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Ogimi C, Kim YJ, Martin ET, Huh HJ, Chiu CH, Englund JA. What's New With the Old Coronaviruses? J Pediatric Infect Dis Soc 2020; 9:210-217. [PMID: 32314790 PMCID: PMC7188130 DOI: 10.1093/jpids/piaa037] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023]
Abstract
Coronaviruses contribute to the burden of respiratory diseases in children, frequently manifesting in upper respiratory symptoms considered to be part of the "common cold." Recent epidemics of novel coronaviruses recognized in the 21st century have highlighted issues of zoonotic origins of transmissible respiratory viruses and potential transmission, disease, and mortality related to these viruses. In this review, we discuss what is known about the virology, epidemiology, and disease associated with pediatric infection with the common community-acquired human coronaviruses, including species 229E, OC43, NL63, and HKU1, and the coronaviruses responsible for past world-wide epidemics due to severe acute respiratory syndrome and Middle East respiratory syndrome coronavirus.
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Affiliation(s)
- Chikara Ogimi
- Department of Pediatrics, Seattle Children’s Hospital Research Institute, University of Washington, Seattle, Washington, USA
| | - Yae Jean Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, Korea
| | - Emily T Martin
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Hee Jae Huh
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Seoul, Korea
| | - Cheng-Hsun Chiu
- Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung Universit,y College of Medicine, Taoyuan, Taiwan
| | - Janet A Englund
- Department of Pediatrics, Seattle Children’s Hospital Research Institute, University of Washington, Seattle, Washington, USA
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Yu J, Qian S, Liu C, Xiao Y, Xu T, Wang Y, Su H, Chen L, Yuan B, Wang X, Xu B, Yang Y, Shen K, Xie Z, Ren L, Wang J. Viral etiology of life-threatening pediatric pneumonia: A matched case-control study. Influenza Other Respir Viruses 2020; 14:452-459. [PMID: 32267084 PMCID: PMC7262399 DOI: 10.1111/irv.12738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Pediatric pneumonia remains a significant health challenge, while the viral risk factors for adverse outcomes in pediatric pneumonia are not yet fully clear. Methods A matched case‐control study of pediatric patients with pneumonia was carried out in Beijing, China, between 2007 and 2015. The study enrolled 334 intensive care unit patients who developed life‐threatening diseases and 522 controls matched to the sex, age, ethnicity, admission dates, and residing district of the cases suffered from pneumonia. Nasopharyngeal aspirates were taken from all participants and tested by PCR for 18 common respiratory viruses. Results At least, one virus was detected in 257 (77%) of the cases and 409 (78%) of the controls. We observed no difference in the prevalence of 17 respiratory viruses between cases and controls but found a higher frequency of influenza A virus (IFV‐A) in the cases than in the controls (7% vs 4%, P = .036). After adjusting for comorbid conditions and a history of reactive airway diseases, IFV‐A was associated with an increase in life‐threatening pneumonia (adjusted odds ratio = 2.55, 95% CI = 1.24‐5.24). Young age and congenital heart disease (aOR = 10.16‐10.27, P < .001) were also independent risk factors. Conclusions The prevention of IFV infection is critical in decreasing the risk of life‐threatening pneumonia in children.
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Affiliation(s)
- Jianxing Yu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Suyun Qian
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chunyan Liu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yan Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Teng Xu
- Vision Medicals, Guangzhou, China
| | - Ying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hang Su
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bin Yuan
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Baoping Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yan Yang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Kunling Shen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lili Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Adema IW, Kamau E, Uchi Nyiro J, Otieno GP, Lewa C, Munywoki PK, Nokes DJ. Surveillance of respiratory viruses among children attending a primary school in rural coastal Kenya. Wellcome Open Res 2020; 5:63. [PMID: 33102784 PMCID: PMC7569485 DOI: 10.12688/wellcomeopenres.15703.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/27/2020] [Indexed: 08/03/2024] Open
Abstract
Background: Respiratory viruses are primary agents of respiratory tract diseases. Knowledge on the types and frequency of respiratory viruses affecting school-children is important in determining the role of schools in transmission in the community and identifying targets for interventions. Methods: We conducted a one-year (term-time) surveillance of respiratory viruses in a rural primary school in Kilifi County, coastal Kenya between May 2017 and April 2018. A sample of 60 students with symptoms of ARI were targeted for nasopharyngeal swab (NPS) collection weekly. Swabs were screened for 15 respiratory virus targets using real time PCR diagnostics. Data from respiratory virus surveillance at the local primary healthcare facility was used for comparison. Results: Overall, 469 students aged 2-19 years were followed up for 220 days. A total of 1726 samples were collected from 325 symptomatic students; median age of 7 years (IQR 5-11). At least one virus target was detected in 384 (22%) of the samples with a frequency of 288 (16.7%) for rhinovirus, 47 (2.7%) parainfluenza virus, 35 (2.0%) coronavirus, 15 (0.9%) adenovirus, 11 (0.6%) respiratory syncytial virus (RSV) and 5 (0.3%) influenza virus. The proportion of virus positive samples was higher among lower grades compared to upper grades (25.9% vs 17.5% respectively; χ 2 = 17.2, P -value <0.001). Individual virus target frequencies did not differ by age, sex, grade, school term or class size. Rhinovirus was predominant in both the school and outpatient setting. Conclusion: Multiple respiratory viruses circulated in this rural school population. Rhinovirus was dominant in both the school and outpatient setting and RSV was of notably low frequency in the school. The role of school children in transmitting viruses to the household setting is still unclear and further studies linking molecular data to contact patterns between the school children and their households are required.
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Affiliation(s)
- Irene Wangwa Adema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Joyce Uchi Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Grieven P. Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Clement Lewa
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Patrick K. Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - D. James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, Coventry, CV4 7AL, UK
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Chowdhury F, Shahid ASMSB, Ghosh PK, Rahman M, Hassan MZ, Akhtar Z, Muneer SME, Shahrin L, Ahmed T, Chisti MJ. Viral etiology of pneumonia among severely malnourished under-five children in an urban hospital, Bangladesh. PLoS One 2020; 15:e0228329. [PMID: 32017782 PMCID: PMC6999894 DOI: 10.1371/journal.pone.0228329] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 01/13/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND In Bangladesh, pneumonia has a higher mortality among malnourished children aged <5 years. Evaluating pneumonia etiology among malnourished children may help improve empiric treatment guidelines. METHODS During April 2015-December 2017, we conducted a case-control study among severe acute malnourished (SAM) children aged <5 years admitted to the Dhaka hospital of International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b). We enrolled hospital admitted SAM children with clinical or radiological pneumonia as cases (during April 2015 to March 2017) and hospital admitted SAM children without any respiratory symptom in the past 10 days before admission as controls (during February 2016 to December 2017). We tested nasopharyngeal wash from both case and control for respiratory syncytial virus (RSV), human metapneumovirus (HMPV), influenza viruses, human parainfluenza viruses (HPIV), rhinovirus and adenovirus by singleplex real-time reverse transcriptase polymerase chain reaction. To identify the independent association of pneumonia with viral pathogens during February 2016 to March 2017, we used multivariable logistic regression for calculating adjusted odds ratios. RESULTS We enrolled 360 cases and 334 controls. For case and control the median age was 8 months (IQR: 5-13) and 11 months (IQR: 6-18) (p = 0.001) respectively. Weight/age Z-score was -4.3 (SD ±0.7) for cases and -4.1 (SD ±1.1) for controls (p = 0.01). Among cases 68% had both clinical and radiological pneumonia, 1% had clinical pneumonia and 31% had only radiological pneumonia. Respiratory virus detection was high in cases compared to controls [69.9% (251) vs. 44.8% (148), p = 0.0001]. The most frequently detected viruses among cases were rhinoviruses (79, 22.0%) followed by RSV (32, 8.9%), adenovirus (23, 6.4%), HPIV (22, 6.1%), influenza virus (16, 4.5%), and HMPV (16, 4.5%). Among the controls, rhinoviruses (82, 24.8%) were most commonly detected one followed by adenovirus (26,7.9%), HMPV (5, 1.5%), HPIV (4, 1.2%), RSV (3, 0.9%), and influenza virus (2, 0.6%). RSV (OR 13.1; 95% CI: 1.6, 106.1), influenza virus (OR 8.7; 95% CI: 1.0, 78.9), HPIV (3.8; 95% CI: 1.0, 14.8), and HMPV (2.7; 95% CI: 1.3, 5.5) were independently associated with pneumonia while compared between 178 cases and 174 controls. CONCLUSION Viral etiology of pneumonia in SAM children were mainly attributable to RSV, influenza, HPIV and HMPV. Our study findings may help in planning further studies targeting vaccines or drugs against common respiratory viruses responsible for pneumonia among SAM children.
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Affiliation(s)
- Fahmida Chowdhury
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | - Probir Kumar Ghosh
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mustafizur Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Md. Zakiul Hassan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Zubair Akhtar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - S. Mah-E- Muneer
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Lubaba Shahrin
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammod Jobayer Chisti
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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Akech SO, Kinuthia DW, Macharia W. Serum Procalcitonin Levels in Children with Clinical Syndromes for Targeting Antibiotic Use at an Emergency Department of a Kenyan Hospital. J Trop Pediatr 2020; 66:29-37. [PMID: 31062031 PMCID: PMC7116410 DOI: 10.1093/tropej/fmz027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Serum procalcitonin (PCT) was measured in 228 children aged 1 month to 15 years at an emergency department of a hospital located in an area without local malaria transmission in children with suspected infections; 21% (49) children had a clinical syndrome for suspected bacterial infections (Syndrome+ve). In children with Syndrome+ve criteria, 27/49 (55.1%) had PCT ≥0.5 µg/l but only 59/179 (32.9%) of those Syndrome-ve had abnormal PCT, χ2 = 8.0, p = 0.005; positive likelihood ratio = 2.0 [95% confidence interval (CI) 1.2-3.3]; negative likelihood ratio = 0.8 (95% CI 0.7-1.0). In patients with pneumonia, 9/15 (60%) with severe pneumonia had PCT ≥0.5 µg/l compared to 11/21 (52.4%) with non-severe pneumonia, χ2 = 0.2, p = 0.65. Children with clinical signs of pneumonia or clinical signs suggestive of bacterial infections fulfilling clinical syndromic definitions for suspected bacterial infections commonly have elevated PCT level. PCT levels are associated with disease severity and antibiotic trials guided by PCT levels may be needed where cultures are not available.
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Affiliation(s)
- Samuel O Akech
- Department of Paediatrics and Child Health, Aga Khan University of Nairobi, P.O. Box 30270-00100, Nairobi, Kenya.,Health Services Unit, Kenya Medical Research Institute/Wellcome Trust Research Programme, P.O. Box 43640-00100, Nairobi, Kenya
| | - Doris W Kinuthia
- Department of Paediatrics and Child Health, Aga Khan University of Nairobi, P.O. Box 30270-00100, Nairobi, Kenya
| | - William Macharia
- Department of Paediatrics and Child Health, Aga Khan University of Nairobi, P.O. Box 30270-00100, Nairobi, Kenya
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Owuor DC, Ngoi JM, Otieno JR, Otieno GP, Nyasimi FM, Nyiro JU, Agoti CN, Chaves SS, Nokes DJ. Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009-2017. Influenza Other Respir Viruses 2020; 14:320-330. [PMID: 31943817 PMCID: PMC7182596 DOI: 10.1111/irv.12717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/01/2022] Open
Abstract
Background Influenza viruses evolve rapidly and undergo immune driven selection, especially in the hemagglutinin (HA) protein. We report amino acid changes affecting antigenic epitopes and receptor‐binding sites of A(H3N2) viruses circulating in Kilifi, Kenya, from 2009 to 2017. Methods Next‐generation sequencing (NGS) was used to generate A(H3N2) virus genomic data from influenza‐positive specimens collected from hospital admissions and health facility outpatients presenting with acute respiratory illness to health facilities within the Kilifi Health and Demographic Surveillance System. Full‐length HA sequences were utilized to characterize A(H3N2) virus genetic and antigenic changes. Results From 186 (90 inpatient and 96 outpatient) influenza A virus‐positive specimens processed, 101 A(H3N2) virus whole genomes were obtained. Among viruses identified in inpatient specimens from 2009 to 2015, divergence of circulating A(H3N2) viruses from the vaccine strains A/Perth/16/2009, A/Texas/50/2012, and A/Switzerland/9715293/2013 formed 6 genetic clades (A/Victoria/208/2009‐like, 3B, 3C, 3C.2a, 4, and 7). Among viruses identified in outpatient specimens from 2015 to 2017, divergence of circulating A(H3N2) viruses from vaccine strain A/Hong Kong/4801/2014 formed clade 3C.2a, subclades 3C.2a2 and 3C.2a3, and subgroup 3C.2a1b. Several amino acid substitutions were associated with the continued genetic evolution of A(H3N2) strains in circulation. Conclusions Our results suggest continuing evolution of currently circulating A(H3N2) viruses in Kilifi, coastal Kenya and suggest the need for continuous genetic and antigenic viral surveillance of circulating seasonal influenza viruses with broad geographic representation to facilitate prompt and efficient selection of influenza strains for inclusion in future influenza vaccines.
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Affiliation(s)
- D Collins Owuor
- Virus Epidemiology and Control Research Group, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce M Ngoi
- Virus Epidemiology and Control Research Group, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - James R Otieno
- Virus Epidemiology and Control Research Group, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Grieven P Otieno
- Virus Epidemiology and Control Research Group, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Festus M Nyasimi
- Virus Epidemiology and Control Research Group, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Joyce U Nyiro
- Virus Epidemiology and Control Research Group, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charles N Agoti
- Virus Epidemiology and Control Research Group, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya.,School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Sandra S Chaves
- Influenza Division, Centres for Disease Control and Prevention (CDC), Nairobi, Kenya
| | - D James Nokes
- Virus Epidemiology and Control Research Group, Kenya Medical Research Institute (KEMRI) - Wellcome Trust Research Programme, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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Kamau E, Oketch JW, de Laurent ZR, Phan MVT, Agoti CN, Nokes DJ, Cotten M. Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia. BMC Genomics 2020; 21:5. [PMID: 31898474 PMCID: PMC6941262 DOI: 10.1186/s12864-019-6400-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/15/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences. RESULTS We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes. CONCLUSION This is the first genomic characterization of HMPV genomes from African patients.
