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Berginc N, Lunar MM, Šramel N, Poljak M. Molecular epidemiology and characterization of enteroviruses detected in cerebrospinal fluid and respiratory samples in Slovenia, 2014-2023. J Med Virol 2024; 96:e29827. [PMID: 39056240 DOI: 10.1002/jmv.29827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/28/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
Enterovirus (EV) infections have various symptoms and severe complications, including death. To determine EV prevalence and EV types in Slovenia, data on over 25 000 EV RNA tests for diagnostics and surveillance from 2014 to 2023 were analyzed. Altogether, 3733 cerebrospinal fluid (CSF) and 21 297 respiratory (sentinel and clinical) samples were tested for EV RNA. EV typing was performed on all residual EV-positive CSF samples and on subset of respiratory specimens. Altogether, 1238 samples tested positive for EV RNA: 238 (6.4%) CSF and 1000 (4.7%) respiratory samples. EV-positive patients were predominantly male (p < 0.001). Many EV-positive CSF samples were from infants under 3 months (33.1%), whereas most EV-positive respiratory samples were from children 1 to 2 years old (49.2%). Echovirus 30 (E-30) was most frequent in CSF (33.0%), followed by CV-B5 (13.8%) and E-6 (13.8%). CV-A6 was most frequent in respiratory samples (16.0%), followed by EV-D68 (7.6%) and CV-A5 (7.4%). EV types in CSF and respiratory samples show diverse dynamics, with some outbreaks indicated. A significant difference was found in the EV detection rate between CSF and respiratory samples by age. Various EV types were characterized, showing that some EV types are more neurotropic or cause more severe infections.
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Affiliation(s)
- Nataša Berginc
- Department of Public Health Microbiology, National Laboratory for Health, Environment, and Food, Maribor, Slovenia
| | - Maja M Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Šramel
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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2
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Berginc N, Sočan M, Prosenc Trilar K, Petrovec M. Seasonality and Genotype Diversity of Human Rhinoviruses during an Eight-Year Period in Slovenia. Microorganisms 2024; 12:341. [PMID: 38399745 PMCID: PMC10893136 DOI: 10.3390/microorganisms12020341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Due to the high socioeconomic burden of rhinoviruses, the development of prevention and treatment strategies is of high importance. Understanding the epidemiological and clinical features of rhinoviruses is essential in order to address these issues. Our study aimed to define the seasonality and molecular epidemiology of rhinoviruses in Slovenia. Over a period of eight years, a total of 20,425 patients from sentinel primary healthcare settings and sentinel hospitals were examined for a panel of respiratory viruses in the national programme for the surveillance of influenza-like illnesses and acute respiratory infections. The patients were from all age groups and had respiratory infections of various severity. Infection with a rhinovirus was confirmed using an RT-rPCR in 1834 patients, and 1480 rhinoviruses were genotyped. The molecular analysis was linked to demographical and meteorological data. We confirmed the year-round circulation of rhinoviruses with clear seasonal cycles, resulting in two seasonal waves with peaks in spring and autumn. High levels of genotype variability and co-circulation were confirmed between and within seasons and were analysed in terms of patient age, the patient source reflecting disease severity, and meteorological factors. Our study provides missing scientific information on the genotype diversity of rhinoviruses in Slovenia. As most previous investigations focused on exclusive segments of the population, such as children or hospitalised patients, and for shorter study periods, our study, with its design, size and length, contributes complementary aspects and new evidence-based knowledge to the regional and global understanding of rhinovirus seasonality and molecular epidemiology.
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Affiliation(s)
- Nataša Berginc
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Maja Sočan
- Centre for Infectious Diseases, National Institute of Public Health, 1000 Ljubljana, Slovenia
| | - Katarina Prosenc Trilar
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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3
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Sugimoto S, Kawase M, Suwa R, Kakizaki M, Kume Y, Chishiki M, Ono T, Okabe H, Norito S, Hosoya M, Hashimoto K, Shirato K. Development of a duplex real-time RT-PCR assay for the detection and identification of two subgroups of human metapneumovirus in a single tube. J Virol Methods 2023; 322:114812. [PMID: 37741464 DOI: 10.1016/j.jviromet.2023.114812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/25/2023]
Abstract
Human metapneumovirus (hMPV) is a common cause of respiratory infections in children. Many genetic diagnostic assays have been developed, but most detect hMPV regardless of the subgroup. In this study, we developed a real-time RT-PCR assay that can detect and identify the two major subgroups of hMPV (A and B) in one tube. Primers and probes were designed based on the sequences of recent clinical isolates in Japan. The assay showed comparable analytical sensitivity to a previously reported real-time RT-PCR assay and specific reactions to hMPV subgroups. The assay also showed no cross-reactivity to clinical isolates of 19 species of other respiratory viruses. In a validation assay using post-diagnosed clinical specimens, 98% (167/170) positivity was confirmed for the duplex assay, and the three specimens not detected were of low copy number. The duplex assay also successfully distinguished the two major subgroups for all 12 clinical specimens, for which the subgroup had already been determined by genomic sequencing analysis. The duplex assay described here will contribute to the rapid and accurate identification and surveillance of hMPV infections.
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Affiliation(s)
- Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan; Management Department of Biosafety, Laboratory Animals, and Pathogen Bank, National Institute of Infectious Disease, Musashimurayama, Tokyo, Japan
| | - Miyuki Kawase
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Reiko Suwa
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Masatoshi Kakizaki
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan
| | - Yohei Kume
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Takashi Ono
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Diseases, Musashimurayama, Tokyo, Japan.
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Morales-Jadán D, Muslin C, Viteri-Dávila C, Coronel B, Castro-Rodríguez B, Vallejo-Janeta AP, Henríquez-Trujillo AR, Garcia-Bereguiain MA, Rivera-Olivero IA. Coinfection of SARS-CoV-2 with other respiratory pathogens in outpatients from Ecuador. Front Public Health 2023; 11:1264632. [PMID: 37965509 PMCID: PMC10641819 DOI: 10.3389/fpubh.2023.1264632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023] Open
Abstract
Worldwide, the COVID-19 pandemic caused by SARS-CoV-2 has enormously impacted healthcare systems, especially in low and middle-income countries. Coinfections with respiratory pathogens in COVID-19 patients may contribute to worse outcomes. This study identified the presence of 12 viral coinfections and pneumococcal carriers among individuals with SARS-CoV-2 infection in outpatient and community settings in Ecuador. From January 2020 to November 2021, 215 nasopharyngeal and nasal swabs were taken from individuals who reported symptoms of COVID-19 or had known exposure to someone with confirmed or suspected COVID-19. One hundred fifty-eight tested positive for SARS-CoV-2 by RT-qPCR and coinfections were detected in 12% (19/158) of SARS-CoV-2-positive patients; the most frequent coinfection was with influenza A virus at 4.4% (7/158; 95% CI: 1.2-7.6), followed by respiratory syncytial virus with 3.1% (5/158; 95% CI: 0.4-5.8), and finally rhinovirus and human coronavirus NL63 with 1.2% (2/158). Pneumococcal carriage was detected in 3.7% (6/158; 95% CI: 0.76-6.64) of SARS-CoV-2 cases. Influenza B, adenovirus, human metapneumovirus (HMPV), parainfluenza virus types 1, 2, and 3, and human coronavirus HKU1 were undetected. To our knowledge, this is the first study of coinfection of SARS-CoV-2 and respiratory pathogens performed on outpatients in Latin America. The high proportion of outpatients with viral coinfections reported in our cohort allows us to suggest that testing for SARS-CoV-2 and other common respiratory pathogens should be carried out to ensure accurate diagnoses, prompt patient treatment, and appropriate isolation.
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Affiliation(s)
| | - Claire Muslin
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
| | | | - Barbara Coronel
- One Health Research Group, Universidad de Las Américas, Quito, Ecuador
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Kamata K, Thein KN, Di Ja L, Win NC, Win SMK, Suzuki Y, Ito A, Osada H, Chon I, Phyu WW, Aizawa Y, Ikuse T, Ota T, Kyaw Y, Tin HH, Shobugawa Y, Watanabe H, Saito R, Saitoh A. Clinical manifestations and outcome of viral acute lower respiratory infection in hospitalised children in Myanmar. BMC Infect Dis 2022; 22:350. [PMID: 35395744 PMCID: PMC8992414 DOI: 10.1186/s12879-022-07342-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/25/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Acute lower respiratory infection (ALRI) remains the leading cause of death in children worldwide, and viruses have been the major cause of ALRI. In Myanmar, ALRI is associated with high morbidity and mortality in children, and detailed information on ALRI is currently lacking. METHODS This prospective study investigated the viral aetiologies, clinical manifestations, and outcomes of ALRI in hospitalised children aged 1 month to 12 years at the Yankin Children Hospital, Yangon, Myanmar from May 2017 to April 2019. The sample size was set to 300 patients for each year. Two nasopharyngeal swabs were obtained for the patients with suspected viral ALRI; one for rapid tests for influenza and respiratory syncytial virus (RSV), and the other for real-time PCR for the 16 ALRI-causing viruses. Pneumococcal colonization rates were also investigated using real-time PCR. Clinical information was extracted from the medical records, and enrolled patients were categorised by age and severity for comparison. RESULTS Among the 5463 patients admitted with a diagnosis of ALRI, 570 (10.4%) were enrolled in this study. The median age of the patients was 8 months (interquartile range, 4-15 months). The most common symptoms were cough (93%) and difficulty in breathing (73%), while the most common signs of ALRI were tachypnoea (78%) and chest indrawing (67%). A total of 16 viruses were detected in 502 of 570 patients' samples (88%), with RSV B (36%) and rhinovirus (28%) being the most commonly detected. Multiple viruses were detected in 221 of 570 samples (37%) collected from 570 patients. Severe ALRI was diagnosed in 107 of 570 patients (19%), and RSV B and human rhinovirus were commonly detected. The mortality rate was 5%; influenza virus A (29%) and RSV B (21%) were commonly detected, and stunting and lack of immunization were frequently observed in such cases. Additionally, 45% (259/570) of the patients had pneumococcal colonization. CONCLUSIONS Viral ALRI in hospitalised children with a median of 8 months has significant morbidity and mortality rates in Myanmar. RSV and rhinovirus were the most commonly detected from nasopharyngeal swabs, while influenza virus and RSV were the most frequently associated with fatal cases.
