIT COMPOSITION | CLINICAL-FEATURES | M-AAA PROTEASE | CEREBELLAR ATAXIAS | SUBSTRATE RECOGNITION | ATPases Associated with Diverse Cellular Activities | Purkinje Cells - metabolism | Saccharomyces cerevisiae - genetics | Cerebellum - metabolism | Humans | Adenosine Triphosphatases - metabolism | Molecular Sequence Data | Mutation, Missense | Spinocerebellar Degenerations - genetics | Genetic Complementation Test | Electron Transport Complex IV - metabolism | Cell Respiration | Base Sequence | Adenosine Triphosphatases - genetics | ATP-Dependent Proteases | Gene mutations | Proteases | Physiological aspects | Ataxia telangiectasia | Genetic aspects | Research | Health aspects | Risk factors | Proteins | Genotype & phenotype | Ataxia | Mutation | Genes
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7. Full Text Can pneumococcal meningitis surveillance be used to assess the impact of pneumococcal conjugate vaccine on total invasive pneumococcal disease? A case-study from South Africa, 2005–2016
by Kleynhans, Jackie and Cohen, Cheryl and McMorrow, Meredith and Tempia, Stefano and Crowther-Gibson, Penny and Quan, Vanessa and de Gouveia, Linda and von Gottberg, Anne and GERMS-SA and for GERMS-SA
Vaccine, ISSN 0264-410X, 2019, Volume 37, Issue 38, pp. 5724 - 5730
AbstractIntroductionSouth Africa introduced seven-valent pneumococcal conjugate vaccine (PCV7) in 2009 and PCV13 in 2011. We aimed to compare the estimated... 
Allergy and Immunology | Meningitis | Invasive disease | Conjugate vaccine | Streptococcus pneumoniae | MEDICINE, RESEARCH & EXPERIMENTAL | IMMUNOLOGY | Medicine, Experimental | Medical research | Pneumonia | Bacterial meningitis | Vaccines | Bacterial pneumonia | Conjugates | Laboratories | Funding | Health risks | Risk reduction | Estimates | Disease control | Manuscripts | Streptococcus infections | Reduction | Surveillance | Serotypes | Population | Trends | Risk management | Age
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8. Full Text Prioritization of risk groups for influenza vaccination in resource limited settings – A case study from South Africa
by McMorrow, Meredith L and Tempia, Stefano and Walaza, Sibongile and Treurnicht, Florette K and Ramkrishna, Wayne and Azziz-Baumgartner, Eduardo and Madhi, Shabir A and Cohen, Cheryl
Vaccine, ISSN 0264-410X, 01/2019, Volume 37, Issue 1, pp. 25 - 33
Due to competing health priorities, low- and middle-income countries (LMIC) may need to prioritize between different influenza vaccine risk groups. Risk group... 
South Africa | Hospitalization | Vaccine policy | Influenza | Mortality | GLOBAL BURDEN | MEDICINE, RESEARCH & EXPERIMENTAL | PANDEMIC INFLUENZA | RESPIRATORY ILLNESS | PREVALENCE | IMMUNOLOGY | SEASONAL INFLUENZA | YOUNG-CHILDREN | MATERNAL INFLUENZA | AGE | VACCINES | Influenza vaccines | Medical research | AIDS vaccines | Vaccination | Case studies | Prevention | Complications and side effects | Tuberculosis | Pregnant women | Medicine, Experimental | Public health | Medical care, Cost of | Immunization | Risk groups | Feasibility studies | Health risks | Vaccines | Morbidity | Pregnancy | Womens health | Risk assessment | Human immunodeficiency virus--HIV | Adults | Children | Chronic illnesses
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9. Full Text Reply to Alonso et al. “Bangladesh and Rwanda: Cases of high burden of influenza in tropical countries?”
by Ahmed, Makhdum and Roguski, Katherine and Tempia, Stefano and Iuliano, Angela D
Influenza and Other Respiratory Viruses, ISSN 1750-2640, 09/2018, Volume 12, Issue 5, pp. 669 - 671
Influenza | Letter to the Editor | Letters to the Editor
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10. Full Text Mortality amongst patients with influenza-associated severe acute respiratory illness, South Africa, 2009-2013
by Cohen, Cheryl and Moyes, Jocelyn and Tempia, Stefano and Groome, Michelle and Walaza, Sibongile and Pretorius, Marthi and Dawood, Halima and Chhagan, Meera and Haffejee, Summaya and Variava, Ebrahim and Kahn, Kathleen and Von Gottberg, Anne and Wolter, Nicole and Cohen, Adam L and Malope-Kgokong, Babatyi and Venter, Marietjie and Madhi, Shabir A and Medicinska fakulteten and Institutionen för folkhälsa och klinisk medicin and Epidemiologi och global hälsa and Umeå universitet
PLoS ONE, ISSN 1932-6203, 03/2015, Volume 10, Issue 3, p. e0118884
Introduction Data on the burden and risk groups for influenza-associated mortality from Africa are limited. We aimed to estimate the incidence and risk-factors... 
