1
|
Ondo GN, Ushijima Y, Abe H, Mahmoudou S, Bikangui R, Nkoma AM, Mbadinga MJVM, More A, Agbanrin MD, Pemba CM, Beh Mba R, Akim AA, Lell B, Yasuda J. Genetic Diversity and Detection of Respiratory Viruses Excluding SARS-CoV-2 during the COVID-19 Pandemic in Gabon, 2020-2021. Viruses 2024; 16:698. [PMID: 38793579 PMCID: PMC11126038 DOI: 10.3390/v16050698] [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: 03/07/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
Acute respiratory infections are a major global burden in resource-limited countries, including countries in Africa. Although COVID-19 has been well studied since the pandemic emerged in Gabon, Central Africa, less attention has been paid to other respiratory viral diseases, and very little data are available. Herein, we provide the first data on the genetic diversity and detection of 18 major respiratory viruses in Gabon during the COVID-19 pandemic. Of 582 nasopharyngeal swab specimens collected from March 2020 to July 2021, which were SARS-CoV-2 negative, 156 were positive (26%) for the following viruses: enterovirus (20.3%), human rhinovirus (HRV) (4.6%), human coronavirus OC43 (1.2%), human adenovirus (0.9%), human metapneumovirus (hMPV) (0.5%), influenza A virus (IAV) (0.3%), and human parainfluenza viruses (0.5%). To determine the genetic diversity and transmission route of the viruses, phylogenetic analyses were performed using genome sequences of the detected viruses. The IAV strain detected in this study was genetically similar to strains isolated in the USA, whereas the hMPV strain belonging to the A2b subtype formed a cluster with Kenyan strains. This study provides the first complete genomic sequences of HRV, IAV, and hMPV detected in Gabon, and provides insight into the circulation of respiratory viruses in the country.
Collapse
Affiliation(s)
- Georgelin Nguema Ondo
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Yuri Ushijima
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan; (Y.U.); (H.A.)
- Division of Biomedical Science, Institute of Medicine, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan; (Y.U.); (H.A.)
- Vietnam Research Station, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan;
| | - Saïdou Mahmoudou
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
| | - Rodrigue Bikangui
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
| | - Anne Marie Nkoma
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
| | - Marien Juliet Veraldy Magossou Mbadinga
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
| | - Ayong More
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
| | - Maradona Daouda Agbanrin
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
| | - Christelle M. Pemba
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan;
| | - Romuald Beh Mba
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
| | - Adegnika Ayola Akim
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
| | - Bertrand Lell
- Centre de Recherches Médicales de Lambaréné, Lambaréné BP.242, Gabon; (G.N.O.); (S.M.); (R.B.); (A.M.N.); (M.J.V.M.M.); (A.M.); (M.D.A.); (R.B.M.); (A.A.A.); (B.L.)
- Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Jiro Yasuda
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki 852-8523, Japan; (Y.U.); (H.A.)
- Department of Emerging Infectious Diseases, National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki 852-8523, Japan;
| |
Collapse
|
2
|
Sojati J, Zhang Y, Williams JV. Clinical human metapneumovirus isolates show distinct pathogenesis and inflammatory profiles but similar CD8 + T cell impairment. mSphere 2024; 9:e0057023. [PMID: 38197640 PMCID: PMC10826344 DOI: 10.1128/msphere.00570-23] [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: 09/27/2023] [Accepted: 12/01/2023] [Indexed: 01/11/2024] Open
Abstract
Human metapneumovirus (HMPV) is a negative-sense single-stranded RNA virus in the Pneumoviridae family and a leading cause of acute upper and lower respiratory infections, particularly in children, immunocompromised patients, and the elderly. Although nearly every person is infected with HMPV during early childhood, re-infections occur often, highlighting difficulty in building long-term immunity. Inflammatory responses, including PD-1-mediated impairment of virus-specific CD8+ T cells (TCD8), contribute to HMPV disease severity. HMPV strains are divided into four lineages: A1, A2, B1, and B2. However, little is known about immune responses to different viral subtypes. Here, we characterize responses to four HMPV clinical isolates-TN/94-344 (A1), TN/94-49 (A2), C2-202 (B1), and TN/96-35 (B2)-in vivo in C57BL/6 (B6) mice. TN/94-49 was avirulent, while TN/94-344, C2-202, and TN/96-35 showed varying degrees of weight loss and clinical disease. Differences in disease did not correlate to virus burden in upper or lower tracts. TN/94-49 HMPV exhibited highest nose titers and delayed lung clearance. Cytokine profiles differed between HMPV isolates, with TN/96-35 inducing the broadest lung inflammatory cytokines. TN/96-35 also showed lower HMPV burden and less weight loss than other virulent