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Grants
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
- 15fm0108009h0001, 19fm0108009h0005 Japan Agency for Medical Research and Development
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Affiliation(s)
- Kazuhiro Kamata
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | | | - Lasham Di Ja
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Nay Chi Win
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Su Mon Kyaw Win
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Yuko Suzuki
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Ai Ito
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Hidekazu Osada
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Irina Chon
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Wint Wint Phyu
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Yuta Aizawa
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Tatsuki Ikuse
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan
| | - Tomomi Ota
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Yadanar Kyaw
- Respiratory Medicine Department, Thingangyun Sanpya General Hospital, Yangon, Myanmar
| | - Htay Htay Tin
- Department of Medical Services, National Health Laboratory, Ministry of Health and Sports, Yangon, Myanmar
| | - Yugo Shobugawa
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Hisami Watanabe
- Infectious Diseases Research Center of Niigata University in Myanmar, Yangon, Myanmar
| | - Reiko Saito
- Division of International Health, Graduate School of Medical and Dental Science, Niigata University, Niigata, Japan
| | - Akihiko Saitoh
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-dori, Chuo-ku, Niigata, Niigata, 951-8510, Japan.
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6
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Lopez SMC, Shaikh N, Johnson M, Liu H, Martin JM, Williams JV. Viral Coinfection and Nasal Cytokines in Children With Clinically Diagnosed Acute Sinusitis. Front Pediatr 2022; 9:783665. [PMID: 35096705 PMCID: PMC8791629 DOI: 10.3389/fped.2021.783665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/07/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: Children with no pathogenic bacteria in the nasopharynx are unlikely to have acute bacterial sinusitis. We evaluated whether information on clinical presentation, viral co-detection, and mucosal cytokine levels could be used to predict presence of bacteria in the nasopharynx. Method: We obtained nasopharyngeal (NP) swabs from children diagnosed with acute sinusitis. NP swabs were processed for bacterial culture, viral PCR testing, and cytokine expression. We examined whether results of the bacterial culture could be predicted based on the presence of clinical information, presence of viruses or mucosal cytokine levels. Results: We enrolled 174 children; 123 (71%) had a positive culture for potentially pathogenic bacteria and 51 (29%) had normal flora. 122/174 (70%) tested positive for one or more viruses. Compared to children with normal flora, children with pathogenic bacteria were more likely to have viruses (p < 0.01), but this relationship disappeared when we adjusted for age. Children with pathogenic bacteria in their nasopharynx and children with normal flora had similar levels of nasal cytokines. Conclusion: In children with clinically diagnosed acute sinusitis, clinical presentation, levels of nasal cytokines, and presence of viruses do not differentiate children with and without pathogenic bacteria in their nasopharynx.
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Affiliation(s)
- Santiago M. C. Lopez
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, United States
- Sanford Research, Environmental Influences on Health and Disease Group, Sioux Falls, SD, United States
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Monika Johnson
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Hui Liu
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Judith M. Martin
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
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7
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Howard LM, Liu Y, Zhu Y, Liu D, Willams JV, Gil AI, Griffin MR, Edwards KM, Lanata CF, Grijalva CG. Assessing the impact of acute respiratory illnesses on the risk of subsequent respiratory illness. J Infect Dis 2021; 225:42-49. [PMID: 34120189 DOI: 10.1093/infdis/jiab313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/09/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Whether acute respiratory illnesses (ARIs), often associated with virus detection, are associated with lower risk for subsequent ARI remains unclear. We assessed the association between symptomatic ARI and subsequent ARI in young children. METHODS In a prospective cohort of Peruvian children <3 years, we examined the impact of index ARI on subsequent ARI risk. Index ARI were matched with ≤3 asymptomatic observations and followed over 28 days. We compared risk of subsequent ARI between groups using conditional logistic regression adjusting for several covariates, accounting for repeat observations from individual children. RESULTS Among 983 index ARI, 339 (34%) had an ARI event during follow-up, compared with 876/2826 (31%) matched asymptomatic observations. We found no significant association of index ARI and subsequent ARI risk during follow-up overall (aOR 1.10, 95% CI 0.98, 1.23) or when limited to index ARI with respiratory viruses detected (aOR 1.03, 95% CI 0.86, 1.24). Similarly, when the outcome was limited to ARI in which viruses were detected, no significant association was seen (aOR 1.05, 95% CI 0.87, 1.27). DISCUSSION ARIs were not associated with short-term protection against subsequent ARI in these children. Additional longitudinal studies are needed to understand drivers of recurrent ARI in young children.
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Affiliation(s)
- Leigh M Howard
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuhan Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dandan Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John V Willams
- Department of Pediatrics, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ana I Gil
- Instituto de Investigación Nutricional, Lima, Peru
| | - Marie R Griffin
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
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8
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Steiner F, Schmutz S, Gosert R, Huder JB, Redli PM, Capaul R, Hirsch HH, Böni J, Zbinden A. Usefulness of the GenMark ePlex RPP assay for the detection of respiratory viruses compared to the FTD21 multiplex RT-PCR. Diagn Microbiol Infect Dis 2021; 101:115424. [PMID: 34111651 DOI: 10.1016/j.diagmicrobio.2021.115424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/26/2021] [Accepted: 05/01/2021] [Indexed: 11/26/2022]
Abstract
Cartridge-based multiplex panels covering numerous pathogens offer an advantage of minimal hands-on-time and short time to result to commercial RT-PCR assays. In this study, we evaluated the performance of the ePlex respiratory pathogen panel (RPP) compared to the Fast Track Diagnostics Respiratory pathogens 21 multiplex RT-PCR assay (FTD21) using 400 clinical respiratory samples. Discrepant results were further analysed by a reference nucleic acid amplification testing (NAT) and a composite reference approach was used for final interpretation. Discordant results were observed in 56 targets corresponding to 54 samples. Sensitivities and specificities were 85.5% and 99.9% for the ePlex RPP and 95.8% and 99.7% for the FTD21 system, respectively. Altogether, the ePlex RPP is a valuable tool for the rapid detection of a number of different respiratory viruses with the exception of the coronavirus family (low sensitivity ranging from 50-80%) and samples with a low pathogen load (Ct values >33).
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Affiliation(s)
- Fiona Steiner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Rainer Gosert
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland; Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Jon B Huder
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Patrick M Redli
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hans H Hirsch
- Transplantation & Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland; Clinical Virology, Laboratory Medicine, University Hospital Basel, Basel, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
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9
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Feldstein LR, Ogokeh C, Rha B, Weinberg GA, Staat MA, Selvarangan R, Halasa NB, Englund JA, Boom JA, Azimi PH, Szilagyi PG, McNeal M, Harrison CJ, Williams JV, Klein EJ, Sahni LC, Singer MN, Lively JY, Payne DC, Fry AM, Patel M, Campbell AP. Vaccine Effectiveness Against Influenza Hospitalization Among Children in the United States, 2015-2016. J Pediatric Infect Dis Soc 2021; 10:75-82. [PMID: 32108879 DOI: 10.1093/jpids/piaa017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/06/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Annual United States (US) estimates of influenza vaccine effectiveness (VE) in children typically measure protection against outpatient medically attended influenza illness, with limited data evaluating VE against influenza hospitalizations. We estimated VE for preventing laboratory-confirmed influenza hospitalization among US children. METHODS We included children aged 6 months-17 years with acute respiratory illness enrolled in the New Vaccine Surveillance Network during the 2015-2016 influenza season. Documented influenza vaccination status was obtained from state immunization information systems, the electronic medical record, and/or provider records. Midturbinate nasal and throat swabs were tested for influenza using molecular assays. We estimated VE as 100% × (1 - odds ratio), comparing the odds of vaccination among subjects testing influenza positive with subjects testing negative, using multivariable logistic regression. RESULTS Of 1653 participants, 36 of 707 (5%) of those fully vaccinated, 18 of 226 (8%) of those partially vaccinated, and 85 of 720 (12%) of unvaccinated children tested positive for influenza. Of those vaccinated, almost 90% were documented to have received inactivated vaccine. The majority (81%) of influenza cases were in children ≤ 8 years of age. Of the 139 influenza-positive cases, 42% were A(H1N1)pdm09, 42% were B viruses, and 14% were A(H3N2). Overall, adjusted VE for fully vaccinated children was 56% (95% confidence interval [CI], 34%-71%) against any influenza-associated hospitalization, 68% (95% CI, 36%-84%) for A(H1N1)pdm09, and 44% (95% CI, -1% to 69%) for B viruses. CONCLUSIONS These findings demonstrate the importance of annual influenza vaccination in prevention of severe influenza disease and of reducing the number of children who remain unvaccinated or partially vaccinated against influenza.
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Affiliation(s)
- Leora R Feldstein
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Constance Ogokeh
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education Fellowship Program, Oak Ridge, Tennessee, USA
| | - Brian Rha
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Geoffrey A Weinberg
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Mary A Staat
- Department of Pediatrics, University of Cincinnati, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Natasha B Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Janet A Englund
- Department of Pediatrics, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Julie A Boom
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Parvin H Azimi
- Department of Infectious Diseases, University of California, San Francisco Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Peter G Szilagyi
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Pediatrics, Mattel Children's Hospital, University of California, Los Angeles, Los Angeles, California, USA
| | - Monica McNeal
- Department of Pediatrics, University of Cincinnati, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Christopher J Harrison
- Department of Infectious Diseases, University of Missouri-Kansas City, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Eileen J Klein
- Department of Pediatrics, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | | | - Monica N Singer
- Department of Infectious Diseases, University of California, San Francisco Benioff Children's Hospital Oakland, Oakland, California, USA
| | - Joana Y Lively
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- IHRC, Atlanta, Georgia, USA
| | - Daniel C Payne
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alicia M Fry
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Manish Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Angela P Campbell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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10
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Mazet JAK, Genovese BN, Harris LA, Cranfield M, Noheri JB, Kinani JF, Zimmerman D, Bahizi M, Mudakikwa A, Goldstein T, Gilardi KVK. Human Respiratory Syncytial Virus Detected in Mountain Gorilla Respiratory Outbreaks. ECOHEALTH 2020; 17:449-460. [PMID: 33345293 PMCID: PMC7750032 DOI: 10.1007/s10393-020-01506-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 06/12/2023]
Abstract
Respiratory illness (RI) accounts for a large proportion of mortalities in mountain gorillas (Gorilla beringei beringei), and fatal outbreaks, including disease caused by human metapneumovirus (HMPV) infections, have heightened concern about the risk of human pathogen transmission to this endangered species, which is not only critically important to the biodiversity of its ecosystem but also to the economies of the surrounding human communities. Our goal was to conduct a molecular epidemiologic study to detect the presence of HRSV and HMPV in fecal samples from wild human-habituated free-ranging mountain gorillas in Rwanda and to evaluate the role of these viruses in RI outbreaks. Fecal samples were collected from gorillas with clinical signs of RI between June 2012 and February 2013 and tested by real-time and conventional polymerase chain reaction (PCR) assays; comparison fecal samples were obtained from gorillas without clinical signs of RI sampled during the 2010 Virunga gorilla population census. PCR assays detected HMPV and HRSV first in spiked samples; subsequently, HRSV-A, the worldwide-circulating ON1 genotype, was detected in 12 of 20 mountain gorilla fecal samples collected from gorillas with RI during outbreaks, but not in samples from animals without respiratory illness. Our findings confirmed that pathogenic human respiratory viruses are transmitted to gorillas and that they are repeatedly introduced into mountain gorilla populations from people, attesting to the need for stringent biosecurity measures for the protection of gorilla health.
