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Luka MM, Otieno JR, Kamau E, Morobe JM, Murunga N, Adema I, Nyiro JU, Macharia PM, Bigogo G, Otieno NA, Nyawanda BO, Rabaa MA, Emukule GO, Onyango C, Munywoki PK, Agoti CN, Nokes DJ. Rhinovirus dynamics across different social structures. NPJ VIRUSES 2023; 1:6. [PMID: 38665239 PMCID: PMC11041716 DOI: 10.1038/s44298-023-00008-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/30/2023] [Indexed: 04/28/2024]
Abstract
Rhinoviruses (RV), common human respiratory viruses, exhibit significant antigenic diversity, yet their dynamics across distinct social structures remain poorly understood. Our study delves into RV dynamics within Kenya by analysing VP4/2 sequences across four different social structures: households, a public primary school, outpatient clinics in the Kilifi Health and Demographics Surveillance System (HDSS), and countrywide hospital admissions and outpatients. The study revealed the greatest diversity of RV infections at the countrywide level (114 types), followed by the Kilifi HDSS (78 types), the school (47 types), and households (40 types), cumulatively representing >90% of all known RV types. Notably, RV diversity correlated directly with the size of the population under observation, and several RV type variants occasionally fuelled RV infection waves. Our findings highlight the critical role of social structures in shaping RV dynamics, information that can be leveraged to enhance public health strategies. Future research should incorporate whole-genome analysis to understand fine-scale evolution across various social structures.
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Affiliation(s)
- Martha M. Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Present Address: School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, G12 8QQ UK
| | - James R. Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - John Mwita Morobe
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Irene Adema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Joyce Uchi Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Peter M. Macharia
- Population & Health Impact Surveillance Group, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Health Informatics, Computing, and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK
- Department of Public Health, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | | | - Maia A. Rabaa
- Coronavirus and Other Respiratory Viruses Division (CORVD), National Center for Immunization and Respiratory Diseases (NCIRD), U.S. Centers of Disease Control and Prevention (CDC), Atlanta, GA USA
| | - Gideon O. Emukule
- U.S. Centers of Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Clayton Onyango
- U.S. Centers of Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Patrick K. Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- U.S. Centers of Disease Control and Prevention (CDC), Nairobi, Kenya
| | - Charles N. Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- Department of Public Health, Pwani University, Kilifi, Kenya
| | - D. James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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Ong HH, Liu J, Oo Y, Thong M, Wang DY, Chow VT. Prolonged Primary Rhinovirus Infection of Human Nasal Epithelial Cells Diminishes the Viral Load of Secondary Influenza H3N2 Infection via the Antiviral State Mediated by RIG-I and Interferon-Stimulated Genes. Cells 2023; 12:cells12081152. [PMID: 37190061 DOI: 10.3390/cells12081152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/23/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023] Open
Abstract
Our previous study revealed that prolonged human rhinovirus (HRV) infection rapidly induces antiviral interferons (IFNs) and chemokines during the acute stage of infection. It also showed that expression levels of RIG-I and interferon-stimulated genes (ISGs) were sustained in tandem with the persistent expression of HRV RNA and HRV proteins at the late stage of the 14-day infection period. Some studies have explored the protective effects of initial acute HRV infection on secondary influenza A virus (IAV) infection. However, the susceptibility of human nasal epithelial cells (hNECs) to re-infection by the same HRV serotype, and to secondary IAV infection following prolonged primary HRV infection, has not been studied in detail. Therefore, the aim of this study was to investigate the effects and underlying mechanisms of HRV persistence on the susceptibility of hNECs against HRV re-infection and secondary IAV infection. We analyzed the viral replication and innate immune responses of hNECs infected with the same HRV serotype A16 and IAV H3N2 at 14 days after initial HRV-A16 infection. Prolonged primary HRV infection significantly diminished the IAV load of secondary H3N2 infection, but not the HRV load of HRV-A16 re-infection. The reduced IAV load of secondary H3N2 infection may be explained by increased baseline expression levels of RIG-I and ISGs, specifically MX1 and IFITM1, which are induced by prolonged primary HRV infection. As is congruent with this finding, in those cells that received early and multi-dose pre-treatment with Rupintrivir (HRV 3C protease inhibitor) prior to secondary IAV infection, the reduction in IAV load was abolished compared to the group without pre-treatment with Rupintrivir. In conclusion, the antiviral state induced from prolonged primary HRV infection mediated by RIG-I and ISGs (including MX1 and IFITM1) can confer a protective innate immune defense mechanism against secondary influenza infection.