isolates, suggesting a more efficient antiviral response. Interestingly, disease correlated with higher expression of T-cell chemoattractant CXCL9. All isolates elicited PD-1 upregulation and decreased IFNγ and CD107a expression in virus-specific TCD8, with little difference between HMPV subtypes. This work uncovers previously uncharacterized variations in immune responses to clinical HMPV isolates of different lineages.IMPORTANCEThis study extensively explored differences in T-cell-mediated immunity between human metapneumovirus (HMPV) clinical isolates. Much existing HMPV research has been done with strains passaged extensively in cell lines, likely acquiring mutations advantageous to in vitro replication. Clinical isolates are collected directly from human patients and have undergone <10 passages, serving as more physiologically relevant models of HMPV infection. Additionally, existing animal studies of HMPV disease mainly focus on lung pathogenesis, while HMPV infects both upper and lower airways of humans. This work highlights distinct differences in HMPV burden in upper and lower tracts between clinical isolates. Lastly, this study uniquely explores differences in host immunity between all four HMPV genetic lineages. The predominant HMPV subtype in circulation varies seasonally; thus, understanding host responses to all subgroups is critical for developing effective HMPV vaccines.
Collapse
Affiliation(s)
- Jorna Sojati
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Program in Microbiology & Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yu Zhang
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John V. Williams
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Institute for Infection, Immunity, and Inflammation in Children, Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
3
|
Global Extension and Predominance of Human Metapneumovirus A2 Genotype with Partial G Gene Duplication. Viruses 2022; 14:v14051058. [PMID: 35632799 PMCID: PMC9146545 DOI: 10.3390/v14051058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/29/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Human metapneumovirus (HMPV) is an important respiratory pathogen and is divided in two main groups (A and B). HMPV strains with partial duplications (111-nt and 180-nt duplication) of the G gene have been reported in recent years. Since the initial reports, viruses with these characteristics have been reported in several countries. We analyzed all complete HMPV G gene ectodomain sequences available at GenBank to determine if viruses with 111-nt or 180-nt duplication have become the leading HMPV strains worldwide, and to describe their temporal and geographic distribution. We identified 1462 sequences that fulfilled study criteria (764 HMPV A and 698 HMPV B) reported from 37 countries. The most frequent HMPV A genotype was A2b2 (n = 366), and the most frequent B genotype was B2 (n = 374). A total of 84 sequences contained the 111-nt duplication, and 90 sequences contained the 180-nt duplication. Since 2016, viruses with a partial duplication comprise the most frequent HMPV A sequences globally and have displaced other HMPV A viruses in Asia, Europe, and South America; no sequences of viruses with partial duplication have been reported in North America or Africa so far. Continued surveillance of HMPV is required to identify the emergence and spread of epidemiologically relevant variants.
Collapse
|
4
|
Lefeuvre C, Salmona M, Bondeelle L, Houdouin V, Feghoul L, Jacquier H, Mercier-Delarue S, Bergeron A, LeGoff J. Frequent lower respiratory tract disease in hematological patients with parainfluenza virus type 3 infection. J Med Virol 2021; 93:6371-6376. [PMID: 34324206 DOI: 10.1002/jmv.27243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/26/2021] [Indexed: 11/12/2022]
Abstract
Human parainfluenza virus type 3 (HPIV-3) may cause lower respiratory tract infection disease (LRTI-D) after hematopoietic stem cell transplantation (HSCT). Most previous have studies focused on recipients of HSCT whereas data on characteristics and outcomes in patients with hematological malignancies (HMs) compared to non-hematological patients are limited. The prognostic value of viral load in respiratory specimens remains elusive. In a 2-year retrospective study, we determined the frequencies of LRTI-D in HM, HSCT, and in non-hematological patients, and HPIV-3 levels in respiratory tract secretions. Among 98 patients with HPIV-3 infection, including 31 HSCT and 40 HM, 36 had a diagnosis of LRTI-D. LRTI-D was significantly more frequent in patients with HM or HSCT (n = 32, 45.1%) than in non-hematological patients (n = 4, 14.8%) (p = 0.006). The median HPIV-3 loads were high in upper respiratory tract secretions regardless of the presence or absence of LRTI-D (8.3 log10 vs. 7.6 log10 TCID50 /106 cells). HPIV-3 loads in respiratory tract samples in HM were not significantly higher than those found in HSCT but significantly higher than in non-hematological patients (p = 0.007). In conclusion, LRTI-D was frequent in HM patients who were diagnosed with HPIV-3 infection.