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Affiliation(s)
- Jonna A K Mazet
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA.
| | - Brooke N Genovese
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
| | - Laurie A Harris
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
| | - Michael Cranfield
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Davis, CA, USA
| | - Jean Bosco Noheri
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Musanze, Rwanda
| | - Jean Felix Kinani
- One Health Approach for Conservation, Gorilla Health, Kigali, Rwanda
| | - Dawn Zimmerman
- National Zoological Park, SCBI Global Health Program, Washington, DC, USA
| | - Methode Bahizi
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Musanze, Rwanda
| | | | - Tracey Goldstein
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
| | - Kirsten V K Gilardi
- Karen C. Drayer Wildlife Health Center, One Health Institute, University of California, 1089 Veterinary Medicine Dr., Davis, CA, 95616, USA
- Gorilla Doctors, Mountain Gorilla Veterinary Project Inc, Davis, CA, USA
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11
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Rha B, Curns AT, Lively JY, Campbell AP, Englund JA, Boom JA, Azimi PH, Weinberg GA, Staat MA, Selvarangan R, Halasa NB, McNeal MM, Klein EJ, Harrison CJ, Williams JV, Szilagyi PG, Singer MN, Sahni LC, Figueroa-Downing D, McDaniel D, Prill MM, Whitaker BL, Stewart LS, Schuster JE, Pahud BA, Weddle G, Avadhanula V, Munoz FM, Piedra PA, Payne DC, Langley G, Gerber SI. Respiratory Syncytial Virus-Associated Hospitalizations Among Young Children: 2015-2016. Pediatrics 2020; 146:peds.2019-3611. [PMID: 32546583 DOI: 10.1542/peds.2019-3611] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a major cause of hospitalized acute respiratory illness (ARI) among young children. With RSV vaccines and immunoprophylaxis agents in clinical development, we sought to update estimates of US pediatric RSV hospitalization burden. METHODS Children <5 years old hospitalized for ARI were enrolled through active, prospective, population-based surveillance from November 1, 2015, to June 30, 2016, at 7 US pediatric hospital sites. Clinical information was obtained from parent interviews and medical records. Midturbinate nasal and throat flocked swabs were collected and tested for RSV by using molecular diagnostic assays at each site. We conducted descriptive analyses and calculated population-based rates of RSV-associated hospitalizations. RESULTS Among 2969 hospitalized children included in analyses, 1043 (35%) tested RSV-positive; 903 (87%) children who were RSV-positive were <2 years old, and 526 (50%) were <6 months old. RSV-associated hospitalization rates were 2.9 per 1000 children <5 years old and 14.7 per 1000 children <6 months old; the highest age-specific rate was observed in 1-month-old infants (25.1 per 1000). Most children who were infected with RSV (67%) had no underlying comorbid conditions and no history of preterm birth. CONCLUSIONS During the 2015-2016 season, RSV infection was associated with one-third of ARI hospitalizations in our study population of young children. Hospitalization rates were highest in infants <6 months. Most children who were RSV-positive had no history of prematurity or underlying medical conditions, suggesting that all young children could benefit from targeted interventions against RSV.
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Affiliation(s)
| | | | - Joana Y Lively
- Division of Viral Diseases and.,IHRC, Inc, Atlanta, Georgia
| | - Angela P Campbell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Julie A Boom
- Texas Children's Hospital, Houston, Texas.,Departments of Pediatrics and
| | - Parvin H Azimi
- University of California, San Francisco Benioff Children's Hospital Oakland, Oakland, California
| | - Geoffrey A Weinberg
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, New York
| | - Mary A Staat
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Rangaraj Selvarangan
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | | | - Monica M McNeal
- Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | | | - Christopher J Harrison
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | - John V Williams
- University of Pittsburgh Medical Center Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Peter G Szilagyi
- Department of Pediatrics, UCLA Mattel Children's Hospital, University of California, Los Angeles, Los Angeles, California
| | - Monica N Singer
- University of California, San Francisco Benioff Children's Hospital Oakland, Oakland, California
| | | | | | - Darius McDaniel
- Division of Viral Diseases and.,Maximus Federal, Atlanta, Georgia
| | | | | | | | - Jennifer E Schuster
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | - Barbara A Pahud
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | - Gina Weddle
- University of Missouri-Kansas City School of Medicine, Children's Mercy, Kansas City, Missouri
| | - Vasanthi Avadhanula
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Flor M Munoz
- Texas Children's Hospital, Houston, Texas.,Departments of Pediatrics and.,Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Pedro A Piedra
- Texas Children's Hospital, Houston, Texas.,Departments of Pediatrics and.,Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
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12
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Lopez SM, Martin JM, Johnson M, Kurs-Lasky M, Horne WT, Marshall CW, Cooper VS, Williams JV, Shaikh N. A method of processing nasopharyngeal swabs to enable multiple testing. Pediatr Res 2019; 86:651-654. [PMID: 31288247 PMCID: PMC6851467 DOI: 10.1038/s41390-019-0498-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/08/2019] [Accepted: 06/08/2019] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To develop a method to perform multiple tests on a single nasopharyngeal (NP) swab. METHODS We collected a NP swab on children aged 2-12 years with acute sinusitis and processed it for bacterial culture, viruses, cytokine expression, and 16S ribosomal RNA gene sequencing analysis. During the course of the study, we expand the scope of evaluation to include RNA-sequencing, which we accomplished by cutting the tip of the swab. RESULTS Of the 174 children enrolled, 126 (72.4%) had a positive bacterial culture and 121 (69.5%) tested positive for a virus. Cytokine measurement, as judged by adequate levels of a housekeeping enzyme (glyceraldehyde 3-phosphate dehydrogenase), appeared successful. From the samples used for 16S ribosomal sequencing we recovered, on average, 16,000 sequences per sample, accounting for a total of 2646 operational taxonomic units across all samples sequenced. Samples used for RNA-sequencing had a mean RNA integrity number of 6.0. Cutting the tip of the swab did not affect the recovery yield for viruses or bacteria, nor did it affect species richness in microbiome analysis. CONCLUSION We describe a minimally invasive sample collection protocol that allows for multiple diagnostic and research investigations in young children.
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Affiliation(s)
- Santiago M.C. Lopez
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Judith M. Martin
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Monika Johnson
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Marcia Kurs-Lasky
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - William T. Horne
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Christopher W Marshall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Nader Shaikh
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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13
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Bernal LJ, Velandia-Romero M, Guevara C, Castellanos JE. Human Metapneumovirus: Laboratory Methods for Isolation, Propagation, and Plaque Titration. Intervirology 2019; 61:301-306. [PMID: 30917376 DOI: 10.1159/000497309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 01/24/2019] [Indexed: 11/19/2022] Open
Abstract
The human metapneumovirus (hMPV) is an important viral agent associated with severe infections of the upper and lower airways, especially in young children and immunosuppressed subjects. Nevertheless, in vitro studies of hMPV are very difficult due to the little knowledge we have on its laboratory manipulation. OBJECTIVE The aim of this study was to isolate and propagate hMPV from patients, and to establish a method to quantify the virus by plaque assay. METHOD As part of a Latin American respiratory virus surveillance study, 12 nasal secretion samples - hMPV-positive by direct fluorescence - were inoculated on LLC-MK2 cells to isolate the virus. The supernatants were re-inoculated and the cytopathic effect and syncytium formation were evaluated daily; the infection was confirmed by immunofluorescence and RT-PCR. A protocol to titrate the harvested virus was established inoculating serial dilutions on LLC-MK2 cells, and agarose was then added as an overlay. After different time periods, the monolayers were fixed and stained with Naphthol blue/black or crystal violet and finally the viral titer was obtained. RESULTS Eight out of 12 hMPV-positive respiratory samples were positive for the isolation and confirmed by RT-PCR and immunofluorescence, but the cytopathic effect and syncytium formation were observed only in 5 cultures. One out of 8 viral isolates was used for propagation and plaque assay standardization. We found that incubation for 7 days in the semisolid overlay yielded plaques with appropriate size and shape to be counted, although crystal violet staining showed slightly larger plaques than those seen with Naphthol blue/black staining. CONCLUSIONS The isolation and propagation from patient-derived hMPV and the standardization of a practical, reliable, and inexpensive method of detection and quantification of hMPV were carried out, without the additional use of antibodies that had not been reported previously. These results offer some important insights for future studies of cellular and molecular biology of hMPV.
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Affiliation(s)
- Lilia J Bernal
- Facultad de Odontología, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Jaime E Castellanos
- Facultad de Odontología, Universidad Nacional de Colombia, Bogotá, Colombia, .,Grupo de Virología, Universidad El Bosque, Bogotá, Colombia,
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14
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Howard LM, Edwards KM, Zhu Y, Griffin MR, Weinberg GA, Szilagyi PG, Staat MA, Payne DC, Williams JV. Clinical Features of Human Metapneumovirus Infection in Ambulatory Children Aged 5-13 Years. J Pediatric Infect Dis Soc 2018; 7:165-168. [PMID: 28369564 PMCID: PMC5954304 DOI: 10.1093/jpids/pix012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/23/2017] [Indexed: 12/15/2022]
Abstract
We detected human metapneumovirus (HMPV) in 54 (5%) of 1055 children aged 5 to 13 years with acute respiratory illness (ARI) identified by outpatient and emergency department surveillance between November and May 2003-2009. Its clinical features were similar to those of HMPV-negative ARI, except a diagnosis of pneumonia was more likely (13% vs 4%, respectively; P = .005) and a diagnosis of pharyngitis (7% vs 24%, respectively; P = .005) was less likely in patients with HMPV- positive ARI than those with HMPV-negative ARI.