A H1N1 VIRUS | UNITED-STATES | HIV | PANDEMIC INFLUENZA | MULTIDISCIPLINARY SCIENCES | ADULTS | INFECTION | HOSPITALIZATIONS | PREVALENCE | SYNCYTIAL VIRUS | CHILDREN | Humans | Middle Aged | Child, Preschool | Infant | Male | Influenza, Human - complications | Incidence | Young Adult | Respiratory Tract Infections - mortality | Influenza, Human - mortality | Adult | Female | Respiratory Tract Infections - complications | Respiratory Tract Infections - virology | Seasons | Child | Risk Factors | South Africa - epidemiology | Influenza, Human - epidemiology | Acute Disease - mortality | Hospitals | Adolescent | Acute Disease - epidemiology | Aged | Respiratory Tract Infections - epidemiology | Sentinel Surveillance | Influenza vaccines | HIV (Viruses) | Influenza | Patient outcomes | Analysis | Risk groups | Catchments | Mortality | Vaccination | Viruses | Infants | Infections | Patients | Risk factors | Polymerase chain reaction | Confidence intervals | Studies | Swine flu | Antiretroviral agents | Respiratory diseases | Human immunodeficiency virus--HIV | Fatalities | Adults | Children | Age | Deoxyribonucleic acid--DNA | Hälsovetenskaper | Folkhälsovetenskap, global hälsa, socialmedicin och epidemiologi | Medical and Health Sciences | Medicin och hälsovetenskap | Public Health, Global Health, Social Medicine and Epidemiology | Health Sciences | Deoxyribonucleic acid | DNA | Human immunodeficiency virus
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11. Full Text Deaths associated with respiratory syncytial and influenza viruses among persons ≥5 years of age in HIV-prevalent area, South Africa, 1998–2009
by Tempia, Stefano and Walaza, Sibongile and Viboud, Cecile and Cohen, Adam L and Madhi, Shabir A and Venter, Marietjie and Von Mollendorf, Claire and Moyes, Jocelyn and McAnerney, Johanna M and Cohen, Cheryl
Emerging Infectious Diseases, ISSN 1080-6040, 2015, Volume 21, Issue 4, pp. 600 - 608
We estimated deaths attributable to influenza and respiratory syncytial virus (RSV) among persons >= 5 years of age in South Africa during 1998-2009 by... 
UNITED-STATES | INFECTIOUS DISEASES | PANDEMIC INFLUENZA | MORTALITY BURDEN | ADULTS | SURVEILLANCE | TRACT INFECTION | HOSPITALIZATIONS | IMMUNOLOGY | EPIDEMIOLOGY | SEVERITY | CHILDREN | Respiratory Syncytial Virus Infections - mortality | Coinfection | Prevalence | Respiratory Syncytial Virus Infections - epidemiology | Age Factors | History, 21st Century | HIV Infections - epidemiology | HIV Infections - history | Humans | Middle Aged | Respiratory Syncytial Virus, Human | Child, Preschool | Infant | Male | Orthomyxoviridae | Risk | Young Adult | Aged, 80 and over | Influenza, Human - mortality | Adult | Female | Child | Infant, Newborn | History, 20th Century | Mortality | South Africa - epidemiology | Respiratory Syncytial Virus Infections - history | Influenza, Human - epidemiology | Adolescent | Aged | Influenza, Human - history | Population Surveillance | viruses | RSV | HIV | viruses, respiratory syncytial virus, RSV, HIV, human immunodeficiency virus, mortality rates, deaths, South Africa | respiratory syncytial virus | Influenza
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12. Full Text Risk factors associated with hospitalisation for influenza-associated severe acute respiratory illness in South Africa: A case-population study
by Abadom, Tochukwu Raphael and Smith, Adrian D and Tempia, Stefano and Madhi, Shabir A and Cohen, Cheryl and Cohen, Adam L
Vaccine, ISSN 0264-410X, 2016, Volume 34, Issue 46, pp. 5649 - 5655
Abstract Background Influenza is a common cause of severe respiratory illness, but risk factors for hospitalisation in low income settings with a high HIV... 
Allergy and Immunology | Vaccine | Influenza | Risk factors | Hospitalisation | UNITED-STATES | MORTALITY | MEDICINE, RESEARCH & EXPERIMENTAL | TUBERCULOSIS | ONTARIO | DEATH | IMMUNOLOGY | PNEUMONIA | CHILDREN | GENDER | INFECTION | EPIDEMIC | Tuberculosis - epidemiology | Influenza Vaccines - administration & dosage | Prevalence | HIV Infections - epidemiology | Humans | Middle Aged | Tuberculosis - complications | Hospitalization - statistics & numerical data | Male | Influenza, Human - complications | Pneumococcal Vaccines - administration & dosage | Young Adult | Adult | Female | Influenza, Human - virology | Respiratory Tract Infections - virology | Child | Asthma - epidemiology | Poverty - statistics & numerical data | Risk Factors | South Africa - epidemiology | Influenza, Human - epidemiology | Vaccination - statistics & numerical data | Asthma - complications | Adolescent | HIV Infections - complications | Sex Factors | Acute Disease - epidemiology | Aged | Respiratory Tract Infections - epidemiology | Influenza, Human - prevention & control | Population Surveillance | Sentinel Surveillance | Medicine, Experimental | Medical research | Influenza vaccines | Vaccination | HIV infection | Immunization | Mortality | Infections | Vaccines | Family medical history | Morbidity | Asthma | Demographics | Hospitals | Illnesses | Tuberculosis | Surveillance | Human immunodeficiency virus--HIV | Respiratory diseases | Population | Age | Viral infections
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