Collapse
Affiliation(s)
- Caroline Lefeuvre
- Département des Agents Infectieux, Hôpital Saint-Louis, Virologie et Greffes, Paris, France
| | - Maud Salmona
- Département des Agents Infectieux, Hôpital Saint-Louis, Virologie et Greffes, Paris, France.,Inserm U976, Insight Team, Université de Paris, Paris, France
| | | | | | - Linda Feghoul
- Département des Agents Infectieux, Hôpital Saint-Louis, Virologie et Greffes, Paris, France.,Inserm U976, Insight Team, Université de Paris, Paris, France
| | - Hervé Jacquier
- Service de Bactériologie-Virologie, Hôpital Lariboisière, Paris, France
| | - Séverine Mercier-Delarue
- Département des Agents Infectieux, Hôpital Saint-Louis, Virologie et Greffes, Paris, France.,Inserm U976, Insight Team, Université de Paris, Paris, France
| | - Anne Bergeron
- Service de Pneumologie, Hôpital Saint-Louis, Paris, France.,ECSTRRA Team, Inserm, Université de Paris, Paris, France
| | - Jérôme LeGoff
- Département des Agents Infectieux, Hôpital Saint-Louis, Virologie et Greffes, Paris, France.,Inserm U976, Insight Team, Université de Paris, Paris, France
| |
Collapse
|
5
|
Abstract
Biological sex affects the outcome of diverse respiratory viral infections. The pathogenesis of respiratory infections caused by viruses ranging from respiratory syncytial virus to influenza viruses and severe acute respiratory syndrome coronavirus 2 differs between the sexes across the life course. Generally, males are more susceptible to severe outcomes from respiratory viral infections at younger and older ages. During reproductive years (i.e., after puberty and prior to menopause), females are often at greater risk than males for severe outcomes. Pregnancy and biological sex affect the pathogenesis of respiratory viral infections. In addition to sex differences in the pathogenesis of disease, there are consistent sex differences in responses to treatments, with females often developing greater immune responses but experiencing more adverse reactions than males. Animal models provide mechanistic insights into the causes of sex differences in respiratory virus pathogenesis and treatment outcomes, where available. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Rebecca L Ursin
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA 21205;
| | - Sabra L Klein
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA 21205; .,W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Maryland, USA 21205
| |
Collapse
|
6
|
Wang C, Wei T, Ma F, Wang H, Guo J, Chen A, Huang Y, Xie Z, Zheng L. Epidemiology and genotypic diversity of human metapneumovirus in paediatric patients with acute respiratory infection in Beijing, China. Virol J 2021; 18:40. [PMID: 33602245 PMCID: PMC7890387 DOI: 10.1186/s12985-021-01508-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute respiratory tract infections (ARTIs) causes high amounts of morbidity and mortality worldwide every year. Human metapneumovirus (HMPV) is a major pathogen of ARTIs in children. In this study, we aimed to investigate the epidemiology and genotypic diversity of HMPV in children hospitalized with ARTIs in Beijing, China. METHODS Hospitalized children aged < 14 years with ARTIs were enrolled from April 2017 to March 2018; nasopharyngeal aspirates were collected and subjected to real-time polymerase chain reaction tests for HMPV. HMPV-positive samples were genotyped based on a partial N gene. Whole genome sequences were determined for samples with high viral loads. RESULTS 4.08% (52/1276) enrolled paediatric patients were identified as having HMPV infection. The epidemic season is winter and early spring, children aged ≤ 4 years were more susceptible to HMPV infection (47/52, 90.38%). The co-infection rate were 36.54% (19/52), the most common co-infected virus were influenza and respiratory syncytial virus. The main diagnoses of HMPV infection were pneumonia (29/52, 55.77%) and bronchitis (23/52, 44.23%), while the main clinical manifestations were cough, fever, rhinorrhoea, and sneeze. Among 48 HMPV-positive specimens, A2b (19/48, 39.58%) and B1 (26/48, 54.17%) were the main epidemic subtypes. Patients with HMPV genotype A infection had a higher viral load compared to genotype B patients (6.07 vs. 5.37 log10 RNA copies/ml). Five complete sequences of HMPV were obtained. This is the first report of a whole genome sequence of HMPV-B1 isolated in China. CONCLUSIONS HMPV is an important respiratory pathogen in paediatric patients. Cases of HMPV infection could burden hospitals in the epidemic season. HMPV viral loads and genotypes have no correlation with co-infection or clinical characteristics.