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Affiliation(s)
- Leigh M Howard
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Yuwei Zhu
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | | | - Peter G Szilagyi
- Mattel Children’s Hospital at University of California at Los Angeles
| | - Mary A Staat
- Cincinnati Children’s Hospital Medical Center, Ohio
| | - Daniel C Payne
- Emory University, Atlanta, Georgia
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John V Williams
- University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of UPMC, Pennsylvania
- Correspondence: J. V. Williams, MD, Children’s Hospital of Pittsburgh, Division of Pediatric Infectious Diseases, 4401 Penn Ave, Rangos 9122, Pittsburgh, PA 15224 ()
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15
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Oong XY, Chook JB, Ng KT, Chow WZ, Chan KG, Hanafi NS, Pang YK, Chan YF, Kamarulzaman A, Tee KK. The role of human Metapneumovirus genetic diversity and nasopharyngeal viral load on symptom severity in adults. Virol J 2018; 15:91. [PMID: 29792212 PMCID: PMC5966857 DOI: 10.1186/s12985-018-1005-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 05/16/2018] [Indexed: 11/21/2022] Open
Abstract
Background Human metapneumovirus (HMPV) is established as one of the causative agents of respiratory tract infections. To date, there are limited reports that describe the effect of HMPV genotypes and/or viral load on disease pathogenesis in adults. This study aims to determine the role of HMPV genetic diversity and nasopharyngeal viral load on symptom severity in outpatient adults with acute respiratory tract infections. Methods Severity of common cold symptoms of patients from a teaching hospital was assessed by a four-category scale and summed to obtain the total symptom severity score (TSSS). Association between the fusion and glycoprotein genes diversity, viral load (quantified using an improved RT-qPCR assay), and symptom severity were analyzed using bivariate and linear regression analyses. Results Among 81/3706 HMPV-positive patients, there were no significant differences in terms of demographics, number of days elapsed between symptom onset and clinic visit, respiratory symptoms manifestation and severity between different HMPV genotypes/sub-lineages. Surprisingly, elderly patients (≥65 years old) had lower severity of symptoms (indicated by TSSS) than young and middle age adults (p = 0.008). Nasopharyngeal viral load did not correlate with nor predict symptom severity of HMPV infection. Interestingly, at 3–5 days after symptom onset, genotype A-infected patients had higher viral load compared to genotype B (4.4 vs. 3.3 log10 RNA copies/μl) (p = 0.003). Conclusions Overall, HMPV genetic diversity and viral load did not impact symptom severity in adults with acute respiratory tract infections. Differences in viral load dynamics over time between genotypes may have important implications on viral transmission. Electronic supplementary material The online version of this article (10.1186/s12985-018-1005-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Jack Bee Chook
- School of Healthcare and Medical Sciences, Sunway University, 47500, Kuala Lumpur, Selangor, Malaysia
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Wei Zhen Chow
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kok Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Nik Sherina Hanafi
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Kok Keng Tee
- School of Healthcare and Medical Sciences, Sunway University, 47500, Kuala Lumpur, Selangor, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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16
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Abstract
Human metapneumovirus (HMPV) is a leading cause of acute respiratory infection, particularly in children, immunocompromised patients, and the elderly. HMPV, which is closely related to avian metapneumovirus subtype C, has circulated for at least 65 years, and nearly every child will be infected with HMPV by the age of 5. However, immunity is incomplete, and re-infections occur throughout adult life. Symptoms are similar to those of other respiratory viral infections, ranging from mild (cough, rhinorrhea, and fever) to more severe (bronchiolitis and pneumonia). The preferred method for diagnosis is reverse transcription-polymerase chain reaction as HMPV is difficult to culture. Although there have been many advances made in the past 16 years since its discovery, there are still no US Food and Drug Administration-approved antivirals or vaccines available to treat HMPV. Both small animal and non-human primate models have been established for the study of HMPV. This review will focus on the epidemiology, transmission, and clinical manifestations in humans as well as the animal models of HMPV pathogenesis and host immune response.
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Affiliation(s)
- Nazly Shafagati
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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17
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Fan RR, Howard LM, Griffin MR, Edwards KM, Zhu Y, Williams JV, Vidal JE, Klugman KP, Gil AI, Lanata CF, Grijalva CG. Nasopharyngeal Pneumococcal Density and Evolution of Acute Respiratory Illnesses in Young Children, Peru, 2009-2011. Emerg Infect Dis 2018; 22:1996-1999. [PMID: 27767919 PMCID: PMC5088003 DOI: 10.3201/eid2211.160902] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We examined nasopharyngeal pneumococcal colonization density patterns surrounding acute respiratory illnesses (ARI) in young children in Peru. Pneumococcal densities were dynamic, gradually increasing leading up to an ARI, peaking during the ARI, and decreasing after the ARI. Rhinovirus co-infection was associated with higher pneumococcal densities.
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18
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Hilmes MA, Dunnavant FD, Singh SP, Ellis WD, Payne DC, Zhu Y, Griffin MR, Edwards KM, Williams JV. Chest radiographic features of human metapneumovirus infection in pediatric patients. Pediatr Radiol 2017; 47:1745-1750. [PMID: 28831577 PMCID: PMC5901753 DOI: 10.1007/s00247-017-3943-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 05/28/2017] [Accepted: 07/06/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Human metapneumovirus (HMPV) was identified in 2001 and is a common cause of acute respiratory illness in young children. The radiologic characteristics of laboratory-confirmed HMPV acute respiratory illness in young children have not been systematically assessed. OBJECTIVE We systematically evaluated the radiographic characteristics of acute respiratory illness associated with HMPV in a prospective cohort of pediatric patients. MATERIALS AND METHODS We included chest radiographs from children <5 years old with acute respiratory illness who were enrolled in the prospective New Vaccine Surveillance Network (NVSN) study from 2003 to 2009 and were diagnosed with HMPV by reverse transcription-polymerase chain reaction (RT-PCR). Of 215 HMPV-positive subjects enrolled at our tertiary care children's hospital, 68 had chest radiographs obtained by the treating clinician that were available for review. Two fellowship-trained pediatric radiologists, independently and then in consensus, retrospectively evaluated these chest radiographs for their radiographic features. RESULTS Parahilar opacities were the most commonly observed abnormality, occurring in 87% of children with HMPV. Hyperinflation also occurred frequently (69%). Atelectasis (40%) and consolidation (18%) appeared less frequently. Pleural effusion and pneumothorax were not seen on any radiographs. CONCLUSION The clinical presentations of HMPV include bronchiolitis, croup and pneumonia. Dominant chest radiographic abnormalities include parahilar opacities and hyperinflation, with occasional consolidation. Recognition of the imaging patterns seen with common viral illnesses like respiratory syncytial virus (RSV) and HMPV might facilitate diagnosis and limit unnecessary antibiotic treatment.
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Affiliation(s)
- Melissa A. Hilmes
- Department of Radiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - F. Daniel Dunnavant
- Department of Radiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Sudha P. Singh
- Department of Radiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wendy D. Ellis
- Department of Radiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Marie R. Griffin
- Department of Health Policy, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kathryn M. Edwards
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, 4401 Penn Ave., Pittsburgh, PA 15224, USA
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19
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Howard LM, Fan R, Zhu Y, Griffin MR, Edwards KM, Hartinger S, Williams JV, Vidal JE, Klugman KP, Gil AI, Lanata CF, Grijalva CG. Nasopharyngeal Pneumococcal Density Is Associated With Viral Activity but Not With Use of Improved Stoves Among Young Andean Children. Open Forum Infect Dis 2017; 4:ofx161. [PMID: 28929126 PMCID: PMC5601081 DOI: 10.1093/ofid/ofx161] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/20/2017] [Indexed: 12/15/2022] Open
Abstract
Background Indoor smoke exposure is common in developing countries and may influence nasopharyngeal (NP) pneumococcal colonization density and risk of acute respiratory illness. We compared colonization density among Andean children living in households previously enrolled in a randomized controlled trial of a home intervention package including improved stoves to reduce smoke, kitchen sinks, and water disinfection. Methods We enrolled 260 children aged <3 years and made weekly household visits to assess for acute respiratory illness (ARI) and collect nasal swabs for respiratory virus polymerase chain reaction (PCR) testing during ARI. At monthly intervals, NP swabs were collected to determine pneumococcal colonization density through quantitative lytA PCR. We used linear quantile mixed-effects models to compare median log-transformed colonization densities among children in households randomized to the control (n = 129) versus intervention (n = 131) in sequential time points, accounting for random effects of multiple samples from individual children. Other covariates included age, sex, month, antibiotic exposure, and timing of sample collection relative to ARI with and without viral detection. Results Age and sociodemographic characteristics were similar between groups. Although no differences were observed in densities between groups, colonization density varied significantly over time in both groups, with highest densities coinciding with spring months. Time during and after virus-associated ARI was also associated with higher pneumococcal colonization density than time remote from ARIs. Conclusions A home intervention package, including improved stoves, was not associated with changes in pneumococcal densities in young Andean children. However, increasing pneumococcal density was observed with spring season and viral-associated ARIs.