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Affiliation(s)
- Everlyn Kamau
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - John W Oketch
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - My V T Phan
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | | | - D James Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute, University of Warwick, Coventry, UK
| | - Matthew Cotten
- MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Yu J, Liu C, Xiao Y, Xiang Z, Zhou H, Chen L, Shen K, Xie Z, Ren L, Wang J. Respiratory Syncytial Virus Seasonality, Beijing, China, 2007-2015. Emerg Infect Dis 2019; 25:1127-1135. [PMID: 31107230 PMCID: PMC6537707 DOI: 10.3201/eid2506.180532] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
During July 2007-June 2015, we enrolled 4,225 hospitalized children with pneumonia in a study to determine the seasonality of respiratory syncytial virus (RSV) infection in Beijing, China. We defined season as the period during which >10% of total PCRs performed each week were RSV positive. We identified 8 distinctive RSV seasons. On average, the season onset occurred at week 41 (mid-October) and lasted 33 weeks, through week 20 of the next year (mid-May); 97% of all RSV-positive cases occurred during the season. RSV seasons occurred 3-5 weeks earlier and lasted ≈6 weeks longer in RSV subgroup A-dominant years than in RSV subgroup B-dominant years. Our analysis indicates that monitoring such RSV subgroup shifts might provide better estimates for the onset of RSV transmission. PCR-based tests could be a flexible or complementary way of determining RSV seasonality in locations where RSV surveillance is less well-established, such as local hospitals throughout China.
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Oketch JW, Kamau E, Otieno GP, Otieno JR, Agoti CN, Nokes DJ. Human metapneumovirus prevalence and patterns of subgroup persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007-2016. BMC Infect Dis 2019; 19:757. [PMID: 31470805 PMCID: PMC6716807 DOI: 10.1186/s12879-019-4381-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/15/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Human metapneumovirus (HMPV) is an important respiratory pathogen that causes seasonal epidemics of acute respiratory illness and contributes significantly to childhood pneumonia. Current knowledge and understanding on its patterns of spread, prevalence and persistence in communities in low resource settings is limited. METHODS We present findings of a molecular-epidemiological analysis of nasal samples from children < 5 years of age admitted with syndromic pneumonia between 2007 and 2016 to Kilifi County Hospital, coastal Kenya. HMPV infection was detected using real-time RT-PCR and positives sequenced in the fusion (F) and attachment (G) genes followed by phylogenetic analysis. The association between disease severity and HMPV subgroup was assessed using Fisher's exact test. RESULTS Over 10 years, 274/6756 (4.1%) samples screened were HMPV positive. Annual prevalence fluctuated between years ranging 1.2 to 8.7% and lowest in the recent years (2014-2016). HMPV detections were most frequent between October of one year to April of the following year. Genotyping was successful for 205/274 (74.8%) positives revealing clades A2b (41.0%) and A2c (10.7%), and subgroups B1 (23.4%) and B2 (24.9%). The dominance patterns were: clade A2b between 2007 and 11, subgroup B1 between 2012 and 14, and clade A2c in more recent epidemics. Subgroup B2 viruses were present in all the years. Temporal phylogenetic clustering within the subgroups for both local and global sequence data was seen. Subgroups occurring in each epidemic season were comprised of multiple variants. Pneumonia severity did not vary by subgroup (p = 0.264). In both the F and G gene, the sequenced regions were found to be predominantly under purifying selection. CONCLUSION Subgroup patterns from this rural African setting temporally map with global strain distribution, suggesting a well-mixed global virus transmission pool of HMPV. Persistence in the local community is characterized by repeated introductions of HMPV variants from the global pool. The factors underlying the declining prevalence of HMPV in this population should be investigated.
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Affiliation(s)
- John W. Oketch
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Everlyn Kamau
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Grieven P. Otieno
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - James R. Otieno
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Charles N. Agoti
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - D. James Nokes
- Kenya Medical Research Institute (KEMRI) -Wellcome Trust Research Programme, Kilifi, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
- School of Life Sciences, and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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Zhao Y, Lu R, Shen J, Xie Z, Liu G, Tan W. Comparison of viral and epidemiological profiles of hospitalized children with severe acute respiratory infection in Beijing and Shanghai, China. BMC Infect Dis 2019; 19:729. [PMID: 31429710 PMCID: PMC6701130 DOI: 10.1186/s12879-019-4385-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/15/2019] [Indexed: 12/16/2022] Open
Abstract
Background No comparison data have been reported on viral and epidemiological profiles of hospitalized children with severe acute respiratory infection (SARI) in Beijing or Shanghai, China. Methods We collected 700 nasopharyngeal aspirates (NPA) from hospitalized children with SARI in Beijing (northern China) and Shanghai (southern China). Multiple respiratory viruses (including 15 common viruses) were screened by validated polymerase chain reaction (PCR) or real-time reverse transcription-PCR assays and confirmed by sequencing. Demographic data and the distribution of viral infections were also examined. Results Of 700 samples, 547 (78.1%) tested positive for viral infections. The picornaviruses (PIC), which included rhinovirus (RV) and enterovirus (EV), were the most common (34.0%), followed by respiratory syncytial virus (RSV) (28.3%), human bocavirus (HBoV) (19.1%), adenovirus (ADV) (13.7%), human coronaviruses (HCoV) (10.7%), influenza A and B (8.9%), parainfluenza virus (PIV 1–3) (7.9%), and human metapneumovirus (HMPV) (5.0%). PIC (RV/EV) and RSV were the most prevalent etiological agents of SARI in both cities. The total and age-matched prevalence of RSV, HCoV, and hMPV among SARI children under 5 years old were significantly higher in Beijing than in Shanghai. Different age and seasonal distribution patterns of the viral infections were found between Beijing and Shanghai. Conclusions Viral infection was tested and shown to be the most prevalent etiological agent among children with SARI in either the Beijing or the Shanghai area, while showing different patterns of viral and epidemiological profiles. Our findings provide a better understanding of the roles of geographic location and climate in respiratory viral infections in hospitalized children with SARI.
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Affiliation(s)
- Yanjie Zhao
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China.,National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China
| | - Roujian Lu
- National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China
| | - Jun Shen
- Children's Hospital of Fudan University, Shanghai, China
| | - Zhengde Xie
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Gaoshan Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China
| | - Wenjie Tan
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China. .,National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China.
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61
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Ferreira HLDS, Costa KLP, Cariolano MS, Oliveira GS, Felipe KKP, Silva ESA, Alves MS, Maramaldo CEC, de Sousa EM, Rego JS, Silva ICPA, Albuquerque RKS, Araújo NSC, Amorim AMM, Costa LD, Pinheiro CS, Guimarães VA, Santos MC, Mello WA, Falcai A, Lima-Neto LG. High incidence of rhinovirus infection in children with community-acquired pneumonia from a city in the Brazilian pre-Amazon region. J Med Virol 2019; 91:1751-1758. [PMID: 31230362 PMCID: PMC7166869 DOI: 10.1002/jmv.25524] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/18/2019] [Indexed: 11/17/2022]
Abstract
Community‐acquired pneumonia (CAP) is the leading cause of child death worldwide. Viruses are the most common pathogens associated with CAP in children, but their incidence varies greatly. This study investigated the presence of respiratory syncytial virus (RSV), adenovirus, human rhinovirus (HRV), human metapneumovirus (HMPV), human coronavirus (HCoV‐OC43 and HCoV‐NL63), and influenza A virus (FluA) in children with CAP and the contributing risk factors. Here, children with acute respiratory infections were screened by pediatrics; and a total of 150 radiographically‐confirmed CAP patients (aged 3 months to 10 years) from two clinical centers in Sao Luis, Brazil were recruited. Patient's clinical and epidemiological data were recorded. Nasopharyngeal swab and tracheal aspirate samples were collected to extract viral nucleic acid. RSV, adenovirus, rhinovirus, FluA, HMPV, HCoV‐OC43, and HCoV‐NL63 were detected by real‐time polymerase chain reaction. The severe CAP was associated with ages between 3 and 12 months. Viruses were detected in 43% of CAP patients. Rhinovirus infections were the most frequently identified (68%). RSV, adenovirus, FluA, and coinfections were identified in 14%, 14%, 5%, and 15% of children with viral infection, respectively. Rhinovirus was associated with nonsevere CAP (P = .014); RSV, FluA, and coinfections were associated with severe CAP (P < .05). New strategies for prevention and treatment of viral respiratory infections, mainly rhinovirus and RSV infections, are necessary. This is the first study conducted in a city in the Brazilian pre‐Amazon region to identify viruses in children with CAP. Rhinovirus infections were the most frequently identified. RSV, adenovirus, FluA, and co‐infections were associated with severe CAP.
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Affiliation(s)
| | | | | | - Gustavo S Oliveira
- Programa de Pós-Graduação, Universidade CEUMA, São Luís, Maranhão, Brasil
| | - Karen K P Felipe
- Programa de Pós-Graduação, Universidade CEUMA, São Luís, Maranhão, Brasil
| | - Elen S A Silva
- Programa de Pós-Graduação, Universidade CEUMA, São Luís, Maranhão, Brasil
| | - Matheus S Alves
- Programa de Pós-Graduação, Universidade CEUMA, São Luís, Maranhão, Brasil
| | | | - Eduardo M de Sousa
- Programa de Pós-Graduação, Universidade CEUMA, São Luís, Maranhão, Brasil
| | - Joseany S Rego
- Complexo Hospitalar Materno Infantil do Maranhão Hospital Dr. Juvêncio Mattos Maternidade Benedito Leite, São Luís, Maranhão, Brasil
| | - Ilana C P A Silva
- Programa de Pós-Graduação, Universidade CEUMA, São Luís, Maranhão, Brasil
| | | | | | - Angela M M Amorim
- Hospital da Criança Dr. Odorico de Amaral Matos, São Luís, Maranhão, Brasil
| | - Luciane D Costa
- Hospital da Criança Dr. Odorico de Amaral Matos, São Luís, Maranhão, Brasil
| | | | - Vinícius A Guimarães
- Hospital Universitário, Universidade Federal do Maranhão, São Luís, Maranhão, Brasil
| | - Mirleide C Santos
- Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brasil
| | - Wyller A Mello
- Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ministério da Saúde, Ananindeua, Pará, Brasil
| | - Angela Falcai
- Mestrado em Meio Ambiente, Universidade CEUMA, São Luís, Maranhão, Brasil
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Derrar F, Izri K, Kaddache C, Boukari R, Hannoun D. Virologic study of acute lower respiratory tract infections in children admitted to the paediatric department of Blida University Hospital, Algeria. New Microbes New Infect 2019; 30:100536. [PMID: 31193119 PMCID: PMC6517316 DOI: 10.1016/j.nmni.2019.100536] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 03/08/2019] [Accepted: 03/18/2019] [Indexed: 02/03/2023] Open
Abstract
Acute lower respiratory tract infections (ALRTI) such as pneumonia and bronchiolitis are major causes of mortality and morbidity in children under 5 years of age. The main microbial agents responsible for ALRTI are either bacterial agents (Streptococcus pneumoniae, Haemophilus influenzae type b, Mycoplasma pneumoniae) or viruses (respiratory syncytial virus (RSV, also known as human orthopneumovirus), Myxovirus influenzae, Myxovirus parainfluenzae, adenovirus) [1]. More recently, other viruses (rhinovirus, metapneumovirus, coronavirus, bocavirus) have been implicated in ALRTI; their identification has been facilitated by new molecular biology techniques such as real-time PCR. To our knowledge, these emerging viruses have never been the subject of epidemiologic studies in our country.
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Affiliation(s)
- F. Derrar
- Viral Respiratory Unit, Virology Department, Institut Pasteur of Algeria, Algiers, Algeria
| | - K. Izri
- Viral Respiratory Unit, Virology Department, Institut Pasteur of Algeria, Algiers, Algeria
| | - C. Kaddache
- Paediatric Department, University Hospital of Blida, Blida, Algeria
| | - R. Boukari
- Paediatric Department, University Hospital of Blida, Blida, Algeria
| | - D. Hannoun
- National Institut of Public Health, Algeria
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63
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Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010-2013. J Infect Public Health 2019; 13:438-445. [PMID: 31229412 DOI: 10.1016/j.jiph.2019.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Data on the viral etiology of acute lower respiratory infections are scarce in Pakistan. Human respiratory syncytial virus (RSV) is an important cause of morbidity in children but no effective vaccine or antiviral therapy is currently available. As vaccines are expected to become available in the future, it is important to understand the epidemiology of locally prevalent RSV subtypes. This study aimed to define the molecular epidemiology of RSV (A and B) genotypes in Pakistani children under 5 years. METHODS World Health Organization case definitions for influenza-like illness (ILI) and severe acute respiratory illness (SARI) were used for case selection. Children under 5 years who presented with ILI or SARI at tertiary care hospitals from all provinces/regions, including the eight influenza sentinel sites, during October-April each year between 2010 and 2013 were enrolled. Demographic and clinical data of the children were recorded and nasopharyngeal/throat swabs taken for analysis. All samples were tested for RSV A and B using real-time polymerase chain reaction for non-influenza respiratory viruses. Specific oligonucleotide primers for RSV A and B were used for subtyping and sequencing of the G protein, followed by phylogenetic analysis. RESULTS A total of 1941 samples were included. RSV was detected in 472 (24%) children, with RSV A detected in 367 (78%) and RSV B in 105 (22%). The G protein of all RSV A strains clustered in the NA1/GA2 genotype while RSV B strains carried the signature 60 nucleotide duplication and were assigned to three BA genotypes: BA-9, BA-10 and the new BA-13 genotype. CONCLUSIONS This study highlights the importance of RSV as a viral etiologic agent of acute respiratory infections in children in Pakistan, and the diversity of RSV viruses. Continued molecular surveillance for early detection of prevalent and newly emerging genotypes is needed to understand the epidemiology of RSV infections in Pakistan.