Collapse
Affiliation(s)
- Chao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Tianli Wei
- Department of Pediatrics, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Fenlian Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Hao Wang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Jianqiang Guo
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Aijun Chen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Yiman Huang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China
| | - Zhiping Xie
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China.
| | - Lishu Zheng
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, China CDC, Beijing, China. .,Center for Biosafety Mega-Science, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
7
|
Widhidewi NW, Wiyatno A, Dewantari AK, Paramasatiari L, Aryastuti SA, Artika IN, Setiawan WD, Soebandrio A, Aye Myint KS, safari D. Identification of viral etiology of acute respiratory tract infections in children and adults in Tabanan, Bali, Indonesia. Access Microbiol 2020; 2:acmi000120. [PMID: 32974585 PMCID: PMC7494194 DOI: 10.1099/acmi.0.000120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/31/2020] [Indexed: 12/04/2022] Open
Abstract
Acute respiratory tract infection (ARTI) is the most common infectious disease in humans worldwide. The morbidity and mortality rates are high, especially in developing countries from Southeast Asia and Africa. While ARTI is commonly associated with viruses, there is limited data on the spectrum of viruses causing ARTI in developing countries, including Indonesia. This study was based on utilizing molecular techniques targeting a panel of 11 endemic and emerging respiratory viral pathogens including zoonotic viruses in a cohort of children and adults presenting at Tabanan General Hospital, Bali, with acute respiratory illness, from January to November 2017. In total, 98 out of 200 samples (49.0 %) tested positive for viruses. Our study confirmed 64.3 % viral etiology in children and 12.2 % in adults. Viruses that were detected were Herpesviridae (15.0 %) followed by enteroviruses (12.0 %), influenza A virus (11.5 %), respiratory syncytial virus (8.0 %), Adenoviridae (6.5 %), human metapneumovirus (3.5 %), Paramyxoviridae (2.0 %), bocavirus (1.0 %) and Coronaviridae (0.5 %). The study sheds light on the viral spectrum of ARTI in children and adults in Tabanan, Bali, Indonesia.