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Affiliation(s)
- Leigh M Howard
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | | | | | - Marie R Griffin
- Department of Health Policy, Vanderbilt University, Nashville, Tennessee
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee.,Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | - Stella Hartinger
- Universidad Peruana Cayetano Heredia, Lima, Peru.,Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pennsylvania
| | - Jorge E Vidal
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Keith P Klugman
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Ana I Gil
- Instituto de Investigacion Nutricional, Lima, Peru
| | - Claudio F Lanata
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee.,Instituto de Investigacion Nutricional, Lima, Peru
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University, Nashville, Tennessee
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Blyth CC, Ford R, Sapura J, Kumani T, Masiria G, Kave J, Yuasi L, Greenhill A, Hwaihwanje I, Lang A, Lehmann D, Pomat W. Childhood pneumonia and meningitis in the Eastern Highlands Province, Papua New Guinea in the era of conjugate vaccines: study methods and challenges. Pneumonia (Nathan) 2017; 9:5. [PMID: 28702307 PMCID: PMC5471671 DOI: 10.1186/s41479-017-0029-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/23/2017] [Indexed: 12/18/2022] Open
Abstract
Background Pneumonia and meningitis are common causes of severe childhood illness in Papua New Guinea (PNG). The etiology of both clinical conditions in PNG has not been recently assessed. Changes in lifestyle, provision and access to healthcare, antimicrobial utilization and resistance, and the national childhood vaccination schedule necessitate reassessment. Methods A prospective case-control study was undertaken, enrolling children <5 years of age to determine the contemporary etiology of clinically defined moderate or severe pneumonia or suspected meningitis. Cases were identified following presentation for inpatient or outpatient care in Goroka town, the major population centre in the Eastern Highlands Province. Following enrolment, routine diagnostic specimens including blood, nasopharyngeal swabs, urine and (if required) cerebrospinal fluid, were obtained. Cases residing within one hour’s drive of Goroka were followed up, and recruitment of healthy contemporaneous controls was undertaken in the cases’ communities. Results 998 cases and 978 controls were enrolled over 3 years. This included 784 cases (78.6%) with moderate pneumonia, 187 (18.7%) with severe pneumonia and 75 (7.5%) with suspected meningitis, of whom 48 (4.8%) had concurrent pneumonia. The median age of cases was 7.8 months (Interquartile range [IQR] 3.9–14.3), significantly lower than community controls, which was 20.8 months (IQR 8.2–36.4). Half the cases were admitted to hospital (500/998; 50.1%). Recruitment of cases and controls and successful collection of diagnostic specimens improved throughout the study, with blood volume increasing and rates of blood culture contamination decreasing. The overall case fatality rate was 18/998 (1.8%). Of cases eligible for follow-up, outcome data was available from 76.7%. Low but increasing coverage of Haemophilus influenzae type B conjugate vaccines on the national schedule was observed during the study period: three dose DTPw-HepB-Hib coverage in children >3 months increased from 14.9 to 43.0% and 29.0 to 47.7% in cases and controls (both p < 0.001). Despite inclusion in the national immunization program in 2014, 2015 PCV13 three-dose coverage in cases and controls >3 months was only 4.0 and 6.5%. Conclusions Recruitment of large numbers of pediatric pneumonia and meningitis cases and community controls in a third-world setting presents unique challenges. Successful enrolment of 998 cases and 978 controls with comprehensive clinical data, biological specimens and follow up was achieved. Increased vaccine coverage remains an ongoing health priority. Electronic supplementary material The online version of this article (doi:10.1186/s41479-017-0029-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher C Blyth
- School of Paediatrics and Child Health, The University of Western Australia, Princess Margaret Hospital for Children, Roberts Road, Subiaco, 6008 WA Australia.,Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, PO Box 855, West Perth, 6872 WA Australia.,Department of Infectious Diseases and PathWest Department of Microbiology, Princess Margaret Hospital for Children, Roberts Road, Subiaco, 6008 WA Australia
| | - Rebecca Ford
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - Joycelyn Sapura
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - Tonny Kumani
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - Geraldine Masiria
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - John Kave
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - Lapule Yuasi
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - Andrew Greenhill
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea.,School of Applied and Biomedical Sciences, Federation University Australia, Gippsland Campus, Northways Road, Churchill, 3842 VIC Australia
| | - Ilomo Hwaihwanje
- Eastern Highlands Provincial Hospital, PO Box 392, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - Amanda Lang
- Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - Deborah Lehmann
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, PO Box 855, West Perth, 6872 WA Australia.,Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
| | - William Pomat
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, PO Box 855, West Perth, 6872 WA Australia.,Papua New Guinea Institute of Medical Research, PO Box 60, Goroka, 441 Eastern Highlands Province Papua New Guinea
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Abstract
It was widely believed in the late 1960s that infectious diseases had been conquered by vaccines and antibiotics and humans were no longer under threat by microbial pathogens. Yet, since that time more than 60 pathogens have been discovered that can cause serious emerging infectious diseases. Molecular methods have played critical roles in the discovery, monitoring, and clinical diagnostics of emerging pathogens. In this chapter, we present well-recognized emerging pathogens. We provide examples of the utility of molecular assays in research and clinical care of emerging infectious diseases. We also discuss some theoretical and practical limitations of molecular tests and the future prospects of expanding molecular diagnostics for emerging pathogens based on new advances of knowledge and technologies.
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Maitre NL, Williams JV. Human metapneumovirus in the preterm neonate: current perspectives. RESEARCH AND REPORTS IN NEONATOLOGY 2016; 6:41-49. [PMID: 27891060 PMCID: PMC5120728 DOI: 10.2147/rrn.s76270] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Premature birth (<37 weeks gestation) occurs in ~11% of all births in the US. These infants are at risk of chronic lung disease and respiratory conditions, including bronchopulmonary dysplasia. Respiratory viruses are important causes of acute respiratory illness (ARI) in preterm infants, leading to rehospitalization, increased health care burden, and long-term morbidity. Human metapneumovirus (HMPV) is a paramyxovirus discovered in 2001 that is related to respiratory syncytial virus. Epidemiologic studies show that HMPV is a leading cause of ARI in children and adults worldwide. Prematurity is a major risk factor for severe HMPV disease, requiring hospitalization. Moreover, limited data suggest that HMPV infection during infancy is associated with asthma and recurrent wheezing, which are common long-term pulmonary complication of prematurity. HMPV causes nosocomial outbreaks of ARI in hospitals and long-term care facilities, although there are few studies of the prevalence of HMPV in neonatal intensive care unit populations. HMPV is a common and important virus in premature infants, and caregivers for preterm infants should consider this virus in patients with acute respiratory symptoms.
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Affiliation(s)
- Nathalie L Maitre
- Center for Perinatal Research, Department of Pediatrics, Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, USA
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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23
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Bates JT, Pickens JA, Schuster JE, Johnson M, Tollefson SJ, Williams JV, Davis NL, Johnston RE, Schultz-Darken N, Slaughter JC, Smith-House F, Crowe JE. Immunogenicity and efficacy of alphavirus-derived replicon vaccines for respiratory syncytial virus and human metapneumovirus in nonhuman primates. Vaccine 2016; 34:950-6. [PMID: 26772634 DOI: 10.1016/j.vaccine.2015.12.045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 12/15/2015] [Accepted: 12/18/2015] [Indexed: 12/14/2022]
Abstract
Human respiratory syncytial virus (hRSV) and human metapneumovirus (hMPV) are major causes of illness among children, the elderly, and the immunocompromised. No vaccine has been licensed for protection against either of these viruses. We tested the ability of two Venezuelan equine encephalitis virus-based viral replicon particle (VEE-VRP) vaccines that express the hRSV or hMPV fusion (F) protein to confer protection against hRSV or hMPV in African green monkeys. Animals immunized with VEE-VRP vaccines developed RSV or MPV F-specific antibodies and serum neutralizing activity. Compared to control animals, immunized animals were better able to control viral load in the respiratory mucosa following challenge and had lower levels of viral genome in nasopharyngeal and bronchoalveolar lavage fluids. The high level of immunogenicity and protective efficacy induced by these vaccine candidates in nonhuman primates suggest that they hold promise for further development.
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Affiliation(s)
- John T Bates
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer A Pickens
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jennifer E Schuster
- The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Monika Johnson
- The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Sharon J Tollefson
- The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John V Williams
- The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nancy L Davis
- The Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Nancy Schultz-Darken
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - James C Slaughter
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Department of Biostatistics of Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Frances Smith-House
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James E Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Department of Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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24
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Abstract
BACKGROUND Human metapneumovirus (HMPV) is a leading cause of acute respiratory tract infection in young children. Our objectives were to define HMPV epidemiology and circulating strains and determine markers of severe disease in Jordanian children. METHODS We conducted a prospective study from March 16, 2010 to March 31, 2013 using quantitative reverse transcription-polymerase chain reaction to determine the frequency of HMPV infection among children <2 years old admitted with fever and/or acute respiratory illness to a major government hospital in Amman, Jordan. RESULTS HMPV was present in 273 of 3168 (8.6%) of children presenting with acute respiratory tract infection. HMPV A2, B1 and B2, but not A1, were detected during the 3-year period. HMPV-infected children were older and more likely to be diagnosed with bronchopneumonia than HMPV-negative children. HMPV-infected children with lower respiratory tract infection had higher rates of cough and shortness of breath than children with lower respiratory tract infection infected with other or no identifiable viruses. Symptoms and severity were not different between children with HMPV only compared with HMPV coinfection. Children with HMPV subgroup A infection were more likely to require supplemental oxygen. In a multivariate analysis, HMPV subgroup A and age <6 months were independently associated with supplemental oxygen requirement. CONCLUSIONS HMPV is a leading cause of acute respiratory tract disease in Jordanian children <2 years old. HMPV A and young age were associated with severe disease. Ninety percent of HMPV-infected hospitalized children were full term and otherwise healthy, in contrast to high-income nations; thus, factors contributing to disease severity likely vary depending on geographic and resource differences.
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25
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Halasa N, Williams J, Faouri S, Shehabi A, Vermund SH, Wang L, Fonnesbeck C, Khuri-Bulos N. Natural history and epidemiology of respiratory syncytial virus infection in the Middle East: Hospital surveillance for children under age two in Jordan. Vaccine 2015; 33:6479-87. [PMID: 26314623 PMCID: PMC7115487 DOI: 10.1016/j.vaccine.2015.08.048] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 12/11/2022]
Abstract
UNLABELLED Respiratory syncytial virus (RSV) is the leading cause of bronchiolitis and viral pneumonia in infants and young children worldwide. In the Middle East and Arab countries, the burden of RSV-associated hospitalizations is not well characterized. We sought to determine the burden and clinical/epidemiological characteristics of RSV hospitalization in young children in Amman, Jordan. We investigated risk factors for severity including vitamin D levels. METHODS We conducted viral surveillance with clinical and demographic data in children <2 years admitted with respiratory symptoms and/or fever at the Al-Bashir Government Hospital from March16, 2010 to March 31, 2013. Nasal/throat swabs were obtained and placed into lysis buffer, and frozen at -80°C until testing by real-time RT-PCR for 11 respiratory viruses. Heel stick blood or sera samples for 25-hydroxyvitamin D [25(OH)D] levels were obtained and sent to a central laboratory for mass spectrometry. RESULTS Of the 3168 children, >80% testing positive for one virus, with RSV the most common virus detected (44%). The RSV-associated hospitalization rate was highest in children <6 months with an annual range of 21.1-25.9 per 1000, compared to 6.0-8.0 in 6-11-month-olds and 1.6-2.5 in 12-23-month-olds. RSV-positive children compared with RSV-negative were more likely to be previously healthy without underlying medical conditions, less likely to be born prematurely, had a higher frequency of supplemental oxygen use, and had lower median vitamin D levels. Risk factors for oxygen use in RSV-positive children included underlying medical conditions, lack of breastfeeding, younger age, and higher viral load. CONCLUSION RSV is a major cause of illness in hospitalized Jordanian children and is associated with increased severity compared to other respiratory viruses. Children with RSV in the Middle East would benefit from future RSV vaccines and antiviral therapy.
