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Feng A, Xu J, Fu Y, Li Z, Liu C, Luan X, Wang X, Sun Q, Yang Y, Rong R. An integrative pharmacology-based study on the efficacy and mechanism of essential oil of Chaihu Guizhi Decoction on influenza A virus induced pneumonia in mice. JOURNAL OF ETHNOPHARMACOLOGY 2025; 336:118654. [PMID: 39098621 DOI: 10.1016/j.jep.2024.118654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/20/2024] [Accepted: 07/31/2024] [Indexed: 08/06/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Chaihu Guizhi Decoction (CGD) has a long history of use in China for the treatment of influenza, which involves the use of a variety of aromatic herbs. Our previous studies have found that the contents of aromatic constituents in CGD affected the efficacy of treatment of influenza-infected mice, suggesting a clue that essential oil from CGD may play a relatively important role in ameliorating influenza induced pneumonia. AIM OF THE STUDY To evaluate the anti-influenza potential of essential oil derived from Chaihu Guizhi Decoction (CGD-EO), to characterize and predict the key active components in CGD-EO, and to explore the mechanism of action of CGD-EO. MATERIALS AND METHODS CGD-EO was obtained by steam distillation, and the components of the essential oil were characterized by gas chromatography-mass spectrometry (GC-MS) in conjunction with the retention index. The constituents absorbed into the blood of mice treated with CGD-EO were analyzed by headspace solid phase microextraction gas chromatography/mass spectrometry (HS-SPME-GC/MS). The potential anti-influenza active constituents and their possible action pathway were predicted by simulation using a network pharmacology approach. The protective effect of CGD-EO and its major components on H1N1/PR8-infected cells was determined using the CCK8 assay kit. Mice infected with influenza A virus H1N1/PR8 were administered different doses of CGD-EO orally and the body weights and lung weights were recorded. Mice with varying degrees of H1N1/PR8 infection were administered CGD-EO orally, and their daily weight, water consumption, and clinical indicators were recorded. Necropsies were conducted on days 3 and 5, during which lung weights were measured and lung tissues were preserved. Furthermore, the mRNA expression of the H1N1/PR8 virus and inflammatory factors in lung tissue was analyzed using RT-qPCR. RESULTS (E)-cinnamaldehyde was the most abundant compound in the CGD-EO. The results of serum medicinal chemistry combined with network pharmacological analysis indicated that (E)-cinnamaldehyde and 3-phenyl-2-propenal may be potential active components of the CGD-EO anti-influenza, and may be involved in the NF-κB signalling pathway. In vitro studies have demonstrated that both CGD-EO and cinnamaldehyde exert a protective effect on MDCK cells infected with H1N1/PR8. In a 0.5 TCID50 H1N1/PR8-induced influenza model, mice treated with CGD-EO at a dose of 63.50 μg/kg exhibited a reduction in lung index, pathological lung lesions, and H1N1/PR8 viral gene levels. In addition, CGD-EO treatment was found to regulate the levels of inflammatory cytokines, including IL-6, TNF-α, and IFN-γ. Moreover, following three days of administration, an upregulation of NF-κB mRNA levels in mouse lung tissue was observed in response to CGD-EO treatment. CONCLUSIONS The findings of our study indicate CGD-EO exerts a protective effect against H1N1-induced cytopathic lesions in vitro and is capable of alleviating H1N1-induced pneumonitis in mice. Moreover, it appears to be more efficacious in the treatment of mild symptoms of H1N1 infection. Studies have demonstrated that CGD-EO has antiviral potential to attenuate influenza-induced lung injury by modulating inflammatory cytokines and NF-κB signalling pathways during the early stages of influenza infection. It is possible that (E)-cinnamaldehyde is a potential active ingredient in the anti-influenza efficacy of CGD-EO.
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Affiliation(s)
- Anjie Feng
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Jinke Xu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China; Shandong Center for Disease Control and Prevention, Jinan, 250014, Shandong, China
| | - Yan Fu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Zhuangzhuang Li
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Chen Liu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Xiumei Luan
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Xu Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China
| | - Qihui Sun
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Yong Yang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China; Collaborative Innovation Center for Antiviral Traditional Chinese Medicine in Shandong Province, Jinan, 250355, China; Experimental Center, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
| | - Rong Rong
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China; Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, Jinan, 250355, China.
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Sanz-Muñoz I, Sánchez-Martínez J, Rodríguez-Crespo C, Arroyo-Hernantes I, Domínguez-Gil M, Rojo-Rello S, Hernández M, Eiros JM. Association of viral loads of influenza A (H3N2) with age and care setting on presentation-a prospective study during the 2022-2023 influenza season in Spain. Int J Infect Dis 2024; 143:107034. [PMID: 38561041 PMCID: PMC11068591 DOI: 10.1016/j.ijid.2024.107034] [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: 01/15/2024] [Revised: 03/14/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024] Open
Abstract
OBJECTIVES The aim of this study was to analyze the viral load (VL) using cycle threshold (Ct) in patients infected with influenza A (H3N2). METHODS This prospective study was conducted during the 2022-2023 influenza season in sentinel, non-sentinel, and hospitalized patients of Castilla y León (Spain). Respiratory samples were obtained from nasopharyngeal swabs and analyzed by quantitative reverse transcription-polymerase chain reaction specific for influenza A (H3N2) to obtain the Ct value. RESULTS A total of 1047 individuals were enrolled (174 [16.6%] sentinel, 200 [19.1%] non-sentinel, 673 [64.3%] hospitalized). The mean Ct value was lower in infants, young children, and in the elderly, with a sharp increase in the last from 65 years until 90 years. In addition, the lower Ct values were observed in non-sentinel patients and then in hospitalized patients, probably because non-sentinel are outpatients in the acute phase of the influenza infection. CONCLUSIONS A higher VL (lower Ct value) is related to the extreme ages of life: children and the elderly. Furthermore, a higher VL is related with the care setting, being probably higher in outpatients because they are in the acute phase of the disease and slightly lower in hospitalized patients because they are attended during the post-acute phase.
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Affiliation(s)
- Iván Sanz-Muñoz
- National Influenza Centre, Valladolid, Spain; Instituto de Estudios de Ciencias de la Salud de Castilla y León, ICSCYL, Soria, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFECC), Madrid, Spain.