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64
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Rhedin SA, Eklundh A, Ryd-Rinder M, Naucler P, Mårtensson A, Gantelius J, Zenk I, Andersson-Svahn H, Nybond S, Rasti R, Lindh M, Andersson M, Peltola V, Waris M, Alfvén T. Introducing a New Algorithm for Classification of Etiology in Studies on Pediatric Pneumonia: Protocol for the Trial of Respiratory Infections in Children for Enhanced Diagnostics Study. JMIR Res Protoc 2019; 8:e12705. [PMID: 31025954 PMCID: PMC6658235 DOI: 10.2196/12705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 03/09/2019] [Accepted: 03/24/2019] [Indexed: 01/20/2023] Open
Abstract
Background There is a need to better distinguish viral infections from antibiotic-requiring bacterial infections in children presenting with clinical community-acquired pneumonia (CAP) to assist health care workers in decision making and to improve the rational use of antibiotics. Objective The overall aim of the Trial of Respiratory infections in children for ENhanced Diagnostics (TREND) study is to improve the differential diagnosis of bacterial and viral etiologies in children aged below 5 years with clinical CAP, by evaluating myxovirus resistance protein A (MxA) as a biomarker for viral CAP and by evaluating an existing (multianalyte point-of-care antigen detection test system [mariPOC respi] ArcDia International Oy Ltd.) and a potential future point-of-care test for respiratory pathogens. Methods Children aged 1 to 59 months with clinical CAP as well as healthy, hospital-based, asymptomatic controls will be included at a pediatric emergency hospital in Stockholm, Sweden. Blood (analyzed for MxA and C-reactive protein) and nasopharyngeal samples (analyzed with real-time polymerase chain reaction as the gold standard and antigen-based mariPOC respi test as well as saved for future analyses of a novel recombinase polymerase amplification–based point-of-care test for respiratory pathogens) will be collected. A newly developed algorithm for the classification of CAP etiology will be used as the reference standard. Results A pilot study was performed from June to August 2017. The enrollment of study subjects started in November 2017. Results are expected by the end of 2019. Conclusions The findings from the TREND study can be an important step to improve the management of children with clinical CAP. International Registered Report Identifier (IRRID) DERR1-10.2196/12705
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Affiliation(s)
- Samuel Arthur Rhedin
- Sachs' Children and Youth Hospital, South General Hospital, Stockholm, Sweden.,Department of Medical Epidemiology and Biostatistics, Karolinska Insitutet, Stockholm, Sweden
| | - Annika Eklundh
- Sachs' Children and Youth Hospital, South General Hospital, Stockholm, Sweden
| | | | - Pontus Naucler
- Division of Infectious Diseases, Department of Medicine, Solna, Karolinska Institutet & Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Uppsala, Sweden
| | - Jesper Gantelius
- Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ingela Zenk
- Sachs' Children and Youth Hospital, South General Hospital, Stockholm, Sweden
| | - Helene Andersson-Svahn
- Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Susanna Nybond
- Science for Life Laboratory, Division of Proteomics and Nanobiotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Reza Rasti
- Sachs' Children and Youth Hospital, South General Hospital, Stockholm, Sweden.,Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Lindh
- Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Maria Andersson
- Department of Infectious Diseases, University of Gothenburg, Gothenburg, Sweden
| | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Matti Waris
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Tobias Alfvén
- Sachs' Children and Youth Hospital, South General Hospital, Stockholm, Sweden.,Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
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65
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Havers FP, Fry AM, Goswami D, Nahar K, Sharmin AT, Rahman M, Brooks WA. Population-based Incidence of Childhood Pneumonia Associated With Viral Infections in Bangladesh. Pediatr Infect Dis J 2019; 38:344-350. [PMID: 30882722 DOI: 10.1097/inf.0000000000002155] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The contribution of respiratory viruses to childhood pneumonia in tropical low- and middle-income countries is poorly understood. We used population-based respiratory illness surveillance in children 5 years of age or younger in Dhaka, Bangladesh, to characterize these illnesses. METHODS We conducted weekly home visits to children who were referred to clinic for fever or respiratory symptoms. Standardized clinical data were collected. Nasopharyngeal washes were collected for one fifth of children diagnosed with a febrile or respiratory syndrome, with virus isolation testing for influenza and reverse transcription polymerase chain reaction testing for other viruses. Pneumonia was defined as age-specific tachypnea and crepitations on chest auscultation by study physicians. RESULTS From April 2004 to February 2008, 17,584 children were followed for 17,644 child-years; 6335 children had 12,499 clinic visits with eligible illnesses, including 6345 pneumonia episodes (incidence of 36 episodes/100 child-years). Annual incidence of pneumonia/100 child-years ranged from 88.3 for children 0-6 months of age to 13.1 for those 36-60 months of age. Of 1248 pneumonia visits with laboratory testing, 803 (64%) had detection of viral pathogens, including 274 respiratory syncytial virus (22% of pneumonia visits with laboratory testing; incidence 7.9/100 child-years), 244 adenovirus (19%; 7.0/100 child-years), 198 human metapneumovirus (16%; 5.7/100 child-years), 174 parainfluenza (14.0%; 5.0/100 child-years), and 81 influenza (6.5%; 2.3/100 child years). CONCLUSIONS Viral pathogens contribute to a majority of childhood pneumonia episodes in Bangladesh, a setting with high pneumonia rates, especially in children 2 years of age or younger. Developing effective prevention strategies targeting these children is a high priority. Given less sensitive laboratory method used for influenza detection, influenza rates may be underestimated.
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Affiliation(s)
- Fiona P Havers
- From the Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alicia M Fry
- From the Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Doli Goswami
- International Center for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Kamrun Nahar
- International Center for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Amina Tahia Sharmin
- International Center for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - Mustafizur Rahman
- International Center for Diarrheal Diseases Research, Bangladesh (ICDDR,B), Dhaka, Bangladesh
| | - W Abdullah Brooks
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Bhuiyan MU, Snelling TL, West R, Lang J, Rahman T, Granland C, de Gier C, Borland ML, Thornton RB, Kirkham LAS, Sikazwe C, Martin AC, Richmond PC, Smith DW, Jaffe A, Blyth CC. The contribution of viruses and bacteria to community-acquired pneumonia in vaccinated children: a case -control study. Thorax 2019; 74:261-269. [PMID: 30337417 PMCID: PMC6467248 DOI: 10.1136/thoraxjnl-2018-212096] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/12/2018] [Accepted: 09/17/2018] [Indexed: 10/31/2022]
Abstract
INTRODUCTION Respiratory pathogens associated with childhood pneumonia are often detected in the upper respiratory tract of healthy children, making their contribution to pneumonia difficult to determine. We aimed to determine the contribution of common pathogens to pneumonia adjusting for rates of asymptomatic detection to inform future diagnosis, treatment and preventive strategies. METHODS A case-control study was conducted among children <18 years in Perth, Western Australia. Cases were children hospitalised with radiologically confirmed pneumonia; controls were healthy children identified from outpatient and local immunisation clinics. Nasopharyngeal swabs were collected and tested for 14 respiratory viruses and 6 bacterial species by Polymerase chain reaction (PCR). For each pathogen, adjusted odds ratio (aOR; 95% CI) was calculated using multivariate logistic regression and population-attributable fraction (95% CI) for pneumonia was estimated. RESULTS From May 2015 to October 2017, 230 cases and 230 controls were enrolled. At least one respiratory virus was identified in 57% of cases and 29% of controls (aOR: 4.7; 95% CI: 2.8 to 7.8). At least one bacterial species was detected in 72% of cases and 80% of controls (aOR: 0.7; 95% CI: 0.4 to 1.2). Respiratory syncytial virus (RSV) detection was most strongly associated with pneumonia (aOR: 58.4; 95% CI: 15.6 to 217.5). Mycoplasma pneumoniae was the only bacteria associated with pneumonia (aOR: 14.5; 95% CI: 2.2 to 94.8). We estimated that RSV, human metapneumovirus (HMPV), influenza, adenovirus and Mycoplasma pneumoniae were responsible for 20.2% (95% CI: 14.6 to 25.5), 9.8% (5.6% to 13.7%), 6.2% (2.5% to 9.7%), 4% (1.1% to 7.1%) and 7.2% (3.5% to 10.8%) of hospitalisations for childhood pneumonia, respectively. CONCLUSIONS Respiratory viruses, particularly RSV and HMPV, are major contributors to pneumonia in Australian children.
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Affiliation(s)
- Mejbah Uddin Bhuiyan
- Division of Paediatrics, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Thomas L Snelling
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Rachel West
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Jurissa Lang
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Western Australia, Australia
| | - Tasmina Rahman
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Caitlyn Granland
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Camilla de Gier
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Meredith L Borland
- Division of Paediatrics, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Emergency Department, Perth Children's Hospital, Perth, Western Australia, Australia
- Division of Emergency Medicine, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ruth B Thornton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Lea-Ann S Kirkham
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Chisha Sikazwe
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Andrew C Martin
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - Peter C Richmond
- Division of Paediatrics, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- Department of General Paediatrics, Perth Children's Hospital, Perth, Western Australia, Australia
| | - David W Smith
- Department of Microbiology, PathWest Laboratory Medicine WA, Perth, Western Australia, Australia
- School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Christopher C Blyth
- Division of Paediatrics, School of Medicine, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Western Australia, Australia
- Department of Infectious Diseases, Perth Children's Hospital, Perth, Western Australia, Australia
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Kim J, Nam J, Jang W, Lim CS. Clinical Performance of the AllplexTM Respiratory Panel 1 Test Compared to SimplexaTM Flu A/B and RSV for Detection of Influenza Virus and Respiratory Syncytial Virus Infection Including Their Subtyping. Med Princ Pract 2019; 28:380-386. [PMID: 30831570 PMCID: PMC6639576 DOI: 10.1159/000499313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/03/2019] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVE TheAllplexTM Respiratory Panel 1 (ARP) is a new assay based on a real-time polymerase chain reaction (RT-PCR) for the detection of influenza A (Flu A), influenza B virus (Flu B), and respiratory syncytial virus (RSV), including subtyping by multiple detection temperature (MuDT) technology. We evaluated the performance of the Allplex Respiratory Panel compared to the SimplexaTM Flu A/B & RSV assay (SP) and other diagnostic tools. MATERIALS AND METHODS A total of 372 samples were collected from patients at the Korea University Guro Hospital in Seoul, Korea. All samples were tested for influenza virus and RSV by ARP, SP, and an in-house RT-PCR. RESULTS The sensitivity of ARP was 95.56, 100, and 95.24% for Flu A, Flu B, and RSV, respectively. The specificity of ARP was 100, 100, and 100% for Flu A, Flu B, and RSV, respectively. SP had sensitivities and specificities of 98.89 and 100% for Flu A, 100 and 100% for Flu B, and 100 and 100% for RSV. CONCLUSION The Allplex panelshowed high sensitivity, specificity, positive predictive, and negative predictive values for the detection of Flu A, Flu B, and RSV. This assay is fast and easy to perform because it takes only about 150 min and there is no need for post-PCR electrophoresis. The ARP can be used as a reliable and convenient assay in clinical laboratories.
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Affiliation(s)
- Jeeyong Kim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Jeonghun Nam
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Woongsik Jang
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University Guro Hospital, Seoul, Republic of Korea,
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68
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Le Geyt J, Hauck S, Lee M, Mackintosh J, Slater J, Razon D, Williams B. Respiratory syncytial virus prevalence in children admitted to five Kenyan district hospitals: a cross-sectional study. BMJ Paediatr Open 2019; 3:e000409. [PMID: 30957029 PMCID: PMC6422239 DOI: 10.1136/bmjpo-2018-000409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/22/2019] [Accepted: 01/28/2019] [Indexed: 11/05/2022] Open
Abstract
Acute respiratory infections (ARIs) are a leading cause of under-five mortality globally. In Kenya, the reported prevalence of respiratory syncytial virus (RSV) infections in single-centre studies has varied widely. Our study sought to determine the prevalence of RSV infection in children admitted with ARI fulfilling the WHO criteria for bronchiolitis. This was a prospective cross-sectional prevalence study in five hospitals across central and highland Kenya from April to June 2015. Two hundred and thirty-four participants were enrolled. The overall RSV positive rate was 8.1%, which is lower than in previous Kenyan studies. RSV-positive cases were on average 5 months younger than RSV-negative cases.
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Affiliation(s)
- Jacqueline Le Geyt
- Paediatric Emergency Department, Royal Alexandra Children's Hospital, Brighton, UK.,Global Links Volunteer, Royal College of Paediatrics and Child Health, London, UK
| | - Stephanie Hauck
- Paediatric Department, Nanyuki Teaching and Referral Hospital, Nanyuki, Kenya
| | - Mark Lee
- Global Links Volunteer, Royal College of Paediatrics and Child Health, London, UK
| | - Jennifer Mackintosh
- Global Links Volunteer, Royal College of Paediatrics and Child Health, London, UK
| | - Jessica Slater
- Global Links Volunteer, Royal College of Paediatrics and Child Health, London, UK
| | - Duke Razon
- Global Links Volunteer, Royal College of Paediatrics and Child Health, London, UK
| | - Bhanu Williams
- Paediatric Department, London North West Healthcare NHS Trust, London, UK
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le Polain de Waroux O, Flasche S, Kucharski AJ, Langendorf C, Ndazima D, Mwanga-Amumpaire J, Grais RF, Cohuet S, Edmunds WJ. Identifying human encounters that shape the transmission of Streptococcus pneumoniae and other acute respiratory infections. Epidemics 2018; 25:72-79. [PMID: 30054196 PMCID: PMC6227246 DOI: 10.1016/j.epidem.2018.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 01/23/2023] Open
Abstract
Although patterns of social contacts are believed to be an important determinant of infectious disease transmission, it remains unclear how the frequency and nature of human interactions shape an individual's risk of infection. We analysed data on daily social encounters individually matched to data on S. pneumoniae carriage and acute respiratory symptoms (ARS), from 566 individuals who took part in a survey in South-West Uganda. We found that the frequency of physical (i.e. skin-to-skin), long (≥1 h) and household contacts - which capture some measure of close (i.e. relatively intimate) contact - was higher among pneumococcal carriers than non-carriers, and among people with ARS compared to those without, irrespective of their age. With each additional physical encounter the age-adjusted risk of carriage and ARS increased by 6% (95%CI 2-9%) and 7% (2-13%) respectively. In contrast, the number of casual contacts (<5 min long) was not associated with either pneumococcal carriage or ARS. A detailed analysis by age of contacts showed that the number of close contacts with young children (<5 years) was particularly higher among older children and adult carriers than non-carriers, while the higher number of contacts among people suffering from ARS was more homogeneous across contacts of all ages. Our findings provide key evidence that the frequency of close interpersonal contact is important for transmission of respiratory infections, but not that of casual contacts. Those results are essential for both improving disease prevention and control efforts as well as informing research on infectious disease dynamics and transmission models, and more studies should be undertaken to further validate our results.
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Affiliation(s)
- Olivier le Polain de Waroux
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom.
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom
| | - Adam J Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom
| | - Celine Langendorf
- Department of Research, Epicentre, 8 Rue Saint-Sabin, 75011, Paris, France
| | - Donny Ndazima
- Epicentre Mbarara Research Centre, PO Box 1956, Mbarara, Uganda
| | - Juliet Mwanga-Amumpaire
- Epicentre Mbarara Research Centre, PO Box 1956, Mbarara, Uganda; Mbarara Universityof Science and Technology, Mbarara University, PO Box 1410, Mbarara, Uganda
| | - Rebecca F Grais
- Department of Research, Epicentre, 8 Rue Saint-Sabin, 75011, Paris, France
| | - Sandra Cohuet
- Department of Field Epidemiology, Epicentre, 8 Rue Saint-Sabin, 75011, Paris, France
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, WC1E 7HT, London, United Kingdom
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Razanajatovo NH, Guillebaud J, Harimanana A, Rajatonirina S, Ratsima EH, Andrianirina ZZ, Rakotoariniaina H, Andriatahina T, Orelle A, Ratovoson R, Irinantenaina J, Rakotonanahary DA, Ramparany L, Randrianirina F, Richard V, Heraud JM. Epidemiology of severe acute respiratory infections from hospital-based surveillance in Madagascar, November 2010 to July 2013. PLoS One 2018; 13:e0205124. [PMID: 30462659 PMCID: PMC6248916 DOI: 10.1371/journal.pone.0205124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/19/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Few comprehensive data exist regarding the epidemiology of severe acute respiratory infections (SARI) in low income countries. This study aimed at identifying etiologies and describing clinical features of SARI-associated hospitalization in Madagascar. METHODS It is a prospective surveillance of SARI in 2 hospitals for 3 years. Nasopharyngeal swabs, sputum, and blood were collected from SARI patients enrolled and tested for viruses and bacteria. Epidemiological and clinical information were obtained from case report forms. RESULTS Overall, 876 patients were enrolled in the study, of which 83.1% (728/876) were tested positive for at least one pathogen. Viral and bacterial infections occurred in 76.1% (667/876) and 35.8% (314/876) of tested samples, respectively. Among all detected viruses, respiratory syncytial virus (RSV) was the most common (37.7%; 348/924) followed by influenza virus A (FLUA, 18.4%; 170/924), rhinovirus (RV, 13.5%; 125/924), and adenovirus (ADV, 8.3%; 77/924). Among bacteria, Streptococcus pneumoniae (S. pneumoniae, 50.3%, 189/370) was the most detected followed by Haemophilus influenzae type b (Hib, 21.4%; 79/370), and Klebsiella (4.6%; 17/370). Other Streptococcus species were found in 8.1% (30/370) of samples. Compared to patients aged less than 5 years, older age groups were significantly less infected with RSV. On the other hand, patients aged more than 64 years (OR = 3.66) were at higher risk to be infected with FLUA, while those aged 15-29 years (OR = 3.22) and 30-64 years (OR = 2.39) were more likely to be infected with FLUB (influenza virus B). CONCLUSION The frequency of influenza viruses detected among SARI patients aged 65 years and more highlights the need for health authorities to develop strategies to reduce morbidity amongst at-risk population through vaccine recommendation. Amongst young children, the demonstrated burden of RSV should guide clinicians for a better case management of children. These findings reveal the need to develop point-of-care tests to avoid overuse of antibiotics and to promote vaccine that could reduce drastically the RSV hospitalizations.