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Affiliation(s)
- Natasha Halasa
- Departments of Pediatrics, Vanderbilt University, Nashville, TN, USA; Institute for Global Health, Vanderbilt University, Nashville, TN, USA.
| | - John Williams
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Samir Faouri
- Department of Pediatrics, Al Bashir Hospital, Amman, Jordan.
| | - Asem Shehabi
- Department of Pathology-Microbiology at University of Jordan, Amman, Jordan.
| | - Sten H Vermund
- Departments of Pediatrics, Vanderbilt University, Nashville, TN, USA; Institute for Global Health, Vanderbilt University, Nashville, TN, USA.
| | - Li Wang
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA.
| | | | - Najwa Khuri-Bulos
- Department of Pathology-Microbiology at University of Jordan, Amman, Jordan.
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26
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Abstract
BACKGROUND Viruses are commonly detected in children with acute respiratory illnesses (ARIs) and in asymptomatic children. Longitudinal studies of viral detections during asymptomatic periods surrounding ARI could facilitate interpretation of viral detections but are currently scant. METHODS We used reverse transcription polymerase chain reaction to analyze respiratory samples from young Andean children for viruses during asymptomatic periods within 8-120 days of index ARI (cough or fever). We compared viral detections over time within children and explored reverse transcription polymerase chain reaction cycle thresholds (CTs) as surrogates for viral loads. RESULTS At least 1 respiratory virus was detected in 367 (43%) of 859 samples collected during asymptomatic periods, with more frequent detections in periods with rhinorrhea (49%) than those without (34%, P < 0.001). Relative to index ARI with human rhinovirus (HRV), adenovirus (AdV), respiratory syncytial virus (RSV) and parainfluenza virus detected, the same viruses were also detected during 32, 22, 10 and 3% of asymptomatic periods, respectively. RSV was only detected 8-30 days after index RSV ARI, whereas HRV and AdV were detected throughout asymptomatic periods. Human metapneumovirus and influenza were rarely detected during asymptomatic periods (<3%). No significant differences were observed in the CT for HRV or AdV during asymptomatic periods relative to ARI. For RSV, CTs were significantly lower during ARI relative to the asymptomatic period (P = 0.03). CONCLUSIONS These findings indicate that influenza, human metapneumovirus, parainfluenza virus and RSV detections in children with an ARI usually indicate a causal relationship. When HRV or AdV is detected during ARI, the causal relationship is less certain.
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Foster MW, Gerhardt G, Robitaille L, Plante PL, Boivin G, Corbeil J, Moseley MA. Targeted Proteomics of Human Metapneumovirus in Clinical Samples and Viral Cultures. Anal Chem 2015; 87:10247-54. [PMID: 26376123 DOI: 10.1021/acs.analchem.5b01544] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The rapid, sensitive, and specific identification of infectious pathogens from clinical isolates is a critical need in the hospital setting. Mass spectrometry (MS) has been widely adopted for identification of bacterial pathogens, although polymerase chain reaction remains the mainstay for the identification of viral pathogens. Here, we explored the capability of MS for the detection of human metapneumovirus (HMPV), a common cause of respiratory tract infections in children. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) sequencing of a single HMPV reference strain (CAN97-83) was used to develop a multiple reaction monitoring (MRM) assay that employed stable isotope-labeled peptide internal standards for quantitation of HMPV. Using this assay, we confirmed the presence of HMPV in viral cultures from 10 infected patients and further assigned genetic lineage based on the presence/absence of variant peptides belonging to the viral matrix and nucleoproteins. Similar results were achieved for primary clinical samples (nasopharyngeal aspirates) from the same individuals. As validation, virus lineages, and variant coding sequences, were confirmed by next-generation sequencing of viral RNA obtained from the culture samples. Finally, separate dilution series of HMPV A and B lineages were used to further refine and assess the robustness of the assay and to determine limits of detection in nasopharyngeal aspirates. Our results demonstrate the applicability of MRM for identification of HMPV, and assignment of genetic lineage, from both viral cultures and clinical samples. More generally, this approach should prove tractable as an alternative to nucleic-acid based sequencing for the multiplexed identification of respiratory virus infections.
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Affiliation(s)
| | - Geoff Gerhardt
- Waters Corporation , Milford, Massachusetts 01757, United States
| | - Lynda Robitaille
- Department of Molecular Medicine, Department of Microbiology, Immunology and Infectious Diseases, Université Laval , Québec City, Québec, Canada G1V 0A6
| | - Pier-Luc Plante
- Department of Molecular Medicine, Department of Microbiology, Immunology and Infectious Diseases, Université Laval , Québec City, Québec, Canada G1V 0A6
| | - Guy Boivin
- Department of Molecular Medicine, Department of Microbiology, Immunology and Infectious Diseases, Université Laval , Québec City, Québec, Canada G1V 0A6
| | - Jacques Corbeil
- Department of Molecular Medicine, Department of Microbiology, Immunology and Infectious Diseases, Université Laval , Québec City, Québec, Canada G1V 0A6
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Miller EK, Linder J, Kraft D, Johnson M, Lu P, Saville BR, Williams JV, Griffin MR, Talbot HK. Hospitalizations and outpatient visits for rhinovirus-associated acute respiratory illness in adults. J Allergy Clin Immunol 2015; 137:734-43.e1. [PMID: 26255695 DOI: 10.1016/j.jaci.2015.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 05/15/2015] [Accepted: 06/05/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND Rhinovirus is linked to asthma exacerbations and chronic obstructive pulmonary disease exacerbations in adults. The severity and rates of rhinovirus acute respiratory illnesses (ARIs) in adults are uncertain. OBJECTIVES We sought to determine rhinovirus-associated ARI rates in adults presenting for care in multiple settings and identify factors associated with rhinovirus detection. METHODS This prospective, population-based cohort enrolled Tennessee residents 18 years or older in the emergency department (ED), outpatient clinics, or hospitalized for ARI from December 2008 to May 2010. Nasal/throat swabs were collected and tested for rhinovirus and other viruses by using RT-PCR. Rates of ED visits and hospitalizations were calculated and rhinovirus-positive and rhinovirus-negative patients were compared. RESULTS Among 2351 enrollees, rhinovirus was detected in 247 (11%). There were 7 rhinovirus-associated ED visits and 3 hospitalizations per 1000 adults annually. Patients with rhinovirus, compared with virus-negative ARI, were more likely to present with wheezing (odds ratio [OR], 1.7; 95% CI, 1.23-2.35; P < .001), to be a current smoker (OR, 2.31; 95% CI, 1.68-3.19) or live with a smoker (OR, 1.72; 95% CI, 1.10-2.67), have a history of chronic respiratory disease (OR, 1.61; 95% CI, 1.17-2.22), and were less likely to be hospitalized versus seen in the outpatient setting (OR, 0.58; 95% CI, 0.41-0.83). CONCLUSIONS Rhinovirus is associated with a substantial number of ED visits and hospitalizations for ARIs in adults. There may be modifiable factors that can reduce the likelihood of presenting with rhinovirus-associated ARIs.
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Affiliation(s)
- E Kathryn Miller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn.
| | - Jodell Linder
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn
| | - David Kraft
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Monika Johnson
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Pengcheng Lu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Benjamin R Saville
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - John V Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pa
| | - Marie R Griffin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn; Department of Healthy Policy, Vanderbilt University Medical Center, Nashville, Tenn; Mid-South Geriatric Research Education and Clinical Center and Clinical Research Center of Excellence, VA TN Valley Health Care System, Nashville, Tenn
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tenn
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29
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Loria C, Domm JA, Halasa NB, Heitman E, Miller EK, Xu M, Saville BR, Frangoul H, Williams JV. Human rhinovirus C infections in pediatric hematology and oncology patients. Pediatr Transplant 2015; 19:94-100. [PMID: 25377237 PMCID: PMC4280346 DOI: 10.1111/petr.12383] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/02/2014] [Indexed: 12/31/2022]
Abstract
Children with cancer and HSCT recipients are at high risk for common viral infections. We sought to define the viral etiology of ARI and identify risk factors. Nasal wash samples were collected from pediatric hematology-oncology patients and HSCT recipients with ARI during the 2003-2005 winter seasons. Real-time RT-PCR was performed to detect Flu A, influenza B, RSV, PIV 1-3, human MPV, and HRV. HRV specimens were sequenced and genotyped. Seventy-eight samples from 62 children were included. Viruses were detected in 31 of 78 samples (40%). HRV were detected most frequently, in 16 (52%) including five HRVC; followed by seven (22%) RSV, five (16%) Flu A, four (13%) MPV, and two (6%) PIV2. There was a trend toward higher risk of viral infection for children in day care. Only 8% of the study children had received influenza vaccine. HRV, including the recently discovered HRVC, are an important cause of infection in pediatric oncology and HSCT patients. Molecular testing is superior to conventional methods and should be standard of care, as HRV are not detected by conventional methods.