| | - Javier Sánchez-Martínez
- National Influenza Centre, Valladolid, Spain; Instituto de Estudios de Ciencias de la Salud de Castilla y León, ICSCYL, Soria, Spain
| | - Carla Rodríguez-Crespo
- National Influenza Centre, Valladolid, Spain; Instituto de Estudios de Ciencias de la Salud de Castilla y León, ICSCYL, Soria, Spain
| | - Irene Arroyo-Hernantes
- BioCritic, Group of Biomedical Research in Critical Medicine, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Marta Domínguez-Gil
- National Influenza Centre, Valladolid, Spain; Microbiology Unit, Hospital Universitario Río Hortega, Valladolid, Spain
| | - Silvia Rojo-Rello
- National Influenza Centre, Valladolid, Spain; Microbiology Unit, Hospital Clínico Universitario de Valladolid, Valladolid, Spain
| | - Marta Hernández
- National Influenza Centre, Valladolid, Spain; Area of Microbiology, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
| | - José M Eiros
- National Influenza Centre, Valladolid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFECC), Madrid, Spain; Microbiology Unit, Hospital Universitario Río Hortega, Valladolid, Spain; Microbiology Unit, Hospital Clínico Universitario de Valladolid, Valladolid, Spain; Area of Microbiology, Faculty of Medicine, Universidad de Valladolid, Valladolid, Spain
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Ehrenzeller S, Zaffini R, Pecora ND, Kanjilal S, Rhee C, Klompas M. Cycle threshold dynamics of non-severe acute respiratory coronavirus virus 2 (SARS-CoV-2) respiratory viruses. Infect Control Hosp Epidemiol 2024; 45:630-634. [PMID: 38234188 DOI: 10.1017/ice.2023.286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
OBJECTIVE Many providers use severe acute respiratory coronavirus virus 2 (SARS-CoV-2) cycle thresholds (Ct values) as approximate measures of viral burden in association with other clinical data to inform decisions about treatment and isolation. We characterized temporal changes in Ct values for non-SARS-CoV-2 respiratory viruses as a first step to determine whether cycle thresholds could play a similar role in the management of non-SARS-CoV-2 respiratory viruses. DESIGN Retrospective cohort study. SETTING Brigham and Women's Hospital, Boston. METHODS We retrospectively identified all adult patients with positive nasopharyngeal PCRs for influenza, respiratory syncytial virus (RSV), parainfluenza, human metapneumovirus (HMPV), rhinovirus, or adenovirus between January 2022 and March 2023. We plotted Ct distributions relative to days since symptom onset, and we assessed whether distributions varied by immunosuppression and other comorbidities. RESULTS We analyzed 1,863 positive samples: 506 influenza, 502 rhinovirus, 430 RSV, 219 HMPV, 180 parainfluenza, 26 adenovirus. Ct values were generally 25-30 on the day of symptom onset, lower over the ensuing 1-3 days, and progressively higher thereafter with Ct values ≥30 after 1 week for most viruses. Ct values were generally higher and more stable over time for rhinovirus. There was no association between immunocompromised status and median intervals from symptom onset until Ct values were ≥30. CONCLUSIONS Ct values relative to symptom onset for influenza, RSV, and other non-SARS-CoV-2 respiratory viruses generally mirror patterns seen with SARS-CoV-2. Further data on associations between Ct values and viral viability, transmissibility, host characteristics, and response to treatment for non-SARS-CoV-2 respiratory viruses are needed to determine how clinicians and infection preventionists might integrate Ct values into treatment and isolation decisions.
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Affiliation(s)
- Selina Ehrenzeller
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
- Department of Medicine, Limmattal Hospital Zurich, Schlieren, Switzerland
| | - Rebecca Zaffini
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Nicole D Pecora
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Sanjat Kanjilal
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Chanu Rhee
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
| | - Michael Klompas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States
- Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States
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Gao P, Fan Y, Kong X, Zhang R, Chen L, Jiang Y, Liu Y, Zhao M, Deng G, Cao Y, Ma L. A novel assay based on DNA melting temperature for multiplexed identification of SARS-CoV-2 and influenza A/B viruses. Front Microbiol 2023; 14:1249085. [PMID: 38173675 PMCID: PMC10762780 DOI: 10.3389/fmicb.2023.1249085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Introduction The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and influenza viruses can cause respiratory illnesses with similar clinical symptoms, making their differential diagnoses challenging. Additionally, in critically ill SARS-CoV-2-infected patients, co-infections with other respiratory pathogens can lead to severe cytokine storm and serious complications. Therefore, a method for simultaneous detection of SARS-CoV-2 and influenza A and B viruses will be clinically beneficial. Methods We designed an assay to detect five gene targets simultaneously via asymmetric PCR-mediated melting curve analysis in a single tube. We used specific probes that hybridize to corresponding single-stranded amplicons at low temperature and dissociate at high temperature, creating different detection peaks representing the targets. The entire reaction was conducted in a closed tube, which minimizes the risk of contamination. The limit of detection, specificity, precision, and accuracy were determined. Results The assay exhibited a limit of detection of <20 copies/μL for SARS-CoV-2 and influenza A and <30 copies/μL for influenza B, with high reliability as demonstrated by a coefficient of variation for melting temperature of <1.16% across three virus concentrations. The performance of our developed assay and the pre-determined assay showed excellent agreement for clinical samples, with kappa coefficients ranging from 0.98 (for influenza A) to 1.00 (for SARS-CoV-2 and influenza B). No false-positive, and no cross-reactivity was observed with six common non-influenza respiratory viruses. Conclusion The newly developed assay offers a straightforward, cost-effective and nucleic acid contamination-free approach for simultaneous detection of the SARS-CoV-2, influenza A, and influenza B viruses. The method offers high analytical sensitivity, reliability, specificity, and accuracy. Its use will streamline testing for co-infections, increase testing throughput, and improve laboratory efficacy.
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Affiliation(s)
- Peng Gao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yanyan Fan
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xiaomu Kong
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Lida Chen
- Department of Blood Transfusion, China-Japan Friendship Hospital, Beijing, China
| | - Yongwei Jiang
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yi Liu
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Meimei Zhao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Guoxiong Deng
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Yongtong Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
| | - Liang Ma
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Beijing, China
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Quirouette C, Cresta D, Li J, Wilkie KP, Liang H, Beauchemin CAA. The effect of random virus failure following cell entry on infection outcome and the success of antiviral therapy. Sci Rep 2023; 13:17243. [PMID: 37821517 PMCID: PMC10567758 DOI: 10.1038/s41598-023-44180-w] [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: 08/24/2022] [Accepted: 10/04/2023] [Indexed: 10/13/2023] Open
Abstract
A virus infection can be initiated with very few or even a single infectious virion, and as such can become extinct, i.e. stochastically fail to take hold or spread significantly. There are many ways that a fully competent infectious virion, having successfully entered a cell, can fail to cause a productive infection, i.e. one that yields infectious virus progeny. Though many stochastic models (SMs) have been developed and used to estimate a virus infection's establishment probability, these typically neglect infection failure post virus entry. The SM presented herein introduces parameter [Formula: see text] which corresponds to the probability that a virion's entry into a cell will result in a productive cell infection. We derive an expression for the likelihood of infection establishment in this new SM, and find that prophylactic therapy with an antiviral reducing [Formula: see text] is at least as good or better at decreasing the establishment probability, compared to antivirals reducing the rates of virus production or virus entry into cells, irrespective of the SM parameters. We investigate the difference in the fraction of cells consumed by so-called extinct versus established virus infections, and find that this distinction becomes biologically meaningless as the probability of establishment approaches zero. We explain why the release of virions continuously over an infectious cell's lifespan, rather than as a single burst at the end of the cell's lifespan, does not result in an increased risk of infection extinction. We show, instead, that the number of virus released, not the timing of the release, affects infection establishment and associated critical antiviral efficacy.
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Affiliation(s)
| | - Daniel Cresta
- Department of Physics, Toronto Metropolitan University, Toronto, Canada
| | - Jizhou Li
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Wako, Japan
| | - Kathleen P Wilkie
- Department of Mathematics, Toronto Metropolitan University, Toronto, Canada
| | - Haozhao Liang
- Nishina Center for Accelerator-Based Science (RNC), RIKEN, Wako, Japan
- Department of Physics, University of Tokyo, Tokyo, Japan
| | - Catherine A A Beauchemin
- Department of Physics, Toronto Metropolitan University, Toronto, Canada.
- Interdisciplinary Theoretical and Mathematical Sciences (iTHEMS), RIKEN, Wako, Japan.