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Affiliation(s)
| | - Julia Guillebaud
- National Influenza Centre, Virology Unit, Pasteur Institute of Madagascar, Antananarivo, Madagascar
| | - Aina Harimanana
- Epidemiology Unit, Pasteur Institute of Madagascar, Antananarivo, Madagascar
| | | | | | | | | | | | - Arnaud Orelle
- National Influenza Centre, Virology Unit, Pasteur Institute of Madagascar, Antananarivo, Madagascar
| | - Rila Ratovoson
- Epidemiology Unit, Pasteur Institute of Madagascar, Antananarivo, Madagascar
| | | | | | - Lovasoa Ramparany
- Center for Biological Analysis, Pasteur Institute of Madagascar, Antananarivo, Madagascar
| | | | - Vincent Richard
- Epidemiology Unit, Pasteur Institute of Madagascar, Antananarivo, Madagascar
| | - Jean-Michel Heraud
- National Influenza Centre, Virology Unit, Pasteur Institute of Madagascar, Antananarivo, Madagascar
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Kenmoe S, Bigna JJ, Well EA, Simo FBN, Penlap VB, Vabret A, Njouom R. Prevalence of human respiratory syncytial virus infection in people with acute respiratory tract infections in Africa: A systematic review and meta-analysis. Influenza Other Respir Viruses 2018; 12:793-803. [PMID: 29908103 PMCID: PMC6185896 DOI: 10.1111/irv.12584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2018] [Indexed: 12/31/2022] Open
Abstract
AIM The epidemiology of human respiratory syncytial virus (HRSV) infection has not yet been systematically investigated in Africa. This systematic review and meta-analysis are to estimate the prevalence of HRSV infections in people with acute respiratory tract infections (ARTI) in Africa. METHOD We searched PubMed, EMBASE, Africa Journal Online, and Global Index Medicus to identify observational studies published from January 1, 2000, to August 1, 2017. We used a random-effects model to estimate the prevalence across studies. Heterogeneity (I2 ) was assessed via the chi-square test on Cochran's Q statistic. Review registration: PROSPERO CRD42017076352. RESULTS A total of 67 studies (154 000 participants) were included. Sixty (90%), seven (10%), and no studies had low, moderate, and high risk of bias, respectively. The prevalence of HRSV infection varied widely (range 0.4%-60.4%). The pooled prevalence was 14.6% (95% CI 13.0-16.4, I2 = 98.8%). The prevalence was higher in children (18.5%; 95% CI 15.8-21.5) compared to adults (4.0%; 95% CI 2.2-6.1) and in people with severe respiratory tract infections (17.9%; 95% CI 15.8-20.1) compared to those with benign forms (9.4%; 95% CI 7.4-11.5); P-values <0.0001. The HRSV prevalence was not associated with sex, subregion in Africa, setting, altitude, latitude, longitude, and seasonality. CONCLUSION This study suggests a high prevalence of HRSV in people with ARTI in Africa, particularly among children and people with severe clinical form. All innovative strategies to curb the burden should first focus on children which present the highest HRSV-related burden.
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Affiliation(s)
- Sebastien Kenmoe
- Department of VirologyNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
| | - Jean Joel Bigna
- Department of Epidemiology and Public HealthNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
- School of Public HealthFaculty of MedicineUniversity of Paris SudLe Kremlin‐BicêtreFrance
| | | | - Fredy Brice N. Simo
- Department of BiochemistryFaculty of SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Véronique B. Penlap
- Department of BiochemistryFaculty of SciencesUniversity of Yaoundé 1YaoundéCameroon
| | - Astrid Vabret
- Normandie UniversitéCaenFrance
- Groupe de Recherche sur l'Adaptation Microbienne (GRAM)Université de CaenCaenFrance
- Laboratoire de VirologieCentre Hospitalo‐Universitaire de CaenCaenFrance
| | - Richard Njouom
- Department of VirologyNational Influenza CenterCentre Pasteur of CameroonYaoundéCameroon
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Bigna JJ, Kenmoe S, Well EA, Simo FBN, Penlap VB, Vabret A, Njouom R. Contemporaneous data on the prevalence of Human Respiratory Syncytial Virus infection in people with acute respiratory tract infections in Africa (2000-2017). Data Brief 2018; 20:940-947. [PMID: 30225305 PMCID: PMC6138983 DOI: 10.1016/j.dib.2018.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/24/2018] [Accepted: 08/15/2018] [Indexed: 11/28/2022] Open
Abstract
Availability of accurate data on the burden of the Human Respiratory Syncytial Virus (HRSV) can help to implement better strategies to curb this burden in Africa continent among people with acute respiratory tract infections (ARTI). We summarize here available contemporaneous data published from January 1, 2000 to August 31, 2017 on the prevalence of HSRV infection among people with ARTI in the continent.
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Affiliation(s)
- Jean Joel Bigna
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Sebastien Kenmoe
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Estelle Amandine Well
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, P.O. Box 1364, Yaoundé, Cameroon
| | - Fredy Brice N. Simo
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Véronique B. Penlap
- Department of Biochemistry, Faculty of Sciences, University of Yaoundé 1, P.O. Box 337, Yaoundé, Cameroon
| | - Astrid Vabret
- Normandie Université, 14032 Caen, France
- Université de Caen, Groupe de Recherche sur l’Adaptation Microbienne (GRAM), F-14000 Caen, France
- Laboratoire de Virologie, Centre Hospitalo-Universitaire de Caen, F-14033 Caen, France
| | - Richard Njouom
- National Influenza Center, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
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Nyiro JU, Munywoki P, Kamau E, Agoti C, Gichuki A, Etyang T, Otieno G, Nokes DJ. Surveillance of respiratory viruses in the outpatient setting in rural coastal Kenya: baseline epidemiological observations. Wellcome Open Res 2018; 3:89. [PMID: 30175247 PMCID: PMC6081997 DOI: 10.12688/wellcomeopenres.14662.1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2018] [Indexed: 11/24/2022] Open
Abstract
Background: Endemic and seasonally recurring respiratory viruses are a major cause of disease and death globally. The burden is particularly severe in developing countries. Improved understanding of the source of infection, pathways of spread and persistence in communities would be of benefit in devising intervention strategies. Methods: We report epidemiological data obtained through surveillance of respiratory viruses at nine outpatient health facilities within the Kilifi Health and Demographic Surveillance System, Kilifi County, coastal Kenya, between January and December 2016. Nasopharyngeal swabs were collected from individuals of all ages presenting with acute respiratory infection (ARI) symptoms (up to 15 swabs per week per facility) and screened for 15 respiratory viruses using real-time PCR. Paediatric inpatient surveillance at Kilifi County Hospital for respiratory viruses provided comparative data. Results: Over the year, 5,647 participants were sampled, of which 3,029 (53.7%) were aged <5 years. At least one target respiratory virus was detected in 2,380 (42.2%) of the samples; the most common being rhinovirus 18.6% (1,050), influenza virus 6.9% (390), coronavirus 6.8% (387), parainfluenza virus 6.6% (371), respiratory syncytial virus (RSV) 3.9% (219) and adenovirus 2.7% (155). Virus detections were higher among <5-year-olds compared to older children and adults (50.3% vs 32.7%, respectively; χ 2(1) =177.3, P=0.0001). Frequency of viruses did not differ significantly by facility (χ 2(8) =13.38, P=0.072). However, prevalence was significantly higher among inpatients than outpatients in <5-year-olds for RSV (22.1% vs 6.0%; χ 2(1) = 159.4, P=0.0001), and adenovirus (12.4% vs 4.4%, χ 2(1) =56.6, P=0.0001). Conclusions: Respiratory virus infections are common amongst ARI outpatients in this coastal Kenya setting, particularly in young children. Rhinovirus predominance warrants further studies on the health and socio-economic implications. RSV and adenovirus were more commonly associated with severe disease. Further analysis will explore epidemiological transmission patterns with the addition of virus sequence data.
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Affiliation(s)
- Joyce Uchi Nyiro
- Virus Epidemiology and Control, KEMRI-Wellcome Trust Research programme, Kilifi, +254, Kenya
| | - Patrick Munywoki
- Virus Epidemiology and Control, KEMRI-Wellcome Trust Research programme, Kilifi, +254, Kenya
- Public Health, Pwani University, Kilifi, +254, Kenya
| | - Everlyn Kamau
- Virus Epidemiology and Control, KEMRI-Wellcome Trust Research programme, Kilifi, +254, Kenya
| | - Charles Agoti
- Virus Epidemiology and Control, KEMRI-Wellcome Trust Research programme, Kilifi, +254, Kenya
- Public Health, Pwani University, Kilifi, +254, Kenya
| | - Alex Gichuki
- Virus Epidemiology and Control, KEMRI-Wellcome Trust Research programme, Kilifi, +254, Kenya
| | - Timothy Etyang
- Virus Epidemiology and Control, KEMRI-Wellcome Trust Research programme, Kilifi, +254, Kenya
| | - Grieven Otieno
- Virus Epidemiology and Control, KEMRI-Wellcome Trust Research programme, Kilifi, +254, Kenya
| | - D. James Nokes
- Virus Epidemiology and Control, KEMRI-Wellcome Trust Research programme, Kilifi, +254, Kenya
- Public Health, Pwani University, Kilifi, +254, Kenya
- School of Life Sciences and Zeeman Institue of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Conventry, UK
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74
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Kadjo HA, Adjogoua E, Dia N, Adagba M, Abdoulaye O, Daniel S, Kouakou B, Ngolo DC, Coulibaly D, Ndahwouh TN, Dosso M. DETECTION OF NON-INFLUENZA VIRUSES IN ACUTE RESPIRATORY INFECTIONS IN CHILDREN UNDER FIVE-YEAR-OLD IN COTE D'IVOIRE (JANUARY - DECEMBER 2013). Afr J Infect Dis 2018; 12:78-88. [PMID: 30109291 PMCID: PMC6085743 DOI: 10.21010/ajid.v12i2.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Influenza sentinel surveillance in Cote d'Ivoire showed that 70% of Acute Respiratory Infections (ARI) cases remained without etiology. This work aims to describe the epidemiological, clinical, and virological pattern of ARI that tested negative for influenza virus, in children under five years old. MATERIALS AND METHODS one thousand and fifty nine samples of patients presenting influenza Like Illness (ILI) or Severe Acute Respiratory Infections (SARI) symptoms were tested for other respiratory viruses using multiplex RT-PCR assays targeting 10 respiratory viruses. RESULTS The following pathogens were detected as follows, hRV 31,92% (98/307), hRSV 24.4% (75/329), PIV 20.5% (63/307), HCoV 229E 12,05% (37/307), hMPV 6.2% (19/307), HCoVOC43 1.0% (3/307) and EnV 1.0% (3/307). Among the 1,059 specimens analyzed, 917 (86.6%) were ILI samples and 142 (23.4%) were SARI samples. The proportion of children infected with at least one virus was 29.8% (273/917) in ILI cases and 23.9% (34/142) in SARI cases. The most prevalent viruses, responsible for ILI cases were hRV with 35.89% (98/273) and hRSV in SARI cases with 41.2% (14/34) of cases. Among the 1,059 patients, only 22 (2.1%) children presented risk factors related to the severity of influenza virus infection. CONCLUSION This study showed that respiratory viruses play an important role in the etiology of ARI in children. For a better understanding of the epidemiology of ARI and improved case management, it would be interesting in this context to expand the surveillance of influenza to other respiratory viruses.
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Affiliation(s)
- Herve A. Kadjo
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | | | - Marius Adagba
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | - Saraka Daniel
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | - Bertin Kouakou
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | - David C. Ngolo
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | - Talla Nzussouo Ndahwouh
- Noguchi Memorial Institute for Medical Research (NMIMR) University of Ghana, Legon, Accra, Ghana
| | - Mireille Dosso
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
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75
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Kiyuka PK, Agoti CN, Munywoki PK, Njeru R, Bett A, Otieno JR, Otieno GP, Kamau E, Clark TG, van der Hoek L, Kellam P, Nokes DJ, Cotten M. Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya. J Infect Dis 2018; 217:1728-1739. [PMID: 29741740 PMCID: PMC6037089 DOI: 10.1093/infdis/jiy098] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
Background Human coronavirus NL63 (HCoV-NL63) is a globally endemic pathogen causing mild and severe respiratory tract infections with reinfections occurring repeatedly throughout a lifetime. Methods Nasal samples were collected in coastal Kenya through community-based and hospital-based surveillance. HCoV-NL63 was detected with multiplex real-time reverse transcription PCR, and positive samples were targeted for nucleotide sequencing of the spike (S) protein. Additionally, paired samples from 25 individuals with evidence of repeat HCoV-NL63 infection were selected for whole-genome virus sequencing. Results HCoV-NL63 was detected in 1.3% (75/5573) of child pneumonia admissions. Two HCoV-NL63 genotypes circulated in Kilifi between 2008 and 2014. Full genome sequences formed a monophyletic clade closely related to contemporary HCoV-NL63 from other global locations. An unexpected pattern of repeat infections was observed with some individuals showing higher viral titers during their second infection. Similar patterns for 2 other endemic coronaviruses, HCoV-229E and HCoV-OC43, were observed. Repeat infections by HCoV-NL63 were not accompanied by detectable genotype switching. Conclusions In this coastal Kenya setting, HCoV-NL63 exhibited low prevalence in hospital pediatric pneumonia admissions. Clade persistence with low genetic diversity suggest limited immune selection, and absence of detectable clade switching in reinfections indicates initial exposure was insufficient to elicit a protective immune response.