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Affiliation(s)
- Hsiao Hui Ong
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Jing Liu
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Yukei Oo
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Mark Thong
- Department of Otolaryngology-Head & Neck Surgery, National University Health System, Singapore 119228, Singapore
| | - De Yun Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Vincent T Chow
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
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Giardina FAM, Piralla A, Ferrari G, Zavaglio F, Cassaniti I, Baldanti F. Molecular Epidemiology of Rhinovirus/Enterovirus and Their Role on Cause Severe and Prolonged Infection in Hospitalized Patients. Microorganisms 2022; 10:microorganisms10040755. [PMID: 35456806 PMCID: PMC9030097 DOI: 10.3390/microorganisms10040755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 02/04/2023] Open
Abstract
Rhinovirus is one of the most common respiratory viruses, causing both upper and lower respiratory tract infections. It affects mainly children and could cause prolonged infections, especially in immunocompromised patients. Here we report our data on a 15-month surveillance of Rhinovirus seasonality and circulation in Lombardy Region, Italy. All rhinovirus/enterovirus-positive samples were amplified with RT-PCR for the VP4-VP2 region to assign the correct genotype. The median age of RV/EV-positive patients is 9 years, with a range of 0–96. RV-A and RV-C were detected in the majority of cases, while RV-B accounted for less than 10% of cases. An enterovirus species was detected in 6.45% of the cases. A total of 7% of the patients included in this study had a prolonged infection with a median duration of 62 days. All these patients were immunocompromised and most of them were pediatric with an RV-A infection. Two outbreaks were identified, mainly in the neonatal intensive care unit (NICU) and Oncohematology Department, caused by RV A89 and C43, respectively. Nearly 4.5% of the patients were admitted to the ICU requiring mechanical ventilation; all of which had preexisting comorbidities.
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Affiliation(s)
- Federica A. M. Giardina
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.A.M.G.); (G.F.); (F.Z.); (I.C.); (F.B.)
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.A.M.G.); (G.F.); (F.Z.); (I.C.); (F.B.)
- Correspondence: ; Tel.: +39-038-250-2420
| | - Guglielmo Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.A.M.G.); (G.F.); (F.Z.); (I.C.); (F.B.)
| | - Federica Zavaglio
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.A.M.G.); (G.F.); (F.Z.); (I.C.); (F.B.)
| | - Irene Cassaniti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.A.M.G.); (G.F.); (F.Z.); (I.C.); (F.B.)
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy; (F.A.M.G.); (G.F.); (F.Z.); (I.C.); (F.B.)
- Department of Clinical-Surgical, Diagnostic and Pediatric Sciences, Università degli Studi di Pavia, 27100 Pavia, Italy
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Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya. Sci Rep 2022; 12:202. [PMID: 34997042 PMCID: PMC8742071 DOI: 10.1038/s41598-021-03987-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/02/2021] [Indexed: 01/30/2023] Open
Abstract
Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.