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Guterres A. Viral load: We need a new look at an old problem? J Med Virol 2023; 95:e29061. [PMID: 37638475 DOI: 10.1002/jmv.29061] [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: 01/27/2023] [Revised: 07/22/2023] [Accepted: 08/17/2023] [Indexed: 08/29/2023]
Abstract
The concept of viral load was introduced in the 1980s to measure the amount of viral genetic material in a person's blood, primarily for human immunodeficiency virus (HIV). It has since become crucial for monitoring HIV infection progression and assessing the efficacy of antiretroviral therapy. However, during the coronavirus disease 2019 pandemic, the term "viral load" became widely popularized, not only for the scientific community but for the general population. Viral load plays a critical role in both clinical patient management and research, providing valuable insights for antiviral treatment strategies, vaccination efforts, and epidemiological control measures. As measuring viral load is so important, why don't researchers discuss the best way to do it? Is it simply acceptable to use raw Ct values? Relying solely on Ct values for viral load estimation can be problematic due to several reasons. First, Ct values can vary between different quantitative polymerase chain reaction assays, platforms, and laboratories, making it difficult to compare data across studies. Second, Ct values do not directly measure the quantity of viral particles in a sample and they can be influenced by various factors such as initial viral load, sample quality, and assay sensitivity. Moreover, variations in viral RNA extraction and reverse-transcription steps can further impact the accuracy of viral load estimation, emphasizing the need for careful interpretation of Ct values in viral load assessment. Interestingly, we did not observe scientific articles addressing different strategies to quantify viral load. The absence of standardized and validated methods impedes the implementation of viral load monitoring in clinical management. The variability in cell quantities within samples and the variation in viral particle numbers within infected cells further challenge accurate viral load measurement and interpretation. To advance the field and improve patient outcomes, there is an urgent need for the development and validation of tailored, standardized methods for precise viral load quantification.
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Affiliation(s)
- Alexandro Guterres
- Laboratório de Hantaviroses e Rickettsioses, Instituto Oswaldo Cruz Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Vice-Diretoria de Desenvolvimento Tecnológico, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
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Detection Methods for H1N1 Virus. Methods Mol Biol 2022; 2610:109-127. [PMID: 36534286 DOI: 10.1007/978-1-0716-2895-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Influenza A virus H1N1, a respiratory virus transmitted via droplets and responsible for the global pandemic in 2009, belongs to the Orthomyxoviridae family, a single-negative-stranded RNA. It possesses glycoprotein spikes neuraminidase (NA), hemagglutinin (HA), and a matrix protein named M2. The Covid-19 pandemic affected the world population belongs to the respiratory virus category is currently mutating, this can also be observed in the case of H1N1 influenza A virus. Mutations in H1N1 can enhance the viral capacity which can lead to another pandemic. This virus affects children below 5 years, pregnant women, old age people, and immunocompromised individuals due to its high viral capacity. Its early detection is necessary for the patient's recovery time. In this book chapter, we mainly focus on the detection methods for H1N1, from traditional ones to the most advance including biosensors, RT-LAMP, multi-fluorescent PCR.
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Comparison of SARS-CoV-2 viral load in asymptomatic and symptomatic children attended in a referral public pediatric hospital in Argentina. Rev Argent Microbiol 2022:S0325-7541(22)00082-7. [PMID: 36402614 PMCID: PMC9618439 DOI: 10.1016/j.ram.2022.09.002] [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: 03/11/2022] [Revised: 07/15/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
At present, different reports have shown that children reach similar SARS-CoV-2 viral load (VL) levels compared to adults; however, the impact of VL on children remains ambiguous when asymptomatic versus symptomatic cases are compared. Thus, the aim of this study was to assess VL at the time of diagnosis in asymptomatic and symptomatic SARS-CoV-2 infected children. VL analysis was retrospectively carried out from nasopharyngeal swabs on 82 SARS-CoV-2 infected children, from March to October 2020. Of the 82 children, 31 were asymptomatic. Symptomatic patients had significantly higher VL values compared to asymptomatic ones (median = 7.41 vs 4.35 log10 copies/ml, respectively). Notwithstanding, 8 out of 31 asymptomatic children had high VL levels, overlapping levels observed above the first quartile in the symptomatic group. Analysis of different age groups revealed that median VL values were higher in the symptomatic groups, although there was only a significant difference in children younger than 5 years of age. On the other hand, there was no significant difference between the VL values from the 82 SARS-CoV-2 infected children according to age, sex, underlying disease, symptoms or severity of COVID-19 related disease. This study emphasizes the importance of VL analysis in SARS-CoV-2 infected children, who could contribute to viral spread in the community. This concern could be extended to healthcare workers, who are in contact with children.
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Gaspard P, Ambert-Balay K, Mosnier A, Chaigne B, Frey C, Uhrig C, Martinot M. Respiratory tract outbreak modeling with case definition criteria: A proposal for a standardized clinical approach in nursing homes. Infect Dis Now 2022; 52:365-370. [DOI: 10.1016/j.idnow.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/31/2022] [Accepted: 07/05/2022] [Indexed: 10/17/2022]
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Van Poelvoorde LAE, Delcourt T, Vuylsteke M, De Keersmaecker SCJ, Thomas I, Van Gucht S, Saelens X, Roosens N, Vanneste K. A general approach to identify low-frequency variants within influenza samples collected during routine surveillance. Microb Genom 2022; 8. [PMID: 36169645 DOI: 10.1099/mgen.0.000867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza viruses exhibit considerable diversity between hosts. Additionally, different quasispecies can be found within the same host. High-throughput sequencing technologies can be used to sequence a patient-derived virus population at sufficient depths to identify low-frequency variants (LFV) present in a quasispecies, but many challenges remain for reliable LFV detection because of experimental errors introduced during sample preparation and sequencing. High genomic copy numbers and extensive sequencing depths are required to differentiate false positive from real LFV, especially at low allelic frequencies (AFs). This study proposes a general approach for identifying LFV in patient-derived samples obtained during routine surveillance. Firstly, validated thresholds were determined for LFV detection, whilst balancing both the cost and feasibility of reliable LFV detection in clinical samples. Using a genetically well-defined population of influenza A viruses, thresholds of at least 104 genomes per microlitre and AF of ≥5 % were established as detection limits. Secondly, a subset of 59 retained influenza A (H3N2) samples from the 2016-2017 Belgian influenza season was composed. Thirdly, as a proof of concept for the added value of LFV for routine influenza monitoring, potential associations between patient data and whole genome sequencing data were investigated. A significant association was found between a high prevalence of LFV and disease severity. This study provides a general methodology for influenza LFV detection, which can also be adopted by other national influenza reference centres and for other viruses such as SARS-CoV-2. Additionally, this study suggests that the current relevance of LFV for routine influenza surveillance programmes might be undervalued.
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Affiliation(s)
- Laura A E Van Poelvoorde
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Thomas Delcourt
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | | | | | - Isabelle Thomas
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Steven Van Gucht
- National Influenza Centre, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Xavier Saelens
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Nancy Roosens
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Juliette Wytsmanstraat 14, Brussels, Belgium
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Andrés P, Blandine P, Victoria D, William M, Justine O, Laurent E, Cedrine M, Bruno L, Aurelien T, Thomas J, Sophie TA, Manuel RC, Olivier T. Interactions Between Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Major Respiratory Viruses in Human Nasal Epithelium. J Infect Dis 2022; 226:2095-2104. [PMID: 36031537 PMCID: PMC9452145 DOI: 10.1093/infdis/jiac357] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 01/04/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), along with extensive nonpharmacological interventions, have profoundly altered the epidemiology of major respiratory viruses. Some studies have described virus-virus interactions, particularly manifested by viral interference mechanisms at different scales. However, our knowledge of the interactions between SARS-CoV-2 and other respiratory viruses remains incomplete. Here, we studied the interactions between SARS-CoV-2 and several respiratory viruses (influenza, respiratory syncytial virus, human metapneumovirus, and human rhinovirus) in a reconstituted human epithelial airway model, exploring different scenarios affecting the sequence and timing of coinfections. We show that the virus type and sequence of infections are key factors in virus-virus interactions, the primary infection having a determinant role in the immune response to the secondary infection.