Collapse
Affiliation(s)
- Ni Wayan Widhidewi
- Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya, No. 6 Jakarta, Indonesia
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - Ageng Wiyatno
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | | | - Lila Paramasatiari
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - Sri Agung Aryastuti
- Faculty of Medicine, Universitas Warmadewa, Jl. Terompong No.24 Denpasar, Bali, Indonesia
| | - I Nengah Artika
- Tabanan General Hospital, Jl. Pahlawan, Tabanan, Bali, Indonesia
| | | | - Amin Soebandrio
- Faculty of Medicine, Universitas Indonesia, Jl. Salemba Raya, No. 6 Jakarta, Indonesia
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | - Khin Saw Aye Myint
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| | - Dodi safari
- Eijkman Institute of Molecular Biology, Jl. Diponegoro No. 69, Jakarta, Indonesia
| |
Collapse
|
8
|
Setianingsih TY, Wiyatno A, Hartono TS, Hindawati E, Rosamarlina, Dewantari AK, Myint KS, Lisdawati V, Safari D. Detection of multiple viral sequences in the respiratory tract samples of suspected Middle East respiratory syndrome coronavirus patients in Jakarta, Indonesia 2015-2016. Int J Infect Dis 2019; 86:102-107. [PMID: 31238156 PMCID: PMC7110706 DOI: 10.1016/j.ijid.2019.06.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES The identification and analysis of viral etiological agents from suspected Middle East respiratory syndrome coronavirus (MERS-CoV) cases admitted to Prof. Dr. Sulianti Saroso Infectious Disease Hospital (IDH) using molecular assays. METHODS Biological samples were collected from 13 hospitalized patients suspected of MERS-CoV infection in Prof. Dr. Sulianti Saroso IDH from July 2015 to December 2016. The majority of patients presented with pneumonia, with symptoms including fever (≥37.5 °C), labored breathing, and cough, and with a history of travel to the Middle East. Viral RNA was isolated and converted to cDNA, which was used as a template for the detection of 12 viral panels using conventional PCR and sequencing. RESULTS Viral etiological agents detected in the patients were enterovirus D68, dengue virus type 3, rhinovirus C, human coronavirus 229E, herpes simplex virus type 1, influenza virus H1N1, influenza virus H3N2, human metapneumovirus, and rhinovirus A60. CONCLUSIONS The sequences of nine viral agents under different taxa were detected in suspected MERS-CoV patients, including influenza virus, paramyxovirus, coronavirus, enterovirus, human metapneumovirus, and herpesvirus.
Collapse
Affiliation(s)
| | - Ageng Wiyatno
- Eijkman Institute of Molecular Biology, Jakarta, Indonesia
| | | | - Evi Hindawati
- Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia
| | - Rosamarlina
- Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia
| | | | - Khin Saw Myint
- Eijkman Institute of Molecular Biology, Jakarta, Indonesia
| | - Vivi Lisdawati
- Prof. Dr. Sulianti Saroso Infectious Disease Hospital, Jakarta, Indonesia
| | - Dodi Safari
- Eijkman Institute of Molecular Biology, Jakarta, Indonesia.
| |
Collapse
|
9
|
Vidaur L, Totorika I, Montes M, Vicente D, Rello J, Cilla G. Human metapneumovirus as cause of severe community-acquired pneumonia in adults: insights from a ten-year molecular and epidemiological analysis. Ann Intensive Care 2019; 9:86. [PMID: 31342206 PMCID: PMC6656825 DOI: 10.1186/s13613-019-0559-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/16/2019] [Indexed: 12/17/2022] Open
Abstract
Background Information on the clinical, epidemiological and molecular characterization of human metapneumovirus in critically ill adult patients with severe community-acquired pneumonia (CAP) and the role of biomarkers identifying bacterial coinfection is scarce. Methods This is a retrospective epidemiological study of adult patients with hMPV severe CAP admitted to ICU during a ten-year period with admission PSI score ≥ 3. Results The 92.8% of the 28 patients with severe CAP due to human metapneumovirus were detected during the first half of the year. Median age was 62 years and 60.7% were male. The genotyping of isolated human metapneumovirus showed group B predominance (60.7%). All patients had acute respiratory failure. Median APACHE II and SOFA score were 13 and 6.55, respectively. The 25% were coinfected with Streptococcus pneumoniae. 60.7% of the patients had shock at admission and 50% underwent mechanical ventilation. Seven patients developed ARDS, three of them younger than 60 years and without comorbidities. Mortality in ICU was 14.3%. Among survivors, ICU and hospital stay were 6.5 and 14 days, respectively. Plasma levels of procalcitonin were higher in patients with bacterial coinfection (18.2 vs 0.54; p < 0.05). The levels of C-reactive protein, however, were similar. Conclusion Human metapneumovirus was associated with severe CAP requiring ICU admission among elderly patients or patients with comorbidities, but also in healthy young subjects. These patients often underwent mechanical ventilation with elevated health resource consumption. While one out of four patients showed pneumococcal coinfection, plasma procalcitonin helped to implement antimicrobial stewardship. Electronic supplementary material The online version of this article (10.1186/s13613-019-0559-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Loreto Vidaur
- Critical Care Department, Donostia University Hospital-Biodonostia Health Research Institute, San Sebastian, Guipuzcoa, Spain. .,CIBERES, Institute of Health Carlos III, Madrid, Spain.