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Mwita Morobe J, Kamau E, Murunga N, Gatua W, Luka MM, Lewa C, Cheruiyot R, Mutunga M, Odundo C, James Nokes D, Agoti CN. Trends and Intensity of Rhinovirus Invasions in Kilifi, Coastal Kenya, Over a 12-Year Period, 2007-2018. Open Forum Infect Dis 2021; 8:ofab571. [PMID: 34988244 PMCID: PMC8694214 DOI: 10.1093/ofid/ofab571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/11/2021] [Indexed: 12/05/2022] Open
Abstract
Background Rhinoviruses (RVs) are ubiquitous pathogens and the principal etiological agents of common cold. Despite the high frequency of RV infections, data describing their long-term epidemiological patterns in a defined population remain limited. Methods Here, we analyzed 1070 VP4/VP2 genomic region sequences sampled at Kilifi County Hospital on the Kenya coast. The samples were collected between 2007 and 2018 from hospitalized pediatric patients (<60 months of age) with acute respiratory illness. Results Of 7231 children enrolled, RV was detected in 1497 (20.7%) and VP4/VP2 sequences were recovered from 1070 samples (71.5%). A total of 144 different RV types were identified (67 Rhinovirus A, 18 Rhinovirus B, and 59 Rhinovirus C) and at any month, several types co-circulated with alternating predominance. Within types, multiple genetically divergent variants were observed. Ongoing RV infections through time appeared to be a combination of (1) persistent types (observed up to 7 consecutive months), (2) reintroduced genetically distinct variants, and (3) new invasions (average of 8 new types annually). Conclusions Sustained RV presence in the Kilifi community is mainly due to frequent invasion by new types and variants rather than continuous transmission of locally established types/variants.
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Affiliation(s)
- John Mwita Morobe
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nickson Murunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Winfred Gatua
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Clement Lewa
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Robinson Cheruiyot
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Martin Mutunga
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Calleb Odundo
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research, Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
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Bioinformatics analysis of rhinovirus capsid proteins VP1-4 sequences for cross-serotype vaccine development. J Infect Public Health 2021; 14:1603-1611. [PMID: 34624714 DOI: 10.1016/j.jiph.2021.09.001] [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: 07/11/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Rhinoviruses (RV) are associated with the development and exacerbations of asthma and chronic obstructive pulmonary disease. They've also been linked to more severe diseases like pneumonia, acute bronchiolitis, croup, and otitis media. Because of the hypervariable sequences in the same serotypes, no effective vaccine against rhinoviruses has been developed to date. With the availability of new full-length genome sequences for all RV-A and RV-B serotyped strains, this study used bioinformatics to find a suitable RV strain with the highest similarity matrices to the other strains. METHODS The full genomic sequences of all known different RV-A and -B prototypes were downloaded from the National Centre for Biotechnology Information (NCBI) and divided into minor low-density lipoprotein receptor (LDLR) and major intercellular adhesion molecule groups (ICAM). The sequences were edited using Biological Sequence Alignment Editor, v 7.2.0 (BioEdit software) to study each capsid protein (VP1, VP2, VP3, and VP4) and analyzed using the EMBL-EBI ClustalW server and the more current Clustal Omega tool for the calculation of the identities and similarities. RESULTS We analyzed and predicted immunogenic motifs from capsid proteins that are conserved across distinct RV serotypes using a bioinformatics technique. The amino acid sequences of VP3 were found to be the most varied, while VP4 was the most conserved protein among all RV-A and RV-B strains. Among all strains studied, RV-74 demonstrated the highest degree of homology to other strains and could be a potential genetic source for recombinant protein production. Nine highly conserved regions with a minimum length of 9-mers were identified, which could serve as potential immune targets against rhinoviruses. CONCLUSION Therefore, bioinformatics analysis conducted in the current study has paved the way for the selection of immunogenic targets. Bioinformatically, the ideal strain's capsid protein is suggested to contain the most common RVs immunogenic sites.