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Affiliation(s)
- Patience K Kiyuka
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
- School of Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Regina Njeru
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Anne Bett
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - James R Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Grieven P Otieno
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Everlyn Kamau
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Academic Medical Center of the University of Amsterdam, the Netherlands
| | - Paul Kellam
- Department of Medicine, Division of Infectious Diseases, Imperial College London
- Kymab Ltd., Babraham Research Campus, Cambridge
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute-Wellcome Trust Research Programme
- School of Life Sciences and Zeeman Institute, University of Warwick, Coventry
| | - Matthew Cotten
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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Caballero MT, Polack FP. Respiratory syncytial virus is an "opportunistic" killer. Pediatr Pulmonol 2018; 53:664-667. [PMID: 29461021 PMCID: PMC5947624 DOI: 10.1002/ppul.23963] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022]
Abstract
Respiratory syncytial virus (RSV), responsible for more than three million yearly hospitalizations and up to 118 000 deaths in children under 5 years, is the leading pulmonary cause of death for this age group that lacks a licensed vaccine. Ninety-nine percent of deaths due to the virus occur in developing countries. In-hospital RSV fatalities affect previously healthy term infants in association with bacterial sepsis, clinically significant pneumothoraxes and, to a lesser extent, comorbid conditions. Community deaths affect low-income children from socially vulnerable families and appear to be as frequent as inpatient fatalities. In industrialized countries, RSV deaths occur almost exclusively in children with premorbid conditions. In a sense, RSV is an "opportunistic" killer. It needs a synergistic premorbid, medical practice-related, infectious, or social co-factor to cause a fatal outcome. But while the complex problems associated with these co-factors await solutions, candidate vaccines, long-lived monoclonal antibodies and antivirals against RSV are under clinical evaluation. It seems reasonable to predict that the landscape of RSV infections will look different in the next decade.
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Affiliation(s)
| | - Fernando P Polack
- Fundacion INFANT, Buenos Aires, Argentina.,Department of Pediatrics, Vanderbilt University, Nashville, Tennessee
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77
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Tempia S, Walaza S, Moyes J, Cohen AL, von Mollendorf C, McMorrow ML, Treurnicht FK, Venter M, Pretorius M, Hellferscee O, Wolter N, von Gottberg A, Nguweneza A, McAnerney JM, Dawood H, Variava E, Madhi SA, Cohen C. Attributable Fraction of Influenza Virus Detection to Mild and Severe Respiratory Illnesses in HIV-Infected and HIV-Uninfected Patients, South Africa, 2012-2016. Emerg Infect Dis 2018. [PMID: 28628462 PMCID: PMC5512492 DOI: 10.3201/eid2307.161959] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
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 <1 and >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.
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78
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Bhuiyan MU, Snelling TL, West R, Lang J, Rahman T, Borland ML, Thornton R, Kirkham LA, Sikazwe C, Martin AC, Richmond PC, Smith DW, Jaffe A, Blyth CC. Role of viral and bacterial pathogens in causing pneumonia among Western Australian children: a case-control study protocol. BMJ Open 2018; 8:e020646. [PMID: 29549211 PMCID: PMC5857668 DOI: 10.1136/bmjopen-2017-020646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/27/2017] [Accepted: 02/12/2018] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Pneumonia is the leading cause of childhood morbidity and mortality globally. Introduction of the conjugate Haemophilus influenzae B and multivalent pneumococcal vaccines in developed countries including Australia has significantly reduced the overall burden of bacterial pneumonia. With the availability of molecular diagnostics, viruses are frequently detected in children with pneumonia either as primary pathogens or predispose to secondary bacterial infection. Many respiratory pathogens that are known to cause pneumonia are also identified in asymptomatic children, so the true contribution of these pathogens to childhood community-acquired pneumonia (CAP) remains unclear. Since the introduction of pneumococcal vaccines, very few comprehensive studies from developed countries have attempted to determine the bacterial and viral aetiology of pneumonia. We aim to determine the contribution of bacteria and viruses to childhood CAP to inform further development of effective diagnosis, treatment and preventive strategies. METHODS AND ANALYSIS We are conducting a prospective case-control study (PneumoWA) where cases are children with radiologically confirmed pneumonia admitted to Princess Margaret Hospital for Children (PMH) and controls are healthy children identified from PMH outpatient clinics and from local community immunisation clinics. The case-control ratio is 1:1 with 250 children to be recruited in each arm. Nasopharyngeal swabs are collected from both cases and controls to detect the presence of viruses and bacteria by PCR; pathogen load will be assessed by quantitative PCR. The prevalence of pathogens detected in cases and controls will be compared, the OR of detection and population attributable fraction to CAP for each pathogen will be determined; relationships between pathogen load and disease status and severity will be explored. ETHICS AND DISSEMINATION This study has been approved by the human research ethics committees of PMH, Perth, Australia (PMH HREC REF 2014117EP). Findings will be disseminated at research conferences and in peer-reviewed journals.
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Affiliation(s)
- Mejbah Uddin Bhuiyan
- Division of Paediatrics, Faculty of Health and Medical Sciences, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
| | - Thomas L Snelling
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
| | - Rachel West
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
| | - Jurissa Lang
- PathWest Laboratory Medicine WA, Perth, Australia
| | - Tasmina Rahman
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Science, The University of Western Australia, Perth, Australia
| | - Meredith L Borland
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
| | - Ruth Thornton
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Science, The University of Western Australia, Perth, Australia
| | - Lea-Ann Kirkham
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Faculty of Health and Medical Sciences, School of Biomedical Science, The University of Western Australia, Perth, Australia
| | | | - Andrew C Martin
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
| | - Peter C Richmond
- Division of Paediatrics, Faculty of Health and Medical Sciences, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
| | | | - Adam Jaffe
- Faculty of Medicine, School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - Christopher C Blyth
- Division of Paediatrics, Faculty of Health and Medical Sciences, School of Medicine, The University of Western Australia, Perth, Western Australia, Australia
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Australia
- PathWest Laboratory Medicine WA, Perth, Australia
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79
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Rodrigues CMC, Groves H. Community-Acquired Pneumonia in Children: the Challenges of Microbiological Diagnosis. J Clin Microbiol 2018; 56:e01318-17. [PMID: 29237789 PMCID: PMC5824044 DOI: 10.1128/jcm.01318-17] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Community-acquired pneumonia (CAP) is the leading cause of mortality in children under 5 years of age globally. To improve the management of CAP, we must distinguish CAP from other common pediatric conditions and develop better diagnostic methods to detect the causative organism, so as to best direct appropriate resources in both industrialized and developing countries. Here, we review the diagnostic modalities available for identifying viruses and bacteria in the upper and lower respiratory tract of children, with a discussion of their utility and limitations in diagnosing CAP in children.
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Affiliation(s)
- C M C Rodrigues
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Paediatric Infectious Diseases and Immunology, Great North Children's Hospital, Newcastle Upon Tyne, United Kingdom
| | - H Groves
- Centre for Experimental Medicine, Queens University, Belfast, United Kingdom
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, United Kingdom
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80
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Higdon MM, Hammitt LL, Deloria Knoll M, Baggett HC, Brooks WA, Howie SRC, Kotloff KL, Levine OS, Madhi SA, Murdoch DR, Scott JAG, Thea DM, Driscoll AJ, Karron RA, Park DE, Prosperi C, Zeger SL, O'Brien KL, Feikin DR. Should Controls With Respiratory Symptoms Be Excluded From Case-Control Studies of Pneumonia Etiology? Reflections From the PERCH Study. Clin Infect Dis 2018; 64:S205-S212. [PMID: 28575354 PMCID: PMC5447853 DOI: 10.1093/cid/cix076] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Many pneumonia etiology case-control studies exclude controls with respiratory illness from enrollment or analyses. Herein we argue that selecting controls regardless of respiratory symptoms provides the least biased estimates of pneumonia etiology. We review 3 reasons investigators may choose to exclude controls with respiratory symptoms in light of epidemiologic principles of control selection and present data from the Pneumonia Etiology Research for Child Health (PERCH) study where relevant to assess their validity. We conclude that exclusion of controls with respiratory symptoms will result in biased estimates of etiology. Randomly selected community controls, with or without respiratory symptoms, as long as they do not meet the criteria for case-defining pneumonia, are most representative of the general population from which cases arose and the least subject to selection bias.
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Affiliation(s)
- Melissa M Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laura L Hammitt
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi.,Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W Abdullah Brooks
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Stephen R C Howie
- Medical Research Council Unit, Basse, The Gambia.,Department of Paediatrics, University of Auckland, and.,Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Orin S Levine
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - David R Murdoch
- Department of Pathology, University of Otago, and.,Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Donald M Thea
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts
| | - Amanda J Driscoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Ruth A Karron
- Department of International Health, Center for Immunization Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Daniel E Park
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland; and
| | - Katherine L O'Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Daniel R Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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81
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Li X, Li J, Meng L, Zhu W, Liu X, Yang M, Yu D, Niu L, Shen X. Viral etiologies and epidemiology of patients with acute respiratory infections based on sentinel hospitals in Gansu Province, Northwest China, 2011-2015. J Med Virol 2018; 90:828-835. [PMID: 29388679 PMCID: PMC7166685 DOI: 10.1002/jmv.25040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/17/2018] [Indexed: 01/01/2023]
Abstract
Understanding etiological role and epidemiological profile is needed to improve clinical management and prevention of acute respiratory infections (ARIs). A 5-year prospective study about active surveillance for outpatients and inpatients with ARIs was conducted in Gansu province, China, from January 2011 to November 2015. Respiratory specimens were collected from patients and tested for eight respiratory viruses using polymerase chain reaction (PCR) or reverse transcription polymerase chain reaction (RT-PCR). In this study, 2768 eligible patients with median age of 43 years were enrolled including pneumonia (1368, 49.2%), bronchitis (435, 15.7%), upper respiratory tract infection or URTI (250, 9.0%), and unclassified ARI (715, 25.8%). Overall, 29.2% (808/2768) were positive for any one of eight viruses, of whom 130 cases were identified with two or more viruses. Human rhinovirus (HRV) showed the highest detection rate (8.6%), followed by influenza virus (Flu, 7.3%), respiratory syncytial virus (RSV, 6.1%), human coronavirus (hCoV, 4.3%), human parainfluenza (PIV, 4.0%), adenovirus (ADV, 2.1%), human metapneumovirus (hMPV, 1.6%), and human bocavirus (hBoV, 0.7%). Compared with URTI, RSV was more likely identified in pneumonia (χ2 = 12.720, P < 0.001) and hCoV was more commonly associated with bronchitis than pneumonia (χ2 = 15.019, P < 0.001). In patients aged less than 5 years, RSV showed the highest detection rate and hCoV was the most frequent virus detected in adults and elderly. The clear epidemical seasons were observed in HRV, Flu, and hCoV infections. These findings could serve as a reference for local health authorities in drawing up further plans to prevent and control ARIs associated with viral etiologies.
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Affiliation(s)
- Xuechao Li
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Juansheng Li
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Lei Meng
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Wanqi Zhu
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Xinfeng Liu
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Mei Yang
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Deshan Yu
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Lixia Niu
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Xiping Shen
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
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82
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Scheltema NM, Gentile A, Lucion F, Nokes DJ, Munywoki PK, Madhi SA, Groome MJ, Cohen C, Moyes J, Thorburn K, Thamthitiwat S, Oshitani H, Lupisan SP, Gordon A, Sánchez JF, O'Brien KL, Gessner BD, Sutanto A, Mejias A, Ramilo O, Khuri-Bulos N, Halasa N, de-Paris F, Pires MR, Spaeder MC, Paes BA, Simões EAF, Leung TF, da Costa Oliveira MT, de Freitas Lázaro Emediato CC, Bassat Q, Butt W, Chi H, Aamir UB, Ali A, Lucero MG, Fasce RA, Lopez O, Rath BA, Polack FP, Papenburg J, Roglić S, Ito H, Goka EA, Grobbee DE, Nair H, Bont LJ. Global respiratory syncytial virus-associated mortality in young children (RSV GOLD): a retrospective case series. LANCET GLOBAL HEALTH 2018; 5:e984-e991. [PMID: 28911764 PMCID: PMC5599304 DOI: 10.1016/s2214-109x(17)30344-3] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/11/2017] [Accepted: 08/16/2017] [Indexed: 01/08/2023]
Abstract
Background Respiratory syncytial virus (RSV) infection is an important cause of pneumonia mortality in young children. However, clinical data for fatal RSV infection are scarce. We aimed to identify clinical and socioeconomic characteristics of children aged younger than 5 years with RSV-related mortality using individual patient data. Methods In this retrospective case series, we developed an online questionnaire to obtain individual patient data for clinical and socioeconomic characteristics of children aged younger than 5 years who died with community-acquired RSV infection between Jan 1, 1995, and Oct 31, 2015, through leading research groups for child pneumonia identified through a comprehensive literature search and existing research networks. For the literature search, we searched PubMed for articles published up to Feb 3, 2015, using the key terms “RSV”, “respiratory syncytial virus”, or “respiratory syncytial viral” combined with “mortality”, “fatality”, “death”, “died”, “deaths”, or “CFR” for articles published in English. We invited researchers and clinicians identified to participate between Nov 1, 2014, and Oct 31, 2015. We calculated descriptive statistics for all variables. Findings We studied 358 children with RSV-related in-hospital death from 23 countries across the world, with data contributed from 31 research groups. 117 (33%) children were from low-income or lower middle-income countries, 77 (22%) were from upper middle-income countries, and 164 (46%) were from high-income countries. 190 (53%) were male. Data for comorbidities were missing for some children in low-income and middle-income countries. Available data showed that comorbidities were present in at least 33 (28%) children from low-income or lower middle-income countries, 36 (47%) from upper middle-income countries, and 114 (70%) from high-income countries. Median age for RSV-related deaths was 5·0 months (IQR 2·3–11·0) in low-income or lower middle-income countries, 4·0 years (2·0–10·0) in upper middle-income countries, and 7·0 years (3·6–16·8) in high-income countries. Interpretation This study is the first large case series of children who died with community-acquired RSV infection. A substantial proportion of children with RSV-related death had comorbidities. Our results show that perinatal immunisation strategies for children aged younger than 6 months could have a substantial impact on RSV-related child mortality in low-income and middle-income countries. Funding Bill & Melinda Gates Foundation.