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Affiliation(s)
- Carolina Loria
- Center for Biomedical Ethics and Society, Vanderbilt University School of Medicine, Nashville, TN
| | - Jennifer A. Domm
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - Natasha B. Halasa
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - Elizabeth Heitman
- Center for Biomedical Ethics and Society, Vanderbilt University School of Medicine, Nashville, TN
| | - E. Kathryn Miller
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - Meng Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN
| | - Benjamin R. Saville
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN
| | - Haydar Frangoul
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN
| | - John V. Williams
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN,Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN
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Chang YF, Tsao KC, Liu YC, Chen YC, Yu PC, Huang YC, Chou C. Diagnosis of human metapneumovirus in patients hospitalized with acute lower respiratory tract infection using a metal-enhanced fluorescence technique. J Virol Methods 2014; 213:151-6. [PMID: 25522922 DOI: 10.1016/j.jviromet.2014.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 11/30/2022]
Abstract
Human metapneumovirus (hMPV) is a common respiratory tract infection in children. However, conventional immunofluorescence assays (IFAs) for detecting hMPV in respiratory samples have limited reliability with a sensitivity and false-negative predictive value of 58.1% and approximately 17.8%, respectively. In this study, hMPV was measured in 91 clinical respiratory samples (55 sputum and 36 nasopharyngeal aspirate samples), which were obtained from children under three years of age, utilizing our previously developed high-throughput metal-enhanced fluorescence (MEF)-based biosensor (HT-MEFB). The sensitivity of HT-MEFB for hMPV detection in the 91 samples was improved by up to 77.4% compared with that obtained with IFAs, and the specificity of HT-MEFB for hMPV detection was 91.7%. In addition, the specificity and accuracy obtained after the selection of 55 sputum samples as the analyzed specimen reached 92.3% and 90.9%, respectively. Thus, in terms of accuracy, high throughput, and sensitivity, HT-MEFB exhibits considerable potential for hMPV detection in clinical settings.
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Affiliation(s)
- Ying-Feng Chang
- Chang Gung University, Graduate Institute of Electro-Optical Engineering, Taoyuan 33371, Taiwan; National Taiwan University, Department of Biochemical Science and Technology, Taipei 10617, Taiwan
| | - Kuo-Chien Tsao
- Linkou Chang Gung Memorial Hospital, Department of Laboratory Medicine, Taoyuan 33305, Taiwan; Chang Gung University, College of Medicine, Department of Medical Biotechnology and Laboratory Science, Taoyuan 33371, Taiwan
| | - Yi-Chun Liu
- Linkou Chang Gung Memorial Hospital, Department of Laboratory Medicine, Taoyuan 33305, Taiwan
| | - Yu-Chi Chen
- Chang Gung University, Graduate Institute of Electro-Optical Engineering, Taoyuan 33371, Taiwan
| | - Pei-Chun Yu
- Chang Gung University, Graduate Institute of Electro-Optical Engineering, Taoyuan 33371, Taiwan
| | - Yhu-Chering Huang
- Linkou Chang Gung Memorial Hospital, Division of Pediatric Infectious Diseases, Taoyuan 33305, Taiwan; Chang Gung University, College of Medicine, Department of Medicine, Taoyuan 33371, Taiwan
| | - Chien Chou
- Chang Gung University, Graduate Institute of Electro-Optical Engineering, Taoyuan 33371, Taiwan; Chang Gung University, Healthy Aging Research Center, Taoyuan 33302, Taiwan.
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Budge PJ, Griffin MR, Edwards KM, Williams JV, Verastegui H, Hartinger SM, Johnson M, Klemenc JM, Zhu Y, Gil AI, Lanata CF, Grijalva CG. A household-based study of acute viral respiratory illnesses in Andean children. Pediatr Infect Dis J 2014; 33:443-7. [PMID: 24378948 PMCID: PMC4223552 DOI: 10.1097/inf.0000000000000135] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Few community studies have measured the incidence, severity and etiology of acute respiratory illness (ARI) among children living at high-altitude in remote rural settings. METHODS We conducted active, household-based ARI surveillance among children aged <3 years in rural highland communities of San Marcos, Cajamarca, Peru from May 2009 through September 2011 (RESPIRA-PERU study). ARI (defined by fever or cough) were considered lower respiratory tract infections if tachypnea, wheezing, grunting, stridor or retractions were present. Nasal swabs collected during ARI episodes were tested for respiratory viruses by real-time, reverse-transcriptase polymerase chain reaction. ARI incidence was calculated using Poisson regression. RESULTS During 755.1 child-years of observation among 892 children in 58 communities, 4475 ARI were observed, yielding an adjusted incidence of 6.2 ARI/child-year (95% confidence interval: 5.9-6.5). Families sought medical care for 24% of ARI, 4% were classified as lower respiratory tract infections and 1% led to hospitalization. Of 5 deaths among cohort children, 2 were attributed to ARI. One or more respiratory viruses were detected in 67% of 3957 samples collected. Virus-specific incidence rates per 100 child-years were: rhinovirus, 236; adenovirus, 73; parainfluenza virus, 46; influenza, 37; respiratory syncytial virus, 30 and human metapneumovirus, 17. Respiratory syncytial virus, metapneumovirus and parainfluenza virus 1-3 comprised a disproportionate share of lower respiratory tract infections compared with other etiologies. CONCLUSIONS In this high-altitude rural setting with low-population density, ARI in young children were common, frequently severe and associated with a number of different respiratory viruses. Effective strategies for prevention and control of these infections are needed.
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Affiliation(s)
- Philip J. Budge
- Division of Infectious Diseases, Department of Internal Medicine, Vanderbilt University, Nashville, TN, USA
| | - Marie R. Griffin
- Department of Preventive Medicine, Vanderbilt University, Nashville, TN, USA
| | - Kathryn M. Edwards
- Vanderbilt Vaccine Research Program, Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University, Nashville, TN, USA
- Department of Pediatrics, Vanderbilt University, Nashville, TN, USA
| | - John V. Williams
- Department of Pediatrics, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN, USA
| | | | - Stella M. Hartinger
- Instituto de Investigacion Nutricional, Lima, Peru
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Monika Johnson
- Department of Pediatrics, Vanderbilt University, Nashville, TN, USA
| | | | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA
| | - Ana I. Gil
- Instituto de Investigacion Nutricional, Lima, Peru
| | | | - Carlos G. Grijalva
- Department of Preventive Medicine, Vanderbilt University, Nashville, TN, USA
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Grijalva CG, Griffin MR, Edwards KM, Johnson M, Gil AI, Verástegui H, Lanata CF, Williams JV. Concordance between RT-PCR-based detection of respiratory viruses from nasal swabs collected for viral testing and nasopharyngeal swabs collected for bacterial testing. J Clin Virol 2014; 60:309-12. [PMID: 24875136 DOI: 10.1016/j.jcv.2014.04.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/07/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND Epidemiologic studies of respiratory infections frequently rely on separate sample collections for the detection of bacteria and viruses. The requirement for two specimens presents cost, logistical, and acceptability challenges. OBJECTIVES To determine the agreement in detection of respiratory viruses using RT-PCR between two different types of samples collected on the same day: nasal swabs preserved in viral transport medium (NS) and nasopharyngeal swabs preserved in skim milk-tryptone-glucose-glycerol [STGG] medium (NP), the current standard for pneumococcal colonization studies. STUDY DESIGN Paired NS and NP samples were collected between May 2009 and September 2011 as part of the RESPIRA-PERU study, a large prospective cohort of Andean children <3 years of age. NS samples used polyester swabs and viral transport medium whereas NP samples used rayon wire-handled swabs and STGG medium. Samples were tested for influenza, human metapneumovirus (MPV), respiratory syncytial virus (RSV), human rhinovirus (HRV), parainfluenza virus 3 (PIV3) and adenovirus (ADV) using real-time RT-PCR. We calculated the agreement, and compared cycle thresholds (CT) between NP and NS samples. RESULTS Among 226 paired NP-NS samples, we observed very high agreement with a Kappa statistic ranging from 0.71 for ADV to 0.97 for MPV. CT values were similar for both strategies. CONCLUSIONS NP samples preserved in STGG provide a simple and reliable strategy for identification of both pneumococcus and respiratory viruses. This single specimen collection strategy could be used for epidemiologic studies, especially in resource-limited settings. Furthermore, archived NP-STGG specimens from previous studies could be reliably tested by RT-PCR for viruses.
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Affiliation(s)
- Carlos G Grijalva
- Department of Health Policy, Vanderbilt University School of Medicine, Nashville, TN, United States.
| | - Marie R Griffin
- Department of Health Policy, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Kathryn M Edwards
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Monika Johnson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Ana I Gil
- Instituto de Investigación Nutricional, Lima, Peru
| | | | | | - John V Williams
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States; Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States
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Human metapneumovirus viral load is an important risk factor for disease severity in young children. J Clin Virol 2014; 60:133-40. [PMID: 24686044 DOI: 10.1016/j.jcv.2014.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 11/23/2022]
Abstract
BACKGROUND The role of viral load in human metapneumovirus (HMPV) disease severity has not yet been clearly determined. OBJECTIVE We evaluated the importance of viral load along with other factors in HMPV disease severity among children aged <3 years old. STUDY DESIGN HMPV-positive cases were selected from a cohort of outpatients and hospitalized children with lower respiratory tract infections. HMPV groups (A or B) and viral loads were determined in their nasopharyngeal aspirates. Disease severity was defined by assessing risk for hospitalization and by using two validated clinical severity scores. RESULTS Of the 118 HMPV cases detected over 4 years for which viral load could be determined, 60 belonged to genotype A and 58 to genotype B. Baseline characteristics were similar in HMPV-A and HMPV-B mono-infected patients. In multivariate analysis, HMPV hospitalization was associated with viral load ≥1000 copies/10(4)cells (OR, 3.2; 95%CI, 1.4-7.4), age <6 months (OR, 3.1; 95%CI, 1.2-8.6) and presence of ≥3 children in the household (OR, 2.7; 95%CI, 1.04-6.9). A high HMPV viral load was also associated with pulmonary rales (p=.03), use of bronchodilators (p=.02) and inhaled corticosteroids (p=.01). CONCLUSION HMPV viral load is associated with disease severity in young children along with young age and household crowding.