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Kiseleva I, Ksenafontov A. COVID-19 Shuts Doors to Flu but Keeps Them Open to Rhinoviruses. BIOLOGY 2021; 10:biology10080733. [PMID: 34439965 PMCID: PMC8389621 DOI: 10.3390/biology10080733] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022]
Abstract
Simple Summary Ten years have passed since the beginning of the H1N1pdm09 flu pandemic. No sooner had humanity recovered from its consequences than a new attack came—the COVID-19 pandemic. What happens to other respiratory infectious diseases during a global disaster such as the COVID-19 pandemic? The pandemic brought about by the novel SARS-CoV-2 virus has disrupted many well-established epidemiological and pathogenetic relationships, as well as mechanisms affecting infections with other respiratory viruses. The level of circulation of many respiratory pathogens has changed significantly. For instance, global influenza activity is at much lower levels than expected. In many regions, the influenza season has not started. Intriguingly, the COVID-19 pandemic did not substantially affect the spread of human rhinoviruses. In this review, the main properties of epidemiologically significant respiratory viruses such as SARS-CoV-2, influenza virus, and human rhinovirus are described. Abstract It is well known that rhinoviruses are distributed across the globe and are the most common cause of the common cold in all age groups. Rhinoviruses are widely considered to be harmless because they are generally perceived as respiratory viruses only capable of causing mild disease. However, they may also infect the lower respiratory tract, inducing chronic obstructive pulmonary disease and exacerbations of asthma, bronchiolitis, etc. The role of rhinoviruses in pathogenesis and the epidemiological process is underestimated, and they need to be intensively studied. In the light of recent data, it is now known that rhinoviruses could be one of the key epidemiological barriers that may influence the spread of influenza and novel coronaviruses. It has been reported that endemic human rhinoviruses delayed the development of the H1N1pdm09 influenza pandemic through viral interference. Moreover, human rhinoviruses have been suggested to block SARS-CoV-2 replication in the airways by triggering an interferon response. In this review, we summarized the main biological characteristics of genetically distinct viruses such as rhinoviruses, influenza viruses, and SARS-CoV-2 in an attempt to illuminate their main discrepancies and similarities. We hope that this comparative analysis will help us to better understand in which direction research in this area should move.
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Affiliation(s)
- Irina Kiseleva
- Department of Virology, Institute of Experimental Medicine, 197376 Saint Petersburg, Russia
- Correspondence:
| | - Andrey Ksenafontov
- Department of Etiology and Epidemiology, Smorodintsev Research Institute of Influenza, 197376 Saint Petersburg, Russia;
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van der Zalm MM, Walters E, Claassen M, Palmer M, Seddon JA, Demers AM, Shaw ML, McCollum ED, van Zyl GU, Hesseling AC. High burden of viral respiratory co-infections in a cohort of children with suspected pulmonary tuberculosis. BMC Infect Dis 2020; 20:924. [PMID: 33276721 PMCID: PMC7716283 DOI: 10.1186/s12879-020-05653-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022] Open
Abstract
Background The presentation of pulmonary tuberculosis (PTB) in young children is often clinically indistinguishable from other common respiratory illnesses, which are frequently infections of viral aetiology. As little is known about the role of viruses in children with PTB, we investigated the prevalence of respiratory viruses in children with suspected PTB at presentation and follow-up. Methods In an observational cohort study, children < 13 years were routinely investigated for suspected PTB in Cape Town, South Africa between December 2015 and September 2017 and followed up for 24 weeks. Nasopharyngeal aspirates (NPAs) were tested for respiratory viruses using multiplex PCR at enrolment, week 4 and 8. Results Seventy-three children were enrolled [median age 22.0 months; (interquartile range 10.0–48.0); 56.2% male and 17.8% HIV-infected. Anti-tuberculosis treatment was initiated in 54.8%; of these 50.0% had bacteriologically confirmed TB. At enrolment, ≥1 virus were detected in 95.9% (70/73) children; most commonly human rhinovirus (HRV) (74.0%). HRV was more frequently detected in TB cases (85%) compared to ill controls (60.6%) (p = 0.02). Multiple viruses were detected in 71.2% of all children; 80% of TB cases and 60.6% of ill controls (p = 0.07). At follow-up, ≥1 respiratory virus was detected in 92.2% (47/51) at week 4, and 94.2% (49/52) at week 8. Conclusions We found a high prevalence of viral respiratory co-infections in children investigated for PTB, irrespective of final PTB diagnosis, which remained high during follow up. Future work should include investigating the whole respiratory ecosystem in combination with pathogen- specific immune responses.