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Affiliation(s)
- Nienke M Scheltema
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Angela Gentile
- Department of Epidemiology, Ricardo Gutiérrez Children's Hospital, Buenos Aires, Argentina
| | - Florencia Lucion
- Department of Epidemiology, Ricardo Gutiérrez Children's Hospital, Buenos Aires, Argentina
| | - D James Nokes
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya; School of Life Sciences, University of Warwick, Coventry, UK
| | - Patrick K Munywoki
- Kenya Medical Research Institute, Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya; Department of Nursing Sciences, Pwani University, Kilifi, Kenya
| | - Shabir A Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit and Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Michelle J Groome
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit and Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa; Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Disease and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Kentigern Thorburn
- Department of Paediatric Intensive Care, Alder Hey Children's Hospital, Liverpool, UK
| | - Somsak Thamthitiwat
- Division of Global Health Protection, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi, Thailand
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai, Miyagi, Japan
| | - Socorro P Lupisan
- Research Institute for Tropical Medicine, Alabang Muntinlupa City, Metro Manila Philippines
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, MI, USA
| | - José F Sánchez
- Department of Medicine, Hospital Infantil Manuel de Jesus Rivera, Managua, Nicaragua
| | - Katherine L O'Brien
- International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | | | - Asuncion Mejias
- Department of Pediatrics, Division of Infectious Diseases, Ohio State University, Columbus, OH, USA; Center for Vaccines and Immunity at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Octavio Ramilo
- Department of Pediatrics, Division of Infectious Diseases, Ohio State University, Columbus, OH, USA; Center for Vaccines and Immunity at Nationwide Children's Hospital, Ohio State University, Columbus, OH, USA
| | - Najwa Khuri-Bulos
- Department of Pediatrics, University of Jordan, Aljubeiha, Amman, Jordan
| | - Natasha Halasa
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fernanda de-Paris
- Molecular Biology Laboratory, Hospital de Clínicas de Porto Alegre, Bairro Santa Cecília, Porto Alegre, Brazil
| | - Márcia Rosane Pires
- Infection Control Commission, Hospital de Clínicas de Porto Alegre, Bairro Santa Cecília, Porto Alegre, Brazil
| | - Michael C Spaeder
- Division of Pediatric Critical Care, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Bosco A Paes
- Neonatal Division, Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Eric A F Simões
- Department of Pediatrics and Center for Global Health, University of Colorado, Aurora, CO, USA
| | - Ting F Leung
- Department of Paediatrics, Faculty of Medicine and Chinese University of Hong Kong-University Medical Center Utrecht Joint Research Laboratory of Respiratory Virus and Immunobiology, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China
| | | | | | - Quique Bassat
- ISGlobal, Barcelona Centre for International Health Research, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain; ICREA, Catalan Institution for Research and Advanced Studies, Barcelona, Spain; Department of Pediatrics, Hospital Sant Joan de Déu, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique; Faculty of Medicine, Universidad Europea de Madrid, Madrid, Spain
| | - Warwick Butt
- Department of Intensive Care, Royal Children's Hospital, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Hsin Chi
- Department of Pediatric Infectious Disease, MacKay Children's Hospital, Taipei, Taiwan
| | - Uzma Bashir Aamir
- Department of Virology, National Institute of Health, Islamabad, Pakistan
| | - Asad Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Marilla G Lucero
- Research Institute for Tropical Medicine, Alabang Muntinlupa City, Metro Manila Philippines
| | | | - Olga Lopez
- Hospital Dr. Ernesto Torres Galdames, Iquique, Chile
| | - Barbara A Rath
- Vienna Vaccine Safety Initiative, Berlin, Germany; University of Nottingham School of Medicine, Nottingham, UK
| | | | - Jesse Papenburg
- Department of Microbiology, Division of Pediatric Infectious Diseases, McGill University Health Centre, Montreal, QC, Canada
| | - Srđan Roglić
- Department of Paediatric Infectious Diseases, University Hospital for Infectious Diseases, Zagreb, Croatia
| | - Hisato Ito
- Department of Pediatrics, Nantan General Hospital, Ueno, Yagichoyagi, Nantan-shi, Kyoto, Japan
| | - Edward A Goka
- School of Health and Related Research, University of Sheffield, Sheffield, UK
| | - Diederick E Grobbee
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands; Julius Clinical Science, Zeist, Netherlands
| | - Harish Nair
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Louis J Bont
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Netherlands; ReSViNET Respiratory Syncytial Virus Network, Utrecht, Netherlands.
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83
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Abstract
The four endemic human coronaviruses HCoV-229E, -NL63, -OC43, and -HKU1 contribute a considerable share of upper and lower respiratory tract infections in adults and children. While their clinical representation resembles that of many other agents of the common cold, their evolutionary histories, and host associations could provide important insights into the natural history of past human pandemics. For two of these viruses, we have strong evidence suggesting an origin in major livestock species while primordial associations for all four viruses may have existed with bats and rodents. HCoV-NL63 and -229E may originate from bat reservoirs as assumed for many other coronaviruses, but HCoV-OC43 and -HKU1 seem more likely to have speciated from rodent-associated viruses. HCoV-OC43 is thought to have emerged from ancestors in domestic animals such as cattle or swine. The bovine coronavirus has been suggested to be a possible ancestor, from which HCoV-OC43 may have emerged in the context of a pandemic recorded historically at the end of the 19th century. New data suggest that HCoV-229E may actually be transferred from dromedary camels similar to Middle East respiratory syndrome (MERS) coronavirus. This scenario provides important ecological parallels to the present prepandemic pattern of host associations of the MERS coronavirus.
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Affiliation(s)
- Victor M Corman
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany
| | - Doreen Muth
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany
| | - Daniela Niemeyer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Christian Drosten
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany; German Center for Infection Research (DZIF), Berlin, Germany.
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84
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Yu J, Xie Z, Zhang T, Lu Y, Fan H, Yang D, Bénet T, Vanhems P, Shen K, Huang F, Han J, Li T, Gao Z, Ren L, Wang J. Comparison of the prevalence of respiratory viruses in patients with acute respiratory infections at different hospital settings in North China, 2012-2015. BMC Infect Dis 2018; 18:72. [PMID: 29422011 PMCID: PMC5806372 DOI: 10.1186/s12879-018-2982-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 01/30/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Acute respiratory infections (ARIs) are a great public health challenge globally. The prevalence of respiratory viruses in patients with ARIs attending at different hospital settings is fully undetermined. METHODS Laboratory-based surveillance for ARIs was conducted at inpatient and outpatient settings of 11 hospitals in North China. The first 2-5 patients with ARIs were recruited in each hospital weekly from 2012 through 2015. The presence of respiratory viruses was screened by PCR assays. The prevalence of respiratory viruses was determined and compared between patients at different hospital settings. RESULTS A total of 3487 hospitalized cases and 6437 outpatients/Emergency Department (ED) patients were enrolled. The most commonly detected viruses in the hospitalized cases were respiratory syncytial virus (RSV, 33.3%) in children less than two years old, adenoviruses (13.0%) in patients 15-34 years old, and influenza viruses (IFVs, 9.6%) in patients ≥65 years. IFVs were the most common virus in outpatient/ED patients across all age groups (22.7%). After controlling for the confounders caused by other viruses and covariates, adenoviruses (adjusted odds ratio [aOR]: 3.97, 99% confidence interval [99% CI]: 2.19-7.20) and RSV (aOR: 2.04, 99% CI: 1.34-3.11) were independently associated with increased hospitalization in children, as well as adenoviruses in adults (aOR: 2.14, 99% CI: 1.19-3.85). Additionally, co-infection of RSV with IFVs was associated with increased hospitalization in children (aOR: 12.20, 99% CI: 2.65-56.18). CONCLUSIONS A substantial proportion of ARIs was associated with respiratory viruses in North China. RSV, adenoviruses, and co-infection of RSV and IFVs were more frequent in hospitalized children (or adenoviruses in adults), which might predict the severity of ARIs. Attending clinicians should be more vigilant of these infections.
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Affiliation(s)
- Jianxing Yu
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Zhengde Xie
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, No. 56 Nan-li-shi Road, Beijing, 100045, People's Republic of China
| | - Tiegang Zhang
- Beijing Center for Disease Control and Prevention, No.16, Hepingli Middle Avenue of Dongcheng district, Beijing, 100013, People's Republic of China
| | - Yanqin Lu
- Shandong Medicinal Biotechnology Centre, Key Laboratory for Modern Medicine and Technology of Shandong Province, Shandong Academy of Medical Sciences, No. 18877 Jingshi Road, Jinan, Shandong, 250062, People's Republic of China
| | - Hongwei Fan
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Donghong Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Thomas Bénet
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Lyon, France.,Laboratoire des Pathogènes Emergents - Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Institut National de la Santé et de la Recherche Médicale U1111, Centre National de la Recherche Scientifique, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 21, Avenue Tony Garnier, 69007, Lyon, France
| | - Philippe Vanhems
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Lyon, France.,Laboratoire des Pathogènes Emergents - Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Institut National de la Santé et de la Recherche Médicale U1111, Centre National de la Recherche Scientifique, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 21, Avenue Tony Garnier, 69007, Lyon, France.,INSERM, F-CRIN, I-REIVAC, Lyon Collaborative Center, Lyon, France
| | - Kunling Shen
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, No. 56 Nan-li-shi Road, Beijing, 100045, People's Republic of China
| | - Fang Huang
- Beijing Center for Disease Control and Prevention, No.16, Hepingli Middle Avenue of Dongcheng district, Beijing, 100013, People's Republic of China
| | - Jinxiang Han
- Shandong Medicinal Biotechnology Centre, Key Laboratory for Modern Medicine and Technology of Shandong Province, Shandong Academy of Medical Sciences, No. 18877 Jingshi Road, Jinan, Shandong, 250062, People's Republic of China
| | - Taisheng Li
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Lili Ren
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, 100730, People's Republic of China.
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, 100730, People's Republic of China.
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85
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Dawa JA, Chaves SS, Nyawanda B, Njuguna HN, Makokha C, Otieno NA, Anzala O, Widdowson MA, Emukule GO. National burden of hospitalized and non-hospitalized influenza-associated severe acute respiratory illness in Kenya, 2012-2014. Influenza Other Respir Viruses 2017; 12:30-37. [PMID: 29243402 PMCID: PMC5818348 DOI: 10.1111/irv.12488] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Influenza-associated respiratory illness was substantial during the emergence of the 2009 influenza pandemic. Estimates of influenza burden in the post-pandemic period are unavailable to guide Kenyan vaccine policy. OBJECTIVES To update estimates of hospitalized and non-hospitalized influenza-associated severe acute respiratory illness (SARI) during a post-pandemic period (2012-2014) and describe the incidence of disease by narrow age categories. METHODS We used data from Siaya County Referral Hospital to estimate age-specific base rates of SARI. We extrapolated these base rates to other regions within the country by adjusting for regional risk factors for acute respiratory illness (ARI), regional healthcare utilization for acute respiratory illness, and the proportion of influenza-positive SARI cases in each region, so as to obtain region-specific rates. RESULTS The mean annual rate of hospitalized influenza-associated SARI among all ages was 21 (95% CI 19-23) per 100 000 persons. Rates of non-hospitalized influenza-associated SARI were approximately 4 times higher at 82 (95% CI 74-90) per 100 000 persons. Mean annual rates of influenza-associated SARI were highest in children <2 years of age with annual hospitalization rates of 147 (95% CI of 134-160) per 100 000 persons and non-hospitalization rates of 469 (95% CI 426-517) per 100 000 persons. For the period 2012-2014, there were between 8153 and 9751 cases of hospitalized influenza-associated SARI and 31 785-38 546 cases of non-hospitalized influenza-associated SARI per year. CONCLUSIONS The highest burden of disease was observed among children <2 years of age. This highlights the need for strategies to prevent influenza infections in this age group.
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Affiliation(s)
- Jeanette A Dawa
- College of Health Sciences, Kenya AIDS Vaccine Institute (KAVI) - Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
| | - Sandra S Chaves
- Centers for Disease Control and Prevention, Nairobi, Kenya.,Influenza Division, National Center for Immunization and Respiratory Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | | | - Omu Anzala
- College of Health Sciences, Kenya AIDS Vaccine Institute (KAVI) - Institute of Clinical Research, University of Nairobi, Nairobi, Kenya
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86
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Ning G, Wang X, Wu D, Yin Z, Li Y, Wang H, Yang W. The etiology of community-acquired pneumonia among children under 5 years of age in mainland China, 2001-2015: A systematic review. Hum Vaccin Immunother 2017; 13:2742-2750. [PMID: 28922613 DOI: 10.1080/21645515.2017.1371381] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The aim of this systematic review was to examine the etiology of community-acquired pneumonia (CAP) among Chinese children younger than 5 y and provide evidence for further cost-effectiveness analyses for vaccine development, diagnostic strategies and empirical treatments. METHODS The literature review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Data were obtained by searching PubMed, Embase, Web-of Science, and the Chinese databases Wanfang Data and China National Knowledge Infrastructure. All CAP etiological studies on children under 5 y of age from China published in Chinese and English between the years of 2001 and 2015 were included. A total of 48 studies were included in the final review, comprising 100 151 hospitalized children with CAP episodes. Heterogeneity and the percentage of variation between studies was analyzed based on Q statistic and I2 indices, respectively. Random effect models were used to calculate the weighted average rate in all analyses. RESULTS The most frequently detected bacterial agents were Klebsiella pneumoniae (5.4%), Streptococcus pneumoniae (5.2%), Escherichia coli (5.2%), Staphylococcus aureus (3.9%), Haemophilus influenza (3.6%) and Haemophilus parainfluenzae (3.3%). The most frequently detected viruses were human rhinovirus (20.3%, in just 2 studies), respiratory syncytial virus (RSV, 17.3%), human bocavirus (9.9%), parainfluenza virus (5.8%), human metapneumovirus (3.9%) and influenza (3.5%). Mycoplasma pneumoniae and Chlamydophila pneumoniae were identified in 9.5% and 2.9%, respectively, of children under 5 y of age with CAP. CONCLUSION This article provides the most comprehensive analysis to date of the factors contributing to CAP in children under 5 y of age. S. pneumoniae, H. influenzae and influenza were the most common vaccine-preventable diseases in children. Corresponding, vaccines should be introduced into Chinese immunization programs, and further economic evaluations should be conducted. RSV is common in Chinese children and preventative measures could have a substantial impact on public health. These data also have major implications for diagnostic strategies and empirical treatments.