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Budge PJ, Griffin MR, Edwards KM, Williams JV, Verastegui H, Hartinger SM, Mäusezahl D, Johnson M, Klemenc JM, Zhu Y, Gil AI, Lanata CF, Grigalva CG. Impact of home environment interventions on the risk of influenza-associated ARI in Andean children: observations from a prospective household-based cohort study. PLoS One 2014; 9:e91247. [PMID: 24622044 PMCID: PMC3951509 DOI: 10.1371/journal.pone.0091247] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 02/08/2014] [Indexed: 11/25/2022] Open
Abstract
Background The Respiratory Infections in Andean Peruvian Children (RESPIRA-PERU) study enrolled children who participated in a community-cluster randomized trial of improved stoves, solar water disinfection, and kitchen sinks (IHIP trial) and children from additional Andean households. We quantified the burden of influenza-associated acute respiratory illness (ARI) in this household-based cohort. Methods From May 2009 to September 2011, we conducted active weekly ARI surveillance in 892 children age <3 years, of whom 272 (30.5%) had participated in the IHIP trial. We collected nasal swabs during ARI, tested for influenza and other respiratory viruses by RT-PCR, and determined influenza incidence and risk factors using mixed-effects regression models. Results The overall incidence of influenza-associated ARI was 36.6/100 child-years; incidence of influenza A, B, and C was 20.5, 8.7, and 5.2/100 child-years, respectively. Influenza C was associated with fewer days of subjective fever (median 1 vs. 2) and malaise (median 0 vs. 2) compared to influenza A. Non-influenza ARI also resulted in fewer days of fever and malaise, and fewer healthcare visits than influenza A-associated ARI. Influenza incidence varied by calendar year (80% occurred in the 2010 season) and IHIP trial participation. Among households that participated in the IHIP trial, influenza-associated ARI incidence was significantly lower in intervention than in control households (RR 0.40, 95% CI: 0.20–0.82). Conclusions Influenza burden is high among Andean children. ARI associated with influenza A and B had longer symptom duration and higher healthcare utilization than influenza C-associated ARI or non-influenza ARI. Environmental community interventions may reduce influenza morbidity.
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Affiliation(s)
- Philip J. Budge
- Division of Infectious Diseases, Department of Internal Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Marie R. Griffin
- Department of Health Policy, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Kathryn M. Edwards
- Vanderbilt Vaccine Research Program, Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - John V. Williams
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
| | | | - Stella M. Hartinger
- Instituto de Investigación Nutricional, Lima, Peru
- Swiss Tropical and Public Health Institute, and University of Basel, Basel, Switzerland
| | - Daniel Mäusezahl
- Swiss Tropical and Public Health Institute, and University of Basel, Basel, Switzerland
| | - Monika Johnson
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jennifer M. Klemenc
- Department of Pediatrics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Ana I. Gil
- Instituto de Investigación Nutricional, Lima, Peru
| | | | - Carlos G. Grigalva
- Department of Health Policy, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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Widmer K, Griffin MR, Zhu Y, Williams JV, Talbot HK. Respiratory syncytial virus- and human metapneumovirus-associated emergency department and hospital burden in adults. Influenza Other Respir Viruses 2014; 8:347-52. [PMID: 24512531 PMCID: PMC3984605 DOI: 10.1111/irv.12234] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2013] [Indexed: 11/30/2022] Open
Abstract
Objective Determine the burden of illness associated with respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) in adults, especially young adults. Design Prospective surveillance study using RT-PCR for the diagnosis of RSV and HMPV. Setting One academic Emergency Department (ED), one academic hospital and three middle Tennessee community hospitals. Sample We prospectively enrolled Middle Tennessee residents ≥18 years old evaluated in the emergency department (ED) or hospitalized for respiratory symptoms May 2009 through April 2010. We collected nose/throat specimens for RSV and HMPV reverse-transcriptase polymerase chain reaction (RT-PCR) testing and obtained demographic and clinical data. Main outcome Measures Rates of ED visits and hospitalizations were calculated using the proportion of enrolled patients positive for each virus multiplied by the number of Middle Tennessee residents evaluated in EDs and/or hospitalized in Tennessee for acute respiratory illness during the study period. Results Three thousand two hundred and fifty six patients were eligible; 1477 (45·4%) were enrolled; 1248 (84·5%) of these consented to additional testing and had adequate samples. RT-PCR identified 32 (2·6%) patients with RSV and 33 (2·6%) with HMPV. The median duration of symptoms before ED presentation was 3·3 days with RSV and 2·8 days with HMPV, and before hospital admission was 4·5 days with RSV and 3·5 days with HMPV. The annual hospitalization and ED visit rates were similar for RSV and HMPV. The hospitalization rate associated with each virus was about 10 per 10 000 persons aged ≥50 years; ED rates were approximately 2 times higher. Hospitalization rates were about 2 per 10 000 persons aged 18–49 years, with ED rates 5–6 times higher. Conclusion RSV and MPV are associated with substantial disease in adults, with hospitalization and ED visits rates increasing with age.
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Affiliation(s)
- Kyle Widmer
- Department of Internal Medicine, Tulane University School of Medicine, New Orleans, LA, USA; Southeast Louisiana Veterans Health Care System, New Orleans, LA, USA
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Kono J, Jonduo MH, Omena M, Siba PM, Horwood PF. Viruses associated with influenza-like-illnesses in Papua New Guinea, 2010. J Med Virol 2013; 86:899-904. [PMID: 24136362 PMCID: PMC7166351 DOI: 10.1002/jmv.23786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2013] [Indexed: 12/31/2022]
Abstract
Influenza‐like‐illness can be caused by a wide range of respiratory viruses. The etiology of influenza‐like‐illness in developing countries such as Papua New Guinea is poorly understood. The etiological agents associated with influenza‐like‐illness were investigated retrospectively for 300 nasopharyngeal swabs received by the Papua New Guinea National Influenza Centre in 2010. Real‐time PCR/RT‐PCR methods were used for the detection of 13 respiratory viruses. Patients with influenza‐like‐illness were identified according to the World Health Organization case definition: sudden onset of fever (>38°C), with cough and/or sore throat, in the absence of other diagnoses. At least one viral respiratory pathogen was detected in 66.3% of the samples tested. Rhinoviruses (17.0%), influenza A (16.7%), and influenza B (12.7%) were the pathogens detected most frequently. Children <5 years of age presented with a significantly higher rate of at least one viral pathogen and a significantly higher rate of co‐infections with multiple viruses, when compared to all other patients >5 years of age. Influenza B, adenovirus, and respiratory syncytial virus were all detected at significantly higher rates in children <5 years of age. This study confirmed that multiple respiratory viruses are circulating and contributing to the presentation of influenza‐like‐illness in Papua New Guinea. J. Med. Virol. 86:899–904, 2014. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- Jacinta Kono
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
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Abstract
BACKGROUND Prospective data on viral etiology and clinical characteristics of bronchiolitis and upper respiratory illness (URI) in infants are limited. METHODS This prospective cohort enrolled previously healthy term infants during inpatient or outpatient visits for acute URI or bronchiolitis during September to May 2004 to 2008. Illness severity was determined using an ordinal bronchiolitis severity score. Common respiratory viruses were identified by real-time reverse-transcriptase polymerase chain reaction. RESULTS Of 648 infants, 67% were enrolled during inpatient visits and 33% during outpatient visits. Seventy percent had bronchiolitis, 3% croup and 27% URI. Among infants with bronchiolitis, 76% had respiratory syncytial virus (RSV), 18% human rhinovirus (HRV), 10% influenza, 2% coronavirus, 3% human metapneumovirus and 1% parainfluenza virus. Among infants with croup, 39% had HRV, 28% parainfluenza virus, 28% RSV, 11% influenza, 6% coronavirus and none human metapneumovirus. Among infants with URI, 46% had HRV, 14% RSV, 12% influenza, 7% coronavirus, 6% parainfluenza virus and 4% human metapneumovirus. Individual viruses exhibited distinct seasonal, demographic and clinical expression. CONCLUSIONS The most common infections among infants seeking care in unscheduled medical visits for URI or bronchiolitis were RSV and HRV. Demographic differences were observed between patients with different viruses, suggesting that host and viral factors play a role in phenotypic expression of viral illness.
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Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India. Arch Virol 2013; 159:217-25. [PMID: 23929232 PMCID: PMC7087245 DOI: 10.1007/s00705-013-1812-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 06/28/2013] [Indexed: 11/09/2022]
Abstract
Human metapneumovirus (HMPV) is an important respiratory virus implicated in respiratory infections. The purpose of this study was to develop a one-step real-time RT-PCR assay that can detect all four lineages of HMPV and to identify the HMPV lineages circulating in Pune, India. Conserved regions of the nucleoprotein gene were used to design real-time primers and a probe. A total of 224 clinical samples that were positive for different respiratory viruses (including 51 samples that were positive for HMPV) were tested using the real time RT-PCR assay, and the specificity of the assay was observed to be 100 %. Using in vitro-synthesized RNA, the sensitivity of the assay was ascertained to be 100 copies of the target gene per reaction. Phylogenetic analysis of the nucleoprotein (N) and attachment glycoprotein (G) genes confirmed that this assay detected all lineages of HMPV. A2, B1 and B2 strains were observed during the study period. Our assay is highly sensitive and specific for all known lineages of HMPV, making it a valuable tool for rapid detection of the virus. A2 and B2 were the predominant subtypes circulating in Pune, Western India.
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Grijalva CG, Griffin MR, Edwards KM, Williams JV, Gil AI, Verastegui H, Hartinger SM, Vidal JE, Klugman KP, Lanata CF. Cohort profile: The study of respiratory pathogens in Andean children. Int J Epidemiol 2013; 43:1021-30. [PMID: 23771719 DOI: 10.1093/ije/dyt065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigated respiratory pathogens in a prospective cohort study of young children living in the Peruvian Andes. In the study we assessed viral respiratory infections among young children, and explored interactions of viruses with common respiratory bacteria, especially Streptococcus pneumoniae. Through weekly household visits, data were collected on the signs and symptoms of acute respiratory illness (ARI), nasal samples were collected to test for viruses during episodes of ARI, and nasopharyngeal samples were collected on a monthly basis to monitor bacterial colonisation. We also collected data on vaccination coverage, patterns of social mixing, geographic information, and environmental and socio-demographic variables. Understanding the interaction of respiratory viruses with bacteria and its impact on the burden and severity of ARIs in rural areas of developing countries is critical to designing strategies for preventing such infections.
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Affiliation(s)
- Carlos G Grijalva
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - Marie R Griffin
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - Kathryn M Edwards
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - John V Williams
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USADepartments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - Ana I Gil
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - Héctor Verastegui
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - Stella M Hartinger
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USADepartments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - Jorge E Vidal
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - Keith P Klugman
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
| | - Claudio F Lanata
- Departments of Preventive Medicine, Vanderbilt University School of Medicine, Nashville TN, USA, Pediatrics-Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville TN, USA, Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville TN, USA, Instituto de Investigación Nutricional, Lima, Perú, Swiss Tropical and Public Health Institute, Basel, Switzerland and Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA, USA
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