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Affiliation(s)
- M M van der Zalm
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - E Walters
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Department of Paediatrics, Great North Children's Hospital, Newcastle-Upon-Tyne Health Trust, Newcastle upon Tyne, UK
| | - M Claassen
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - M Palmer
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - J A Seddon
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,Department of Infectious Diseases, Imperial College London, London, UK
| | - A M Demers
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - M L Shaw
- Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - E D McCollum
- Eudowood Division of Pediatric Respiratory Sciences, School of Medicine, Johns Hopkins University, Baltimore, USA.,Global Program in Respiratory Sciences, Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA.,Health Systems Program, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - G U van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University and National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - A C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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9
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Luka MM, Kamau E, Adema I, Munywoki PK, Otieno GP, Gicheru E, Gichuki A, Kibinge N, Agoti CN, Nokes DJ. Molecular Epidemiology of Human Rhinovirus From 1-Year Surveillance Within a School Setting in Rural Coastal Kenya. Open Forum Infect Dis 2020; 7:ofaa385. [PMID: 33094115 PMCID: PMC7568438 DOI: 10.1093/ofid/ofaa385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/21/2020] [Indexed: 01/12/2023] Open
Abstract
Background Human rhinovirus (HRV) is the most common cause of the common cold but may also lead to more severe respiratory illness in vulnerable populations. The epidemiology and genetic diversity of HRV within a school setting have not been previously described. The objective of this study was to characterize HRV molecular epidemiology in a primary school in a rural location of Kenya. Methods Between May 2017 and April 2018, over 3 school terms, we collected 1859 nasopharyngeal swabs (NPS) from pupils and teachers with symptoms of acute respiratory infection in a public primary school in Kilifi County, coastal Kenya. The samples were tested for HRV using real-time reverse transcription polymerase chain reaction. HRV-positive samples were sequenced in the VP4/VP2 coding region for species and genotype classification. Results A total of 307 NPS (16.4%) from 164 individuals were HRV positive, and 253 (82.4%) were successfully sequenced. The proportion of HRV in the lower primary classes was higher (19.8%) than upper primary classes (12.2%; P < .001). HRV-A was the most common species (134/253; 53.0%), followed by HRV-C (73/253; 28.9%) and HRV-B (46/253; 18.2%). Phylogenetic analysis identified 47 HRV genotypes. The most common genotypes were A2 and B70. Numerous (up to 22 in 1 school term) genotypes circulated simultaneously, there was no individual re-infection with the same genotype, and no genotype was detected in all 3 school terms. Conclusions HRV was frequently detected among school-going children with mild acute respiratory illness symptoms, particularly in the younger age groups (<5-year-olds). Multiple HRV introductions were observed that were characterized by considerable genotype diversity.
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Affiliation(s)
- Martha M Luka
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Irene Adema
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Grieven P Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Elijah Gicheru
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Alex Gichuki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Nelson Kibinge
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya
| | - Charles N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,Department of Public Health, Pwani University, Kilifi, Kenya
| | - D James Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research - Coast, Kilifi, Kenya.,School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
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10
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Abstract
Viral pneumonia is an important cause of death and morbidity among infants worldwide. Transmission of non-influenza respiratory viruses in households can inform preventative interventions and has not been well-characterised in South Asia. From April 2011 to April 2012, household members of pregnant women enrolled in a randomised trial of influenza vaccine in rural Nepal were surveyed weekly for respiratory illness until 180 days after birth. Nasal swabs were tested by polymerase chain reaction for respiratory viruses in symptomatic individuals. A transmission event was defined as a secondary case of the same virus within 14 days of initial infection within a household. From 555 households, 825 initial viral illness episodes occurred, resulting in 79 transmission events. The overall incidence of transmission was 1.14 events per 100 person-weeks. Risk of transmission incidence was associated with an index case age 1–4 years (incidence rate ratio (IRR) 2.35; 95% confidence interval (CI) 1.40–3.96), coinfection as initial infection (IRR 1.94; 95% CI 1.05–3.61) and no electricity in household (IRR 2.70; 95% CI 1.41–5.00). Preventive interventions targeting preschool-age children in households in resource-limited settings may decrease the risk of transmission to vulnerable household members, such as young infants.
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11
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Morobe JM, Nyiro JU, Brand S, Kamau E, Gicheru E, Eyase F, Otieno GP, Munywoki PK, Agoti CN, Nokes DJ. Human rhinovirus spatial-temporal epidemiology in rural coastal Kenya, 2015-2016, observed through outpatient surveillance. Wellcome Open Res 2019; 3:128. [PMID: 30483602 PMCID: PMC6234744 DOI: 10.12688/wellcomeopenres.14836.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Human rhinovirus (HRV) is the predominant cause of upper respiratory tract infections, resulting in a significant public health burden. The virus circulates as many different types (168), each generating strong homologous, but weak heterotypic, immunity. The influence of these features on transmission patterns of HRV in the community is understudied. Methods: Nasopharyngeal swabs were collected from patients with symptoms of acute respiratory infection (ARI) at nine out-patient facilities across a Health and Demographic Surveillance System between December 2015 and November 2016. HRV was diagnosed by real-time RT-PCR, and the VP4/VP2 genomic region of the positive samples sequenced. Phylogenetic analysis was used to determine the HRV types. Classification models and G-test statistic were used to investigate HRV type spatial distribution. Demographic characteristics and clinical features of ARI were also compared. Results: Of 5,744 NPS samples collected, HRV was detected in 1057 (18.4%), of which 817 (77.3%) were successfully sequenced. HRV species A, B and C were identified in 360 (44.1%), 67 (8.2%) and 390 (47.7%) samples, respectively. In total, 87 types were determined: 39, 10 and 38 occurred within species A, B and C, respectively. HRV types presented heterogeneous temporal patterns of persistence. Spatially, identical types occurred over a wide distance at similar times, but there was statistically significant evidence for clustering of types between health facilities in close proximity or linked by major road networks. Conclusion: This study records a high prevalence of HRV in out-patient presentations exhibiting high type diversity. Patterns of occurrence suggest frequent and independent community invasion of different types. Temporal differences of persistence between types may reflect variation in type-specific population immunity. Spatial patterns suggest either rapid spread or multiple invasions of the same type, but evidence of similar types amongst close health facilities, or along road systems, indicate type partitioning structured by local spread.
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Affiliation(s)
- John Mwita Morobe
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, +254, Kenya.,Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Joyce U Nyiro
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Samuel Brand
- Zeeman Institute of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK
| | - Everlyn Kamau
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Elijah Gicheru
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Fredrick Eyase
- Institute of Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, +254, Kenya
| | - Grieven P Otieno
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya
| | - Patrick K Munywoki
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Public Health, Pwani University, Kilifi, +254, Kenya
| | - C N Agoti
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Public Health, Pwani University, Kilifi, +254, Kenya
| | - D J Nokes
- Epidemiology and Demography Department, KEMRI-Wellcome Trust Research Programme, Kilifi, +254, Kenya.,Zeeman Institute of Systems Biology and Infectious Disease Research (SBIDER), University of Warwick, Coventry, UK.,School of Life Sciences, University of Warwick, Coventry, UK.,Public Health, Pwani University, Kilifi, +254, Kenya
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