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Affiliation(s)
- Guijun Ning
- a Department of National Immunization Program , Chinese Center for Disease Control and Prevention , Beijing , China
| | - Xuxia Wang
- b Immunization Program Department , Gansu Provincial Center for Disease Control and Prevention , Lanzhou , Gansu , China
| | - Dan Wu
- a Department of National Immunization Program , Chinese Center for Disease Control and Prevention , Beijing , China
| | - Zundong Yin
- a Department of National Immunization Program , Chinese Center for Disease Control and Prevention , Beijing , China
| | - Yixing Li
- a Department of National Immunization Program , Chinese Center for Disease Control and Prevention , Beijing , China
| | - Huaqing Wang
- a Department of National Immunization Program , Chinese Center for Disease Control and Prevention , Beijing , China
| | - Weizhong Yang
- a Department of National Immunization Program , Chinese Center for Disease Control and Prevention , Beijing , China
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87
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Bénet T, Picot VS, Awasthi S, Pandey N, Bavdekar A, Kawade A, Robinson A, Rakoto-Andrianarivelo M, Sylla M, Diallo S, Russomando G, Basualdo W, Komurian-Pradel F, Endtz H, Vanhems P, Paranhos-Baccalà G, For The Gabriel Network. Severity of Pneumonia in Under 5-Year-Old Children from Developing Countries: A Multicenter, Prospective, Observational Study. Am J Trop Med Hyg 2017; 97:68-76. [PMID: 28719310 PMCID: PMC5508893 DOI: 10.4269/ajtmh.16-0733] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Pneumonia is the leading cause of death in children. The objectives were to evaluate the microbiological agents linked with hypoxemia in hospitalized children with pneumonia from developing countries, to identify predictors of hypoxemia, and to characterize factors associated with in-hospital mortality. A multicenter, observational study was conducted in five hospitals, from India (Lucknow, Vadu), Madagascar (Antananarivo), Mali (Bamako), and Paraguay (San Lorenzo). Children aged 2-60 months with radiologically confirmed pneumonia were enrolled prospectively. Respiratory and whole blood specimens were collected, identifying viruses and bacteria by real-time multiplex polymerase chain reaction (PCR). Microbiological agents linked with hypoxemia at admission (oxygen saturation < 90%) were analyzed by multivariate logistic regression, and factors associated with 14-day in-hospital mortality were assessed by bivariate Cox regression. Overall, 405 pneumonia cases (3,338 hospitalization days) were analyzed; 13 patients died within 14 days of hospitalization. Hypoxemia prevalence was 17.3%. Detection of human metapneumovirus (hMPV) and respiratory syncytial virus (RSV) in respiratory samples was independently associated with increased risk of hypoxemia (adjusted odds ratio [aOR] = 2.4, 95% confidence interval [95% CI] = 1.0-5.8 and aOR = 2.5, 95% CI = 1.1-5.3, respectively). Lower chest indrawing and cyanosis were predictive of hypoxemia (positive likelihood ratios = 2.3 and 2.4, respectively). Predictors of death were Streptococcus pneumoniae detection by blood PCR (crude hazard ratio [cHR] = 4.6, 95% CI = 1.5-14.0), procalcitonin ≥ 50 ng/mL (cHR = 22.4, 95% CI = 7.3-68.5) and hypoxemia (cHR = 4.8, 95% CI = 1.6-14.4). These findings were consistent on bivariate analysis. hMPV and RSV in respiratory samples were linked with hypoxemia, and S. pneumoniae in blood was associated with increased risk of death among hospitalized children with pneumonia in developing countries.
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Affiliation(s)
- Thomas Bénet
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS, UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Valentina Sanchez Picot
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS, UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | | | - Nitin Pandey
- Chhatrapati Shahu Ji Maharaj University, Lucknow, India
| | | | | | | | | | | | | | | | - Wilma Basualdo
- Hospital Pediátrico "Niños de Acosta Ñu," San Lorenzo, Paraguay
| | - Florence Komurian-Pradel
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS, UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Hubert Endtz
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS, UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Philippe Vanhems
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS, UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Gláucia Paranhos-Baccalà
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), INSERM U1111, CNRS, UMR5308, ENS de Lyon, UCBL1, Lyon, France
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88
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Feikin DR, Hammitt LL, Murdoch DR, O'Brien KL, Scott JAG. The Enduring Challenge of Determining Pneumonia Etiology in Children: Considerations for Future Research Priorities. Clin Infect Dis 2017; 64:S188-S196. [PMID: 28575369 PMCID: PMC5447852 DOI: 10.1093/cid/cix143] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Pneumonia kills more children each year worldwide than any other disease. Nonetheless, accurately determining the causes of childhood pneumonia has remained elusive. Over the past century, the focus of pneumonia etiology research has shifted from studies of lung aspirates and postmortem specimens intent on identifying pneumococcal disease to studies of multiple specimen types distant from the lung that are tested for multiple pathogens. Some major challenges facing modern pneumonia etiology studies include the use of nonspecific and variable case definitions, poor access to pathologic lung tissue and to specimens from fatal cases, poor diagnostic accuracy of assays (especially when testing nonpulmonary specimens), and the interpretation of results when multiple pathogens are detected in a given individual. The future of childhood pneumonia etiology research will likely require integrating data from complementary approaches, including applications of advanced molecular diagnostics and vaccine probe studies, as well as a renewed emphasis on lung aspirates from radiologically confirmed pneumonia and postmortem examinations.
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Affiliation(s)
- Daniel R Feikin
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Laura L Hammitt
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - David R Murdoch
- Department of Pathology, University of Otago, and
- Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
| | - Katherine L O'Brien
- International Vaccine Access Center, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
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89
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Mwangome M, Ngari M, Fegan G, Mturi N, Shebe M, Bauni E, Berkley JA. Diagnostic criteria for severe acute malnutrition among infants aged under 6 mo. Am J Clin Nutr 2017; 105:1415-1423. [PMID: 28424189 PMCID: PMC5445677 DOI: 10.3945/ajcn.116.149815] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 03/15/2017] [Indexed: 11/14/2022] Open
Abstract
Background: There is an increasing recognition of malnutrition among infants under 6 mo of age (U6M). Current diagnosis criteria use weight-for-length z scores (WLZs), but the 2006 WHO standards exclude infants shorter than 45 cm. In older children, midupper arm circumference (MUAC) predicts mortality better than does WLZ. Outcomes may also be influenced by exposure to HIV and size or gestational age at birth. Diagnostic thresholds for WLZ, MUAC, and other indexes have not been fully evaluated against mortality risk among U6M infants.Objective: The aim was to determine the association of anthropometric indexes with risks of inpatient and postdischarge mortality among U6M infants recruited at the time of hospitalization.Design: We analyzed data from a cohort of U6M infants admitted to Kilifi County Hospital (2007-2013), Kenya. The primary outcomes were inpatient death and death during follow-up over 1 y after discharge. We calculated adjusted RRs for inpatient mortality and HRs for postdischarge mortality for different anthropometric measures and thresholds. Discriminatory value was assessed by using receiver operating characteristic curves.Results: A total of 2882 infants were admitted: 140 (4.9%) died in the hospital and 1405 infants were followed up after discharge. Of these, 75 (5.3%) died within 1 y during 1318 child-years of observation. MUAC and weight-for-age z score (WAZ) predicted inpatient and postdischarge mortality better than did WLZ (P < 0.0001). A single MUAC threshold of <11.0 cm performed similarly to MUAC thresholds that varied with age (all P > 0.05) and performed better than WLZ <-3 for both inpatient and postdischarge mortality (both P < 0.001). Reported small size at birth did not reduce the risk of death associated with anthropometric indexes.Conclusions: U6M infants at the highest risk of death are best targeted by using MUAC or WAZ. Further research into the effectiveness of potential interventions is required.
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Affiliation(s)
- Martha Mwangome
- Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Program, Kilifi, Kenya; .,Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Moses Ngari
- Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Program, Kilifi, Kenya;,Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Greg Fegan
- Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Program, Kilifi, Kenya;,Swansea Trials Unit, Swansea University Medical School, Swansea, United Kingdom; and
| | - Neema Mturi
- Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Program, Kilifi, Kenya
| | - Mohammed Shebe
- Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Program, Kilifi, Kenya
| | - Evasius Bauni
- Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Program, Kilifi, Kenya
| | - James A Berkley
- Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Program, Kilifi, Kenya;,Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya;,Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford, Oxford, United Kingdom
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90
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Nyiro JU, Kombe IK, Sande CJ, Kipkoech J, Kiyuka PK, Onyango CO, Munywoki PK, Kinyanjui TM, Nokes DJ. Defining the vaccination window for respiratory syncytial virus (RSV) using age-seroprevalence data for children in Kilifi, Kenya. PLoS One 2017; 12:e0177803. [PMID: 28531224 PMCID: PMC5439681 DOI: 10.1371/journal.pone.0177803] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/03/2017] [Indexed: 11/19/2022] Open
Abstract
Background Respiratory syncytial virus (RSV) is an important cause of lower respiratory tract disease in early life and a target for vaccine prevention. Data on the age-prevalence of RSV specific antibodies will inform on optimizing vaccine delivery. Methods Archived plasma samples were randomly selected within age strata from 960 children less than 145 months of age admitted to Kilifi County Hospital pediatric wards between 2007 and 2010. Samples were tested for antibodies to RSV using crude virus IgG ELISA. Seroprevalence (and 95% confidence intervals) was estimated as the proportion of children with specific antibodies above a defined cut-off level. Nested catalytic models were used to explore different assumptions on antibody dynamics and estimate the rates of decay of RSV specific maternal antibody and acquisition of infection with age, and the average age of infection. Results RSV specific antibody prevalence was 100% at age 0-<1month, declining rapidly over the first 6 months of life, followed by an increase in the second half of the first year of life and beyond. Seroprevalence was lowest throughout the age range 5–11 months; all children were seropositive beyond 3 years of age. The best fit model to the data yielded estimates for the rate of infection of 0.78/person/year (95% CI 0.65–0.97) and 1.69/person/year (95% CI 1.27–2.04) for ages 0-<1 year and 1-<12 years, respectively. The rate of loss of maternal antibodies was estimated as 2.54/year (95% CI 2.30–2.90), i.e. mean duration 4.7 months. The mean age at primary infection was estimated at 15 months (95% CI 13–18). Conclusions The rate of decay of maternal antibody prevalence and subsequent age-acquisition of infection are rapid, and the average age at primary infection early. The vaccination window is narrow, and suggests optimal targeting of vaccine to infants 5 months and above to achieve high seroconversion.
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Affiliation(s)
- Joyce U. Nyiro
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Ivy K. Kombe
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- * E-mail:
| | - Charles J. Sande
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
| | - James Kipkoech
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Patience K. Kiyuka
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Clayton O. Onyango
- Kenya Medical Research Institute/ Centre for Disease Control and Prevention, Kisumu, Kenya
| | - Patrick K. Munywoki
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | | | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
- School of Life Sciences and WIDER, University of Warwick, Coventry, United Kingdom
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91
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Ngari MM, Fegan G, Mwangome MK, Ngama MJ, Mturi N, Scott JAG, Bauni E, Nokes DJ, Berkley JA. Mortality after Inpatient Treatment for Severe Pneumonia in Children: a Cohort Study. Paediatr Perinat Epidemiol 2017; 31:233-242. [PMID: 28317139 PMCID: PMC5434848 DOI: 10.1111/ppe.12348] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Although pneumonia is a leading cause of inpatient mortality, deaths may also occur after discharge from hospital. However, prior studies have been small, in selected groups or did not fully evaluate risk factors, particularly malnutrition and HIV. We determined 1-year post-discharge mortality and risk factors among children diagnosed with severe pneumonia. METHODS A cohort study of children aged 1-59 months admitted to Kilifi County Hospital with severe pneumonia (2007-12). The primary outcome was death <1 year after discharge, determined through Kilifi Health and Demographic Surveillance System (KHDSS) quarterly census rounds. RESULTS Of 4184 children (median age 9 months) admitted with severe pneumonia, 1041 (25%) had severe acute malnutrition (SAM), 267 (6.4%) had a positive HIV antibody test, and 364 (8.7%) died in hospital. After discharge, 2279 KHDSS-resident children were followed up; 70 (3.1%) died during 2163 child-years: 32 (95% confidence interval (CI) 26, 41) deaths per 1000 child years. Post-discharge mortality was greater after admission for severe pneumonia than for other diagnoses, hazard ratio 2.5 (95% CI 1.2, 5.3). Malnutrition, HIV status, age and prolonged hospitalisation, but not signs of pneumonia severity, were associated with post-discharge mortality. Fifty-two per cent (95% CI 37%, 63%) of post-discharge deaths were attributable to low mid-upper arm circumference and 11% (95% CI 3.3%, 18%) to a positive HIV test. CONCLUSIONS Admission with severe pneumonia is an important marker of vulnerability. Risk stratification and better understanding of the mechanisms underlying post-discharge mortality, especially for undernourished children, are needed to reduce mortality after treatment for pneumonia.
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Affiliation(s)
- Moses M. Ngari
- KEMRI/Wellcome Trust Research ProgrammeKilifiKenya,The Childhood Acute Illness & Nutrition (CHAIN) NetworkNairobiKenya
| | - Greg Fegan
- KEMRI/Wellcome Trust Research ProgrammeKilifiKenya,Swansea Trials UnitSwansea University Medical SchoolSwanseaUK
| | - Martha K. Mwangome
- KEMRI/Wellcome Trust Research ProgrammeKilifiKenya,The Childhood Acute Illness & Nutrition (CHAIN) NetworkNairobiKenya
| | | | - Neema Mturi
- KEMRI/Wellcome Trust Research ProgrammeKilifiKenya
| | - John Anthony Gerard Scott
- KEMRI/Wellcome Trust Research ProgrammeKilifiKenya,London School of Hygiene & Tropical MedicineLondonUK
| | | | - David James Nokes
- KEMRI/Wellcome Trust Research ProgrammeKilifiKenya,School of Life SciencesUniversity of WarwickCoventryUK
| | - James A. Berkley
- KEMRI/Wellcome Trust Research ProgrammeKilifiKenya,The Childhood Acute Illness & Nutrition (CHAIN) NetworkNairobiKenya,Centre for Tropical Medicine & Global HealthUniversity of OxfordOxfordUK
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92
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Huang S, Feng C, Zhai YZ, Zhou X, Li B, Wang LL, Chen W, Lv FQ, Li TS. Identification of miRNA biomarkers of pneumonia using RNA-sequencing and bioinformatics analysis. Exp Ther Med 2017; 13:1235-1244. [PMID: 28413462 PMCID: PMC5377245 DOI: 10.3892/etm.2017.4151] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/10/2016] [Indexed: 11/05/2022] Open
Abstract
Pneumonia is a lower respiratory tract infection that causes dramatic mortality worldwide. The present study aimed to investigate the pathogenesis of pneumonia and identify microRNA (miRNA) biomarkers as candidates for targeted therapy. RNA from the peripheral blood plasma of participants with pneumonia (severe, n=9; non-severe, n=9) and controls (n=9) was isolated and paired-end sequencing was performed on an Illumina HiSeq4000 system. Following the processing of raw reads, the sequences were aligned against the Genome Reference Consortium human genome assembly 38 reference genome using Bowtie2 software. Reads per kilobase of transcript per million mapped read values were obtained and the limma software package was used to identify differentially expressed miRNAs (DE-miRs). Then, DE-miR targets were predicted and subjected to enrichment analysis. In addition, a protein-protein interaction (PPI) network of the predicted targets was constructed. This analysis identified 11 key DE-miRs in pneumonia samples, including 6 upregulated miRNAs (including hsa-miR-34a and hsa-miR-455) and 5 downregulated miRNAs (including hsa-let-7f-1). All DE-miRs kept their upregulation/downregulation pattern in the control, non-severe pneumonia and severe pneumonia samples. Predicted target genes of DE-miRs in the subjects with non-severe pneumonia vs. the control and the subjects with severe pneumonia vs. the non-severe pneumonia group were markedly enriched in the adherens junction and Wnt signaling pathways. KALRN, Ras homolog family member A (RHOA), β-catenin (CTNNB1), RNA polymerase II subunit K (POLR2K) and amyloid precursor protein (APP) were determined to encode crucial proteins in the PPI network constructed. KALRN was predicted to be a target of hsa-mir-200b, while RHOA, CTNNB1, POLR2K and APP were predicted targets of hsa-let-7f-1. The results of the present study demonstrated that hsa-let-7f-1 may serve a role in the development of cancer and the Notch signaling pathway. Conversely, hsa-miR-455 may be an inhibitor of pneumonia pathogenesis. Furthermore, hsa-miR-200b might promote pneumonia via targeting KALRN.