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Affiliation(s)
- Pizzorno Andrés
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Padey Blandine
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,Signia Therapeutics SAS, Lyon, France
| | - Dulière Victoria
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Mouton William
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,Laboratoire Commun de Recherche, Hospices Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | - Oliva Justine
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Emilie Laurent
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Milesi Cedrine
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Lina Bruno
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France
| | - Traversier Aurelien
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Julien Thomas
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,VirNext, Faculté de Médecine RTH Laennec, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France
| | - Trouillet Assant Sophie
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France,Laboratoire Commun de Recherche, Hospices Civils de Lyon, bioMérieux, Centre Hospitalier Lyon Sud, Pierre-Bénite, France
| | | | - Terrier Olivier
- Correspondence to: Olivier Terrier. CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France, ()
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12
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El-Malah SS, Saththasivam J, Jabbar KA, K K A, Gomez TA, Ahmed AA, Mohamoud YA, Malek JA, Abu Raddad LJ, Abu Halaweh HA, Bertollini R, Lawler J, Mahmoud KA. Application of human RNase P normalization for the realistic estimation of SARS-CoV-2 viral load in wastewater: A perspective from Qatar wastewater surveillance. ENVIRONMENTAL TECHNOLOGY & INNOVATION 2022; 27:102775. [PMID: 35761926 PMCID: PMC9220754 DOI: 10.1016/j.eti.2022.102775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/30/2022] [Accepted: 06/19/2022] [Indexed: 05/06/2023]
Abstract
The apparent uncertainty associated with shedding patterns, environmental impacts, and sample processing strategies have greatly influenced the variability of SARS-CoV-2 concentrations in wastewater. This study evaluates the use of a new normalization approach using human RNase P for the logic estimation of SARS-CoV-2 viral load in wastewater. SARS-CoV-2 variants outbreak was monitored during the circulating wave between February and August 2021. Sewage samples were collected from five major wastewater treatment plants and subsequently analyzed to determine the viral loads in the wastewater. SARS-CoV-2 was detected in all the samples where the wastewater Ct values exhibited a similar trend as the reported number of new daily positive cases in the country. The infected population number was estimated using a mathematical model that compensated for RNA decay due to wastewater temperature and sewer residence time, and which indicated that the number of positive cases circulating in the population declined from 765,729 ± 142,080 to 2,303 ± 464 during the sampling period. Genomic analyses of SARS-CoV-2 of thirty wastewater samples collected between March 2021 and April 2021 revealed that alpha (B.1.1.7) and beta (B.1.351) were among the dominant variants of concern (VOC) in Qatar. The findings of this study imply that the normalization of data allows a more realistic assessment of incidence trends within the population.
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Affiliation(s)
- Shimaa S El-Malah
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Jayaprakash Saththasivam
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Khadeeja Abdul Jabbar
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Arun K K
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Tricia A Gomez
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Ayeda A Ahmed
- Genomics Laboratory, Weill Cornell Medicine-Qatar (WCM-Q), Cornell University, Doha, Qatar
| | - Yasmin A Mohamoud
- Genomics Laboratory, Weill Cornell Medicine-Qatar (WCM-Q), Cornell University, Doha, Qatar
| | - Joel A Malek
- Genomics Laboratory, Weill Cornell Medicine-Qatar (WCM-Q), Cornell University, Doha, Qatar
| | - Laith J Abu Raddad
- Infectious Disease Epidemiology Group, Weill Cornell Medicine-Qatar, Cornell University, Doha, Qatar
| | - Hussein A Abu Halaweh
- Drainage Network Operation & Maintenance Department, Public Works Authority, Doha, Qatar
| | | | - Jenny Lawler
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Khaled A Mahmoud
- Qatar Environment and Energy Research Institute (QEERI), Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
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13
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Silverman RA, Ceci A, Cohen A, Helmick M, Short E, Bordwine P, Friedlander MJ, Finkielstein CV. Vaccine Effectiveness during Outbreak of COVID-19 Alpha (B.1.1.7) Variant in Men's Correctional Facility, United States. Emerg Infect Dis 2022; 28:1313-1320. [PMID: 35731137 PMCID: PMC9239860 DOI: 10.3201/eid2807.220091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In April 2021, a COVID-19 outbreak occurred at a correctional facility in rural Virginia, USA. Eighty-four infections were identified among 854 incarcerated persons by facilitywide testing with reverse transcription quantitative PCR (qRT-PCR). We used whole-genome sequencing to link all infections to 2 employees infected with the B.1.1.7α (UK) variant. The relative risk comparing unvaccinated to fully vaccinated persons (mRNA-1273 [Moderna, https://www.modernatx.com]) was 7.8 (95% CI 4.8–12.7), corresponding to a vaccine effectiveness of 87.1% (95% CI 79.0%–92.1%). Average qRT-PCR cycle threshold values were lower, suggesting higher viral loads, among unvaccinated infected than vaccinated cases for the nucleocapsid, envelope, and spike genes. Vaccination was highly effective at preventing SARS-CoV-2 infection in this high-risk setting. This approach can be applied to similar settings to estimate vaccine effectiveness as variants emerge to guide public health strategies during the ongoing pandemic.
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14
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Pereira LA, Lapinscki BA, Debur MC, Santos JS, Petterle RR, Nogueira MB, Vidal LRR, De Almeida SM, Raboni SM. Standardization of a high-performance RT-qPCR for viral load absolute quantification of influenza A. J Virol Methods 2021; 301:114439. [PMID: 34942203 DOI: 10.1016/j.jviromet.2021.114439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 12/26/2022]
Abstract
Influenza is an acute viral infectious respiratory disease worldwide, presenting in different clinical forms, from influenza-like illness (ILI) to severe acute respiratory infection (SARI). Although real-time quantitative polymerase chain reaction (qPCR) is already an important tool for both diagnosis and treatment monitoring of several viral infections, the correlation between the clinical aspects and the viral load of influenza is still unclear. This lack of clarity is primarily due to the low accuracy and reproducibility of the methodologies developed to quantify the influenza virus. Thus, this study aimed to develop and standardize a universal absolute quantification for influenza A by reverse transcription-quantitative PCR (RT-qPCR), using a plasmid DNA. The assay showed efficiency (Eff%) 98.6, determination coefficient (R2) 0.998, linear range 10^1 to 10^10, limit of detection (LOD) 6.77, limit of quantification (LOQ) 20.52 copies/reaction. No inter and intra assay variability was shown, and neither was the matrix effect observed. Serial measurements of clinical samples collected at a 72h interval showed no change in viral load. By contrast, immunocompetent patients have a significantly lower viral load than immunosuppressed ones. Absolute quantification in clinical samples showed some predictors associated with increased viral load: (H1N1)pdm09 (0.045); women (p = 0.049) and asthmatics (p = 0.035). The high efficiency, precision, and previous performance in clinical samples suggest the assay can be used as an accurate universal viral load quantification of influenza A. Its applicability in predicting severity and response to antivirals needs to be evaluated.
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Affiliation(s)
- L A Pereira
- Graduate Program in Internal Medicine and Health Science, Universidade Federal, do Paraná, Curitiba, Brazil
| | - B A Lapinscki
- Graduate Program in Internal Medicine and Health Science, Universidade Federal, do Paraná, Curitiba, Brazil
| | - M C Debur
- Public Health Laboratory, Curitiba, Brazil
| | - J S Santos
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - R R Petterle
- Sector of Health Sciences, Medical School, Universidade Federal do Paraná, Curitiba, Brazil
| | - M B Nogueira
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - L R R Vidal
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - S M De Almeida
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil
| | - S M Raboni
- Virology Laboratory, Hospital de Clínicas, Universidade Federal do Paraná, Brazil; Infectious Diseases Division, Hospital de Clínicas, Universidade Federal do Paraná, Brazil.