| | - Izarne Totorika
- Critical Care Department, Donostia University Hospital-Biodonostia Health Research Institute, San Sebastian, Guipuzcoa, Spain
| | - Milagrosa Montes
- Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, San Sebastian, Guipuzcoa, Spain
| | - Diego Vicente
- Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, San Sebastian, Guipuzcoa, Spain.,Faculty of Medicine, University of Basque Country (UPV/EHU), San Sebastian, Guipuzcoa, Spain
| | - Jordi Rello
- CIBERES, Institute of Health Carlos III, Madrid, Spain.,Research Institute Vall d`Hebron University Hospital (VHIR), Barcelona, Spain
| | - Gustavo Cilla
- Microbiology Department, Donostia University Hospital-Biodonostia Health Research Institute, San Sebastian, Guipuzcoa, Spain
| |
Collapse
|
10
|
Rahman MZ, Sumiya M, Sahabuddin M, Pell LG, Gubbay JB, Rahman R, Momtaz F, Azmuda N, Shanta SS, Jahan I, Rahman M, Mahmud AA, Roth DE, Morris SK. Genetic characterization of human metapneumovirus identified through community and facility-based surveillance of infants in Dhaka, Bangladesh. J Med Virol 2018; 91:549-554. [PMID: 30372530 DOI: 10.1002/jmv.25351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/16/2018] [Indexed: 11/09/2022]
Abstract
BACKGROUND Acute respiratory infection (ARI) is a leading cause of morbidity and mortality in children in low and middle-income countries. Human metapneumovirus (hMPV) is one of the most common viral etiological agents for ARIs in children. OBJECTIVES In this study, we explored the genotypic diversity and the epidemiology of hMPV among infants in Dhaka, Bangladesh. STUDY DESIGN Between December 2014 and August 2016, a total of 3810 mid-turbinate nasal swab samples were collected from infants (0 to 6 months of age) who met clinical ARI criteria, as a part of a prospective ARI cohort study. hMPV was detected using polymerase chain reaction, and genotyped by sequencing and phylogenetic analysis. RESULTS hMPV was identified in 206 (5.4%) nasal swab specimens. One-tenth of the hMPV-positive swabs (n = 19) were also positive for other respiratory viruses. hMPV activity peaked in January and September in 2015; however, no seasonal pattern of hMPV infection was detected. Phylogenetic analyses of the N and F gene-fragments revealed that the hMPV strains circulating in Dhaka, Bangladesh, belonged to three genotypes: A2b, A2c, and B1. Genotype A (57%) was the predominant hMPV genotype circulating in Bangladesh during the study period. CONCLUSION This study describes both the epidemiology of hMPV infection and its genotypic strain diversity in Dhaka, Bangladesh.
Collapse
Affiliation(s)
| | - Mariya Sumiya
- Infectious Diseases Division (IDD), icddr,b, Dhaka, Bangladesh
| | | | - Lisa G Pell
- Centre for Global Child Health and Child Health Evaluative Sciences, Sick Kids Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jonathan B Gubbay
- Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada.,Public Health Ontario, Toronto, Ontario, Canada
| | - Rajibur Rahman
- Infectious Diseases Division (IDD), icddr,b, Dhaka, Bangladesh
| | - Farhana Momtaz
- Infectious Diseases Division (IDD), icddr,b, Dhaka, Bangladesh
| | - Nafisa Azmuda
- Department of Microbiology, Jahangirnagar University, Dhaka, Bangladesh
| | - Shaila S Shanta
- Nutrition and Clinical Services Division (NCSD), icddr,b, Dhaka, Bangladesh
| | - Ishrat Jahan
- Maternal and Child Health Training Institute (MCHTI), Ministry of Health and Family Welfare, Government of Bangladesh, Dhaka, Bangladesh
| | | | - Abdullah A Mahmud
- Nutrition and Clinical Services Division (NCSD), icddr,b, Dhaka, Bangladesh
| | - Daniel E Roth
- Centre for Global Child Health and Child Health Evaluative Sciences, Sick Kids Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Shaun K Morris
- Centre for Global Child Health and Child Health Evaluative Sciences, Sick Kids Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|