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Affiliation(s)
- Sai Huang
- Department of Hematology, People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Cong Feng
- Department of Emergency, People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Yong-Zhi Zhai
- Department of Emergency, People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Xuan Zhou
- Department of Emergency, People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Bei Li
- Department of Emergency, People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Li-Li Wang
- Department of Emergency, People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Wei Chen
- Department of Emergency, People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Fa-Qin Lv
- Department of Ultrasound, People's Liberation Army General Hospital, Beijing 100853, P.R. China
| | - Tan-Shi Li
- Department of Emergency, People's Liberation Army General Hospital, Beijing 100853, P.R. China
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You HL, Chang SJ, Yu HR, Li CC, Chen CH, Liao WT. Simultaneous detection of respiratory syncytial virus and human metapneumovirus by one-step multiplex real-time RT-PCR in patients with respiratory symptoms. BMC Pediatr 2017; 17:89. [PMID: 28347279 PMCID: PMC5368990 DOI: 10.1186/s12887-017-0843-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Both respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are important viral pathogens causing respiratory tract infection (RTI) in the pediatric population. However, the clinical manifestations of RSV and hMPV infections are similar. Therefore, a reliable and rapid diagnostic tool is needed for diagnostic performance. METHODS In order to optimize diagnosis efficiency of RTI, the aim of this study is to establish a rapid and advanced method for simultaneous detecting RSV and hMPV in nasopharyngeal aspirates specimens from patients. We designed a one-step triplex real-time RT-PCR (qRT-PCR) protocol using TaqMan probes for detecting RSV and hMPV. The plasmid clones containing RSV nucleoprotein gene and hMPV fusion gene were established as reference standards. We used virus culture supernatants from 86 known pediatric RTI patient to test the specificity and sensitivity of our assay. Then we used total 222 nasopharyngeal aspirates specimens from pediatric patients hospitalized with respiratory symptoms to evaluate our assay. RESULTS Our one-step triplex qRT-PCR assay showed 100% sensitivity and specificity in testing RSV and hMPV in 86 known virus culture supernatants, with excellent linearity (R2 > 0.99) and reliable reproducibility (CV lower than 1.04%). This assay has a wide dynamic range 102-109copies/reaction (limit of detection; LOD = 100 copies/reaction). A total of 222 patients hospitalized with respiratory symptoms were enrolled for clinical evaluation. In these samples, our qRT-PCR assay detected 68 RSV positive and 18 hMPV positive cases. However, standard virus culture only detected 8 RSV positive cases and 0 hMPV cases. Based on this improved triplex qRT-PCR assay, we found that RSV infection was associated with severe inflammation by chest X-ray and occurrence of pneumonia which were not observed previously. CONCLUSIONS In summary, we have developed a highly specific and sensitive one-step triplex qRT-PCR assay to detect hMPV and RSV simultaneously. This assay offers a valuable tool for routine diagnosis.
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Affiliation(s)
- Huey-Ling You
- Departments of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Department of Medical Laboratory Sciences and Biotechnology, Fooyin University, Kaohsiung, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung, Taiwan
| | - Hong-Ren Yu
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Chin Li
- Departments of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chang-Han Chen
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Department of Applied Chemistry, and Graduate Institute of Biomedicine and Biomedical Technology, National Chi Nan University, Nanto, Taiwan
| | - Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, No. 100 Shih-Chuan 1st Road, Kaohsiung, 807, Taiwan. .,Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan.
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94
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Huang M, Luo R, Fu Z. [Risk factors for poor prognosis in children with severe adenovirus pneumonia]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2017; 19:159-162. [PMID: 28202112 PMCID: PMC7389467 DOI: 10.7499/j.issn.1008-8830.2017.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 10/15/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To investigate the risk factors for poor prognosis of severe adenovirus pneumonia (SAP) in children. METHODS The clinical data of 189 children with SAP were retrospectively analyzed. Univariate logistic regression analysis was performed to assess the risk factors for poor prognosis. RESULTS The univariate logistic regression analysis showed that the patients with hemoglobin <90 g/L, plasma albumin <30 g/L, C-reactive protein >30 mg/L, procalcitonin >10 ng/mL, alanine aminotransferase >100 U/L, or aspartate aminotransferase >100 U/L had poor prognosis (P<0.05), and that those with congenital dysplasia of the airway, acute respiratory distress syndrome, circulatory complications, electrolyte and acid-base disturbance, or more than three complications also had poor prognosis (P<0.05). CONCLUSIONS Poor prognosis of severe adenovirus pneumonia in children is associated with anemia, low serum albumin, inflammatory response, concurrent multiple complications and underlying lung diseases.
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Affiliation(s)
- Miao Huang
- Deparment of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China.
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95
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Huang M, Luo R, Fu Z. [Risk factors for poor prognosis in children with severe adenovirus pneumonia]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2017; 19:159-162. [PMID: 28202112 PMCID: PMC7389467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 10/15/2016] [Indexed: 08/01/2024]
Abstract
OBJECTIVE To investigate the risk factors for poor prognosis of severe adenovirus pneumonia (SAP) in children. METHODS The clinical data of 189 children with SAP were retrospectively analyzed. Univariate logistic regression analysis was performed to assess the risk factors for poor prognosis. RESULTS The univariate logistic regression analysis showed that the patients with hemoglobin <90 g/L, plasma albumin <30 g/L, C-reactive protein >30 mg/L, procalcitonin >10 ng/mL, alanine aminotransferase >100 U/L, or aspartate aminotransferase >100 U/L had poor prognosis (P<0.05), and that those with congenital dysplasia of the airway, acute respiratory distress syndrome, circulatory complications, electrolyte and acid-base disturbance, or more than three complications also had poor prognosis (P<0.05). CONCLUSIONS Poor prognosis of severe adenovirus pneumonia in children is associated with anemia, low serum albumin, inflammatory response, concurrent multiple complications and underlying lung diseases.
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Affiliation(s)
- Miao Huang
- Deparment of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China.
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96
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Recent sequence variation in probe binding site affected detection of respiratory syncytial virus group B by real-time RT-PCR. J Clin Virol 2017; 88:21-25. [PMID: 28107671 PMCID: PMC5331890 DOI: 10.1016/j.jcv.2016.12.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/20/2016] [Accepted: 12/31/2016] [Indexed: 12/26/2022]
Abstract
BACKGROUND Direct immuno-fluorescence test (IFAT) and multiplex real-time RT-PCR have been central to RSV diagnosis in Kilifi, Kenya. Recently, these two methods showed discrepancies with an increasing number of PCR undetectable RSV-B viruses. OBJECTIVES Establish if mismatches in the primer and probe binding sites could have reduced real-time RT-PCR sensitivity. STUDY DESIGN Nucleoprotein (N) and glycoprotein (G) genes were sequenced for real-time RT-PCR positive and negative samples. Primer and probe binding regions in N gene were checked for mismatches and phylogenetic analyses done to determine molecular epidemiology of these viruses. New primers and probe were designed and tested on the previously real-time RT-PCR negative samples. RESULTS N gene sequences revealed 3 different mismatches in the probe target site of PCR negative, IFAT positive viruses. The primers target sites had no mismatches. Phylogenetic analysis of N and G genes showed that real-time RT-PCR positive and negative samples fell into distinct clades. Newly designed primers-probe pair improved detection and recovered previous PCR undetectable viruses. CONCLUSIONS An emerging RSV-B variant is undetectable by a quite widely used real-time RT-PCR assay due to polymorphisms that influence probe hybridization affecting PCR accuracy.
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97
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Chen H, Weng H, Lin M, He P, Li Y, Xie Q, Ke C, Jiao X. The Clinical Significance of FilmArray Respiratory Panel in Diagnosing Community-Acquired Pneumonia. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7320859. [PMID: 29018819 PMCID: PMC5606103 DOI: 10.1155/2017/7320859] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/11/2017] [Indexed: 02/05/2023]
Abstract
AIM FilmArray Respiratory Panel (FilmArray RP) test is an emerging diagnostic method in fast detecting multiple respiratory pathogens; the methodology and clinical significance of FilmArray RP in community-acquired pneumonia (CAP) diagnosis were evaluated in this study. METHODS Specimens from 74 patients with CAP were analyzed and compared using FilmArray RP, traditional multiple PCR assay, bacterial (or fungal) culture, and serological detection. RESULTS FilmArray RP and multiplex PCR showed 100% coincidence rate in detecting coronaviruses 229E, OC43, HKU1, and NL63, human metapneumovirus, influenza A and B, and parainfluenza viruses (PIV1, PIV2, and PIV4). There were 15 viral specimens tested as disagreement positive results. FilmArray RP had higher detection rate in detecting dual viral and Mycoplasma pneumoniae infection. The positive bacteria (or fungi) were found in 25 specimens. CONCLUSIONS This study demonstrated the capability of FilmArray RP for simultaneous detection of broad-spectrum respiratory pathogens and potential use in facilitating better patient care.
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Affiliation(s)
- Huanzhu Chen
- Cell Biology and Genetics Department, Shantou University Medical College, Shantou 515041, China
| | - Huilan Weng
- First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Meirui Lin
- First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China
| | - Ping He
- Cell Biology and Genetics Department, Shantou University Medical College, Shantou 515041, China
| | - Yazhen Li
- Cell Biology and Genetics Department, Shantou University Medical College, Shantou 515041, China
| | - Qingdong Xie
- Cell Biology and Genetics Department, Shantou University Medical College, Shantou 515041, China
| | - Changwen Ke
- Cell Biology and Genetics Department, Shantou University Medical College, Shantou 515041, China
| | - Xiaoyang Jiao
- Cell Biology and Genetics Department, Shantou University Medical College, Shantou 515041, China
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98
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Affiliation(s)
- Seema Jain
- Influenza Division, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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99
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Epidemiological and Virological Characteristics of Influenza in Chongqing, China, 2011-2015. PLoS One 2016; 11:e0167866. [PMID: 27936139 PMCID: PMC5148009 DOI: 10.1371/journal.pone.0167866] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/21/2016] [Indexed: 11/21/2022] Open
Abstract
Background Chongqing is the largest municipality and located in Southwestern of China, with over 30 million registered inhabitants. There are few reports regarding the epidemiology of influenza in Chongqing. The objective of the paper is to explore the epidemiology of influenza in Chongqing, in order to provide scientific basis for prevention and control of influenza. Methodology /Principal Findings From 2011 to 2015, we collected information on influenza-like illness (ILI) patients fulfilling the case definition, and took nasalpharyngeal or throat swabs specimens from ILI cases per week at the 7 sentinel hospitals. Specimens were tested by reverse transcription-polymerase chain reaction(RT-PCR) for influenza. Descriptive epidemiology was applied to analyze the epidemiology and etiology of influenza. A total of 9,696,212 cases were enrolled, of which 111,589 were ILI. Of those 24,868 samples from ILI cases, 13.3% (3,314/24,868) tested positive for influenza virus (65.7% influenza A, 34.1% influenza B, and 0.2% influenza A and B co-infection). Among the influenza A viruses, 71.3% were seasonal influenza A(H3N2) and 28.7% were influenza A(H1N1)pdm09. No cases of seasonal A(H1N1) were detected. The isolation rate was highest in children aged 5–14 years old. Influenza activity consistently peaked during January-March in 2011–2015, and June-July in 2012, 2014 and 2015. Conclusions Influenza is an important public health problem among ILI patients in Chongqing, especially among school-aged children. It might be beneficial to prioritize influenza vaccination for school-aged children and implement the school-based intervention to prevent and mitigating influenza outbreaks in Chongqing, particularly during the seasonal peaks.
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100
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Bashir U, Nisar N, Arshad Y, Alam MM, Ashraf A, Sadia H, Kazi BM, Zaidi SSZ. Respiratory syncytial virus and influenza are the key viral pathogens in children <2 years hospitalized with bronchiolitis and pneumonia in Islamabad Pakistan. Arch Virol 2016; 162:763-773. [PMID: 27885562 DOI: 10.1007/s00705-016-3146-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/30/2016] [Indexed: 10/20/2022]
Abstract
Pneumonia remains a leading cause of morbidity and mortality in developing countries. Comprehensive surveillance data are needed to review the prevention and control strategies. We conducted active surveillance of acute lower respiratory infections among children aged <2 years hospitalized at two hospitals of Islamabad, Pakistan. Viral etiology was determined using real-time PCR on respiratory specimens collected during March 2011-April 2012. The overall mean age was 7.83 ± 5.25 months while no statistical difference between age or sex distribution of patients with positive and negative viral etiology (p > 0.05). The average weight of the study group was 6.1 ± 2.25 kg. ≥1 viral pathogens were detected in 75% cases. Major respiratory viruses included RSV-A: 44%, RSV-B: 23%, Influenza-A: 24.5%, Influenza-B: 7%, Adenovirus: 8.4% and HmPV: 5.2%. A single, dual or multiple viral pathogens were detected in 43%, 27% and 5.2% patients respectively. Common symptoms were cough (95%), apnoea (84%), fever (78%), wheeze (64.5%), nasal congestion (55%) and rhinorrhea (48%). Among the RSV positive cases, 2-6 months age group had highest detection rate for RSV-A (30%, n = 21/69) and RSV-B (20%, n = 14/69) while patients infected with Influenza-A were in 2.1-6 months age group (61%, 23/38). Statistically significant difference was observed between RSV-positive and negative cases for nutrition status (p = 0.001), cigarette/wood smoke exposure (p = 0.001) and concomitant clinical findings. Most patients had successful outcome on combination therapy with bronchodilators, inhaled steroids and antibiotics. Our findings underscore high burden of ALRI in Pakistan. Interventions targeting viral pathogens coupled with improved diagnostic approaches are critical for better prevention and control.
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Affiliation(s)
- Uzma Bashir
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, 44000, Pakistan
| | - Nadia Nisar
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, 44000, Pakistan
| | - Yasir Arshad
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, 44000, Pakistan
| | - Muhammad Masroor Alam
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, 44000, Pakistan
| | - Asiya Ashraf
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, 44000, Pakistan
| | - Hajra Sadia
- Atta-Ur-Rahman School of Applied Sciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Birjees Mazher Kazi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, 44000, Pakistan
| | - Syed Sohail Zahoor Zaidi
- Department of Virology, National Institute of Health, Chak Shahzad, Park Road, Islamabad, 44000, Pakistan.
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