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15
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Bouzid D, Vila J, Hansen G, Manissero D, Pareja J, Rao SN, Visseaux B. Systematic review on the association between respiratory virus real-time PCR cycle threshold values and clinical presentation or outcomes. J Antimicrob Chemother 2021; 76:iii33-iii49. [PMID: 34555159 PMCID: PMC8460103 DOI: 10.1093/jac/dkab246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Objectives It is unclear whether real-time (rt)-PCR cycle threshold (Ct) values can be utilized to guide clinical and infection-control decisions. This systematic review assesses the association between respiratory pathogen rt-PCR Ct values and clinical presentation or outcomes. Methods We searched MEDLINE, EMBASE and Cochrane library databases on 14–17 January 2020 for studies reporting the presence or absence of an association between Ct values and clinical presentation or outcomes, excluding animal studies, reviews, meta-analyses, and non-English language studies. Results Among 33 studies identified (reporting on between 9 and 4918 participants by pathogen), influenza (n = 11 studies; 4918 participants), human rhinovirus (HRV, n = 11; 2012) and respiratory syncytial virus (RSV, n = 8; 3290) were the most-studied pathogens. Low influenza Ct values were associated with mortality in 1/3 studies, with increased disease severity/duration or ICU admission in 3/9, and with increased hospitalization or length of hospital stay (LOS) in 1/6. Low HRV Ct values were associated with increased disease severity/duration or ICU admission in 3/10 studies, and with increased hospitalization or LOS in 1/3. Low RSV Ct values were associated with increased disease severity/duration or ICU admission in 3/6 studies, and with increased hospitalization or LOS in 4/4. Contradictory associations were also identified for other respiratory pathogens. Conclusions Respiratory infection Ct values may inform clinical and infection-control decisions. However, the study heterogeneity observed in this review highlights the need for standardized workflows to utilize Ct values as a proxy of genomic load and confirm their value for respiratory infection management.
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Affiliation(s)
- Donia Bouzid
- Université de Paris, IAME, INSERM, Paris, France.,Université de Paris, Service d'Accueil des Urgences, Hôpital Bichat Claude Bernard, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jordi Vila
- Department of Clinical Microbiology, Biomedical Diagnostic Centre, Hospital Clinic, School of Medicine, University of Barcelona, Institute of Global Health, Barcelona, Spain
| | - Glen Hansen
- Microbiology and Molecular Diagnostics, Hennepin County Medical Center, Department of Infectious Diseases, University of Minnesota School of Medicine, Minneapolis, MN, USA.,Department of Pathology & Laboratory Medicine, University of Minnesota, School of Medicine, Minneapolis, MN, USA
| | | | - Josep Pareja
- STAT-Dx Life, S.L. (a QIAGEN Company), Medical Affairs, Barcelona, Spain
| | - Sonia N Rao
- QIAGEN Inc., Medical Affairs, Germantown, MD, USA
| | - Benoit Visseaux
- Université de Paris, IAME, INSERM, Paris, France.,Université de Paris, Laboratoire de Virologie, Hôpital Bichat Claude Bernard, Assistance Publique-Hôpitaux de Paris, Paris, France
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16
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Elzein R, Abdel-Sater F, Fakhreddine S, Hanna PA, Feghali R, Hamad H, Ayoub F. In vivo evaluation of the virucidal efficacy of chlorhexidine and povidone-iodine mouthwashes against salivary SARS-CoV-2. A randomized-controlled clinical trial. J Evid Based Dent Pract 2021; 21:101584. [PMID: 34479668 PMCID: PMC8080510 DOI: 10.1016/j.jebdp.2021.101584] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/18/2021] [Accepted: 04/21/2021] [Indexed: 12/15/2022]
Abstract
Objectives The oral cavity is potentially high-risk transmitter of COVID-19. Antimicrobial mouthrinses are used in many clinical preprocedural situations for decreasing the risk of cross-contamination in the dental setting. It is important to investigate the efficacy of mouthwash solutions against salivary SARS-CoV-2 in order to reduce the exposure of the dental team during dental procedures. Aims The aim of this in vivo study was to evaluate the efficacy of 2 preprocedural mouthrinses in the reduction of salivary SARS-CoV-2 viral load and to compare the results of the mouthwashes to a control group. Materials and Methods In this randomized-controlled clinical trial, studied group comprised laboratory-confirmed COVID-19 positive patients through nasopharyngeal swabs. Participants were divided into 3 groups. For 30 s, the control group mouthrinsed with distilled water, the Chlorhexidine group mouthrinsed with 0.2% Chlorhexidine and the Povidone-iodine group gargled with 1% Povidone-iodine. Saliva samples were collected before and 5 min after mouthwash. SARS-CoV-2 rRT-PCR was then performed for each sample. Evaluation of the efficacy was based on difference in cycle threshold (Ct) value. The analysis of data was carried out using GraphPad Prism version 5 for Windows. Kristal wullis and Paired t-test were used. A probability value of less than 0.05 was regarded as statistically significant. Results Sixty-one compliant participants (36 female and 25 male) with a mean age 45.3 ± 16.7 years-old were enrolled. A significant difference was noted between the delta Ct of distilled water wash and each of the 2 solutions Chlorhexidine 0.2% (P = .0024) and 1% Povidone-iodine (P = .012). No significant difference was found between the delta Ct of patients using Chlorhexidine 0.2% and 1% Povidone-iodine solutions (P = .24). A significant mean Ct value difference (P < .0001) between the paired samples in Chlorhexidine group (n = 27) and also in Povidone-iodine group (n = 25) (P < .0001) was found. In contrast, no significant difference (P = .566) existed before and after the experiment in the control group (n = 9). Conclusion Chlorhexidine 0.2% and 1% Povidone-iodine oral solutions are effective preprocedural mouthwashes against salivary SARS-CoV-2 in dental treatments. Their use as a preventive strategy to reduce the spread of COVID-19 during dental practice should be considered.
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Affiliation(s)
- Rola Elzein
- Department of Pediatric Dentistry and Public Dental Health, Faculty of Dental Medicine, Lebanese University, Beirut, Lebanon.
| | - Fadi Abdel-Sater
- Laboratory of Cancer Biology and Cellular Immunology, Department of Biological Sciences, Faculty of Sciences, Lebanese University, Beirut, Lebanon
| | - Soha Fakhreddine
- Infectious Diseases division, Rafik Hariri University Hospital, Beirut, Lebanon
| | - Pierre Abi Hanna
- Infectious Diseases division, Rafik Hariri University Hospital, Beirut, Lebanon
| | - Rita Feghali
- Department of Laboratory Medicine, Rafik Hariri University Hospital, Beirut, Lebanon
| | - Hassan Hamad
- Medical care Laboratory, Faculty of Public Health IV, Lebanese University, Zahle, Lebanon
| | - Fouad Ayoub
- Department of Forensic Odontology, Human Identification and Anthropology, Faculty of Dental Medicine, Lebanese University, Beirut, Lebanon
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17
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Meena GG, Wright JG, Hawkins AR, Schmidt H. Greatly Enhanced Single Particle Fluorescence Detection Using High Refractive Index Liquid-Core Waveguides. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2021; 27:6900407. [PMID: 33994767 PMCID: PMC8117828 DOI: 10.1109/jstqe.2021.3055078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
High sensitivity and easy integration with microfabrication techniques has made silicon photonics one of the leading technologies used to build biosensors for diagnostic applications. Here we introduce a new silicon dioxide based optofluidic platform having a planar solid-core (SC) waveguide orthogonally intersecting a liquid-core (LC) waveguide with high refractive index ZnI2 salt solution as core. This enables both more uniform collection of particle fluorescence by the core mode and its propagation to an off-chip detector. This approach results in ultra-high sensitivity performance, demonstrated by achieving 8X enhancement in signal-to-noise ratio, a 45x increase in detection efficiency, and a 100x lower detection limit of 80 aM of fluorescent nanobeads. This represents a key step towards an ultrasensitive biosensor system for analyzing pathogens at clinical concentrations.
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Affiliation(s)
| | - Joel G Wright
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT 84602 USA
| | - Aaron R Hawkins
- Electrical and Computer Engineering Department, Brigham Young University, Provo, UT 84602 USA
| | - Holger Schmidt
- School of Engineering, University of California Santa Cruz, Santa Cruz, CA 95064 USA
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18
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Khoris IM, Ganganboina AB, Park EY. Self-Assembled Chromogenic Polymeric Nanoparticle-Laden Nanocarrier as a Signal Carrier for Derivative Binary Responsive Virus Detection. ACS APPLIED MATERIALS & INTERFACES 2021; 13:36868-36879. [PMID: 34328304 DOI: 10.1021/acsami.1c08813] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In the current biosensor, the signal generation is limited to single virus detection in the reaction chamber. An adaptive strategy is required to enable the recognition of multiple viruses for diagnostics and surveillance. In this work, a nanocarrier is deployed to bring specific signal amplification into the biosensor, depending on the target viruses. The nanocarrier is designed using pH-sensitive polymeric nanoparticle-laden nanocarriers (PNLNs) prepared by sequential nanoprecipitation. The nanoprecipitation of two chromogens, phenolphthalein (PP) and thymolphthalein (TP), is investigated in three different solvent systems in which PNLNs demonstrate a high loading of the chromogen up to 59.75% in dimethylformamide (DMF)/dimethyl sulfoxide (DMSO)/ethanol attributing to the coprecipitation degree of the chromogens and the polymer. The PP-encapsulated PNLNs (PP@PNLNs) and TP-encapsulated PNLNs (TP@PNLNs) are conjugated to antibodies specific to target viruses, influenza virus A subtype H1N1 (IV/A/H1N1) and H3N2 (IV/A/H3N2), respectively. After the addition of anti-IV/A antibody-conjugated magnetic nanoparticles (MNPs) and magnetic separation, the enriched PNLNs/virus/MNPs sandwich structure is treated in an alkaline solution. It demonstrates a synergy reaction in which the degradation of the polymeric boundary and the pH-induced colorimetric development of the chromogen occurred. The derivative binary biosensor shows feasible detection on IV/A with excellent specificities of PP@PNLNs on IV/A/H1N1 and TP@PNLNs on IV/A/H3N2 with LODs of 27.56 and 28.38 fg mL-1, respectively. It intrigues the distinguished analytical signal in human serum with a variance coefficient of 25.8% and a recovery of 93.6-110.6% for one-step subtype influenza virus detection.
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Affiliation(s)
- Indra Memdi Khoris
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan
| | - Akhilesh Babu Ganganboina
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan
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19
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Profiling of Intestinal Microbiota in Patients Infected with Respiratory Influenza A and B Viruses. Pathogens 2021; 10:pathogens10060761. [PMID: 34204203 PMCID: PMC8233933 DOI: 10.3390/pathogens10060761] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/06/2021] [Accepted: 06/09/2021] [Indexed: 12/23/2022] Open
Abstract
Little is known about the association between respiratory viral infections and their impact on intestinal microbiota. Here, we compared the effect of influenza types, A and B, and influenza shedding in patients’ stools on the gut microbiota diversity and composition. Deep sequencing analysis was performed for the V4 region of the 16S rRNA gene. Fecal samples were collected from 38 adults with active respiratory influenza infection and 11 age-matched healthy controls. Influenza infection resulted in variations in intestinal bacterial community composition rather than in overall diversity. Overall, infected patients experienced an increased abundance of Bacteroidetes and a corresponding decrease in Firmicutes. Differential abundance testing illustrated that differences in gut microbiota composition were influenza type-dependent, identifying ten differentially abundant operational taxonomic units (OTUs) between influenza A- and influenza B-infected patients. Notably, virus shedding in fecal samples of some patients had significantly reduced gut bacterial diversity (p = 0.023). Further taxonomic analysis revealed that the abundance of Bacteroides fragilis was significantly higher among shedders compared to non-shedders (p = 0.037). These results provide fundamental evidence of the direct effect of influenza infection on gut microbiota diversity, as reported in patients shedding the virus.
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20
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Martinez RJ, Pankratz N, Schomaker M, Daniel J, Beckman K, Karger AB, Thyagarajan B, Ferreri P, Yohe SL, Nelson AC. Prediction of False-Positive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Molecular Results in a High-Throughput Open-Platform System. J Mol Diagn 2021; 23:1085-1096. [PMID: 34116245 PMCID: PMC8186061 DOI: 10.1016/j.jmoldx.2021.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/14/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Widespread high-throughput testing for identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by RT-PCR has been a foundation in the response to the coronavirus disease 2019 (COVID-19) pandemic. Quality assurance metrics for these RT-PCR tests are still evolving as testing is widely implemented. As testing increases, it is important to understand performance characteristics and the errors associated with these tests. Herein, we investigate a high-throughput, laboratory-developed SARS-CoV-2 RT-PCR assay to determine whether modeling can generate quality control metrics that identify false-positive (FP) results due to contamination. This study reviewed repeated clinical samples focusing on positive samples that test negative on re-extraction and PCR, likely representing false positives. To identify and predict false-positive samples, we constructed machine learning-derived models based on the extraction method used. These models identified variables associated with false-positive results across all methods, with sensitivities for predicting FP results ranging between 67% and 100%. Application of the models to all results predicted a total FP rate of 0.08% across all samples, or 2.3% of positive results, similar to reports for other RT-PCR tests for RNA viruses. These models can predict quality control parameters, enabling laboratories to generate decision trees that reduce interpretation errors, allow for automated reflex testing of samples with a high FP probability, improve workflow efficiency, and increase diagnostic accuracy for patient care.
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Affiliation(s)
- Ryan J Martinez
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Matthew Schomaker
- M Health Fairview Molecular Diagnostics Laboratory, University of Minnesota, Minneapolis, Minnesota
| | - Jerry Daniel
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota
| | - Kenneth Beckman
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, Minnesota
| | - Amy B Karger
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Patricia Ferreri
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minnesota, Minneapolis, Minnesota
| | - Sophia L Yohe
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota.
| | - Andrew C Nelson
- Division of Molecular Pathology and Genomics, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota.
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21
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Cruz JS, de Souza Luna LK, Alves VRG, Conte DD, Bellei NCJ. Viral load of respiratory syncytial virus among children from primary care and hospital settings admitted to a university hospital in Brazil (2009-2013). J Med Virol 2021; 93:3397-3400. [PMID: 32543739 DOI: 10.1002/jmv.26185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/08/2020] [Accepted: 06/14/2020] [Indexed: 11/09/2022]
Abstract
Respiratory syncytial virus (RSV) is a relevant cause of acute respiratory infection among children. Viral replication and immune conditions may account for severity. RSV viral load (VL) was assessed in 486 children (290 hospitalized and 196 from primary care) attended at São Paulo Hospital from 2009 to 2013. VL was calculated by real-time reverse transcription-polymerase chain reaction and expressed in Log10 RNA copies/mL. Coinfection with rhinovirus (RV) and influenza A virus was also tested. Young children (<1 year of age) had a higher mean VL than older children at primary care (6.35 and 4.34 Log10 RNA copies/mL, respectively; P = .0006). Conversely, hospitalized children ≥2 years of age, presented higher mean VL compared with the same age children of primary care (6.10 and 4.26, respectively; P = .0024). RV was the most codetected virus in RSV positive patients (20% from primary care and 14% in hospitalized), and influenza A virus was found in 11% of primary care and 0.4% in hospitalized children with RSV, without RSV VL association (P = .2903). These findings may guide future therapies and immunization policies considering the role of viral load on clinical presentation among older hospitalized children and also the change of infection transmissions.
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Affiliation(s)
- Jéssica Santiago Cruz
- Clinical Virology Laboratory, Infectious Diseases Unit, Medicine Department, São Paulo Federal University, São Paulo, Brazil
| | - Luciano Kleber de Souza Luna
- Clinical Virology Laboratory, Infectious Diseases Unit, Medicine Department, São Paulo Federal University, São Paulo, Brazil
| | | | - Danielle Dias Conte
- Clinical Virology Laboratory, Infectious Diseases Unit, Medicine Department, São Paulo Federal University, São Paulo, Brazil
| | - Nancy Cristina Junqueira Bellei
- Clinical Virology Laboratory, Infectious Diseases Unit, Medicine Department, São Paulo Federal University, São Paulo, Brazil
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22
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Yuan S, Jiang SC, Zhang ZW, Fu YF, Hu J, Li ZL. Quantification of Cytokine Storms During Virus Infections. Front Immunol 2021; 12:659419. [PMID: 34079547 PMCID: PMC8165266 DOI: 10.3389/fimmu.2021.659419] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022] Open
Abstract
Highly pathogenic virus infections usually trigger cytokine storms, which may have adverse effects on vital organs and result in high mortalities. The two cytokines interleukin (IL)-4 and interferon (IFN)-γ play key roles in the generation and regulation of cytokine storms. However, it is still unclear whether the cytokine with the largest induction amplitude is the same under different virus infections. It is unknown which is the most critical and whether there are any mathematical formulas that can fit the changing rules of cytokines. Three coronaviruses (SARS-CoV, MERS-CoV, and SARS-CoV-2), three influenza viruses (2009H1N1, H5N1 and H7N9), Ebola virus, human immunodeficiency virus, dengue virus, Zika virus, West Nile virus, hepatitis B virus, hepatitis C virus, and enterovirus 71 were included in this analysis. We retrieved the cytokine fold change (FC), viral load, and clearance rate data from these highly pathogenic virus infections in humans and analyzed the correlations among them. Our analysis showed that interferon-inducible protein (IP)-10, IL-6, IL-8 and IL-17 are the most common cytokines with the largest induction amplitudes. Equations were obtained: the maximum induced cytokine (max) FC = IFN-γ FC × (IFN-γ FC/IL-4 FC) (if IFN-γ FC/IL-4 FC > 1); max FC = IL-4 FC (if IFN-γ FC/IL-4 FC < 1). For IFN-γ-inducible infections, 1.30 × log2 (IFN-γ FC) = log10 (viral load) − 2.48 − 2.83 × (clearance rate). The clinical relevance of cytokines and their antagonists is also discussed.
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Affiliation(s)
- Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Si-Cong Jiang
- Chengdu KangHong Pharmaceutical Group Comp. Ltd., Chengdu, China
| | - Zhong-Wei Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yu-Fan Fu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Jing Hu
- School of Medicine, Northwest University, Xi'an, China
| | - Zi-Lin Li
- Department of Cardiovascular Surgery, Xijing Hospital, Medical University of the Air Force, Xi'an, China
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23
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Chen PZ, Bobrovitz N, Premji Z, Koopmans M, Fisman DN, Gu FX. Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols. eLife 2021; 10:e65774. [PMID: 33861198 PMCID: PMC8139838 DOI: 10.7554/elife.65774] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/15/2021] [Indexed: 01/08/2023] Open
Abstract
Background Which virological factors mediate overdispersion in the transmissibility of emerging viruses remains a long-standing question in infectious disease epidemiology. Methods Here, we use systematic review to develop a comprehensive dataset of respiratory viral loads (rVLs) of SARS-CoV-2, SARS-CoV-1 and influenza A(H1N1)pdm09. We then comparatively meta-analyze the data and model individual infectiousness by shedding viable virus via respiratory droplets and aerosols. Results The analyses indicate heterogeneity in rVL as an intrinsic virological factor facilitating greater overdispersion for SARS-CoV-2 in the COVID-19 pandemic than A(H1N1)pdm09 in the 2009 influenza pandemic. For COVID-19, case heterogeneity remains broad throughout the infectious period, including for pediatric and asymptomatic infections. Hence, many COVID-19 cases inherently present minimal transmission risk, whereas highly infectious individuals shed tens to thousands of SARS-CoV-2 virions/min via droplets and aerosols while breathing, talking and singing. Coughing increases the contagiousness, especially in close contact, of symptomatic cases relative to asymptomatic ones. Infectiousness tends to be elevated between 1 and 5 days post-symptom onset. Conclusions Intrinsic case variation in rVL facilitates overdispersion in the transmissibility of emerging respiratory viruses. Our findings present considerations for disease control in the COVID-19 pandemic as well as future outbreaks of novel viruses. Funding Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant program, NSERC Senior Industrial Research Chair program and the Toronto COVID-19 Action Fund.
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Affiliation(s)
- Paul Z Chen
- Department of Chemical Engineering & Applied Chemistry, University of TorontoTorontoCanada
| | - Niklas Bobrovitz
- Temerty Faculty of Medicine, University of TorontoTorontoCanada
- Department of Critical Care Medicine, Cumming School of Medicine, University of CalgaryCalgaryCanada
- O'Brien Institute of Public Health, University of CalgaryCalgaryCanada
| | - Zahra Premji
- Libraries & Cultural Resources, University of CalgaryCalgaryCanada
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical CenterRotterdamNetherlands
| | - David N Fisman
- Division of Epidemiology, Dalla Lana School of Public Health, University of TorontoTorontoCanada
- Division of Infectious Diseases, Temerty Faculty of Medicine, University of TorontoTorontoCanada
| | - Frank X Gu
- Department of Chemical Engineering & Applied Chemistry, University of TorontoTorontoCanada
- Institute of Biomedical Engineering, University of TorontoTorontoCanada
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24
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Chu DKW, Perera RAPM, Ali A, Oladipo JO, Mamo G, So RTY, Zhou Z, Chor YY, Chan CK, Belay D, Tayachew A, Mengesha M, Regassa F, Lam NT, Poon LLM, Peiris M. Influenza A Virus Infections in Dromedary Camels, Nigeria and Ethiopia, 2015-2017. Emerg Infect Dis 2021; 26:173-176. [PMID: 31855544 PMCID: PMC6924894 DOI: 10.3201/eid2601.191165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We examined nasal swabs and serum samples acquired from dromedary camels in Nigeria and Ethiopia during 2015–2017 for evidence of influenza virus infection. We detected antibodies against influenza A(H1N1) and A(H3N2) viruses and isolated an influenza A(H1N1)pdm09–like virus from a camel in Nigeria. Influenza surveillance in dromedary camels is needed.
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25
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Miranda RL, Guterres A, de Azeredo Lima CH, Filho PN, Gadelha MR. Misinterpretation of viral load in COVID-19 clinical outcomes. Virus Res 2021; 296:198340. [PMID: 33592214 PMCID: PMC7881726 DOI: 10.1016/j.virusres.2021.198340] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/30/2022]
Abstract
Knowledge of viral load is essential to formulate strategies for antiviral treatment, vaccination, and epidemiological control of COVID-19. Moreover, identification of patients with high viral loads can also be useful to understand risk factors such as age, comorbidities, severity of symptoms and hypoxia, to decide on the need for hospitalization. Several ongoing studies are analyzing viral load in different types of samples and evaluating its relationship with clinical outcomes and viral transmission pathways. However, in a great number of emerging studies, cycle threshold (Ct) values alone are often used as viral load indicators, which may be a mistake. In this study, we compared tracheal aspirate with nasopharyngeal swab samples obtained from critically ill COVID-19 patients and here we report how the raw Ct can lead to misinterpretation of results. Furthermore, based on analysis of nasopharyngeal swab samples we propose a method to reduce evaluation errors that could occur from using raw Ct data. Based on these findings, we show the impact that normalization of Ct values has on interpretation of SARS-CoV-2 viral load from different biological samples.
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Affiliation(s)
- Renan Lyra Miranda
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, RJ, Brazil
| | - Alexandro Guterres
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, RJ, Brazil.
| | | | | | - Mônica R Gadelha
- Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do Cérebro Paulo Niemeyer, Rio de Janeiro, RJ, Brazil; Neuroendocrinology Research Center, Endocrinology Division, - Medical School and Hospital Universitário Clementino Fraga Filho - Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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26
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Tsuneki-Tokunaga A, Kanai K, Itagaki A, Tsuchie H, Okada T, Kasagi M, Tanaka K, Aoki M, Hinay AJA, Kageyama S. Growth capability of epidemic influenza viruses in Japan since the 2009 H1N1 pandemic. Arch Virol 2021; 166:1193-1196. [PMID: 33580378 PMCID: PMC7880649 DOI: 10.1007/s00705-021-04976-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 11/26/2022]
Abstract
The correlation of viral growth capability (n = 156) with the viral load in nasopharyngeal swabs (n = 76) was assessed. Epidemic influenza A/H1N1, A/H3N2, and B viruses showed a wide range of growth capability (104-1011 copies/mL) in Madin-Darby canine kidney cells. The growth was correlated with the nasopharyngeal viral load (r = 0.53). Six selected strains showed growth-dependent cell death (r = 0.96) in a growth kinetics assay. Epidemic influenza viruses exhibit a wide range of growth capability. Growth capability should be considered one of the key factors in disease prognosis.
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Affiliation(s)
- Akeno Tsuneki-Tokunaga
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Kyosuke Kanai
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Asao Itagaki
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
| | - Hideaki Tsuchie
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Tsuchie Internal Medicine and Pediatric Clinic, Sakaiminato, Japan
| | - Takayoshi Okada
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Department of Pediatrics, Tottori Prefectural Kousei Hospital, Kurayoshi, Japan
| | - Masaaki Kasagi
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Kasagi Children's Clinic for Health Service, Yonago, Japan
| | - Kiyoshi Tanaka
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan
- Tanaka Pediatric Clinic, Tottori, Japan
| | - Miho Aoki
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Alfredo Jr A Hinay
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan
| | - Seiji Kageyama
- Division of Virology, Department of Microbiology and Immunology, Tottori University Faculty of Medicine, Yonago, Japan.
- Tottori Infectious Diseases Forum, Tottori prefecture, Japan.
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27
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Barry MA, Arinal F, Talla C, Hedible BG, Sarr FD, Ba IO, Diop B, Dia N, Vray M. Performance of case definitions and clinical predictors for influenza surveillance among patients followed in a rural cohort in Senegal. BMC Infect Dis 2021; 21:31. [PMID: 33413174 PMCID: PMC7790019 DOI: 10.1186/s12879-020-05724-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 12/18/2020] [Indexed: 11/18/2022] Open
Abstract
Background Influenza is a major cause of morbidity and mortality in Africa. However, a lack of epidemiological data remains for this pathology, and the performances of the influenza-like illness (ILI) case definitions used for sentinel surveillance have never been evaluated in Senegal. This study aimed to i) assess the performance of three different ILI case definitions, adopted by the WHO, USA-CDC (CDC) and European-CDC (ECDC) and ii) identify clinical factors associated with a positive diagnosis for Influenza in order to develop an algorithm fitted for the Senegalese context. Methods All 657 patients with a febrile pathological episode (FPE) between January 2013 and December 2016 were followed in a cohort study in two rural villages in Senegal, accounting for 1653 FPE observations with nasopharyngeal sampling and influenza virus screening by rRT-PCR. For each FPE, general characteristics and clinical signs presented by patients were collected. Sensitivity, Specificity, Positive Predictive Value (PPV) and Negative Predictive Value (NPV) for the three ILI case definitions were assessed using PCR result as the reference test. Associations between clinical signs and influenza infection were analyzed using logistic regression with generalized estimating equations. Sore throat, arthralgia or myalgia were missing for children under 5 years. Results WHO, CDC and ECDC case definitions had similar sensitivity (81.0%; 95%CI: 77.0–85.0) and NPV (91.0%; 95%CI: 89.0–93.1) while the WHO and CDC ILI case definitions had the highest specificity (52.0%; 95%CI: 49.1–54.5) and PPV (32.0%; 95%CI: 30.0–35.0). These performances varied by age groups. In children < 5 years, the significant predictors of influenza virus infection were cough and nasal discharge. In patients from 5 years, cough, nasal discharge, sore throat and asthenia grade 3 best predicted influenza infection. The addition of “nasal discharge” as a symptom to the WHO case definition decreased sensitivity but increased specificity, particularly in the pediatric population. Conclusion In summary, all three definitions studies (WHO, ECDC & CDC) have similar performance, even by age group. The revised WHO ILI definition could be chosen for surveillance purposes for its simplicity. Symptomatic predictors of influenza virus infection vary according the age group. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-020-05724-x.
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Affiliation(s)
- Mamadou Aliou Barry
- Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, 36, Avenue Pasteur, Dakar, Sénégal.
| | - Florent Arinal
- Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, 36, Avenue Pasteur, Dakar, Sénégal
| | - Cheikh Talla
- Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, 36, Avenue Pasteur, Dakar, Sénégal
| | - Boris Gildas Hedible
- Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, 36, Avenue Pasteur, Dakar, Sénégal
| | - Fatoumata Diene Sarr
- Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, 36, Avenue Pasteur, Dakar, Sénégal
| | | | - Boly Diop
- Ministère de la Santé et de l'Action Sociale, Direction de la Prévention, Dakar, Sénégal
| | - Ndongo Dia
- Institut Pasteur de Dakar, Pôle de Virologie, Dakar, Sénégal
| | - Muriel Vray
- Institut Pasteur de Dakar, Unité d'Epidémiologie des maladies infectieuses, 36, Avenue Pasteur, Dakar, Sénégal
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28
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Mu HY, Lu YL, Hsiao TH, Huang JH. Microfluidic-based approaches for COVID-19 diagnosis. BIOMICROFLUIDICS 2020; 14:061504. [PMID: 33343780 PMCID: PMC7725537 DOI: 10.1063/5.0031406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/23/2020] [Indexed: 05/05/2023]
Abstract
Novel coronavirus, COVID-19, erupted in Wuhan, China, in 2019 and has now spread to almost all countries in the world. Until the end of November 2020, there were over 50 × 106 people diagnosed with COVID-19 worldwide and it caused at least 1 × 106 deaths. These numbers are still increasing. To control the spread of the pandemic and to choose a suitable treatment plan, a fast, accurate, effective, and ready-to-use diagnostic method has become an important prerequisite. In this Review, we introduce the principles of multiple off-site and on-site detection methods for virus diagnosis, including qPCR-based, ELISA-based, CRISPR-based methods, etc. All of these methods have been successfully implanted on the microfluidic platform for rapid screening. We also summarize currently available diagnostic methods for the detection of SARS, MERS, and COVID-19. Some of them not only can be used to analyze the SARS and MERS but also have the potential for COVID-19 detection after modifications. Finally, we hope that understanding of current microfluidic-based detection approaches can help physicians and researchers to develop advanced, rapid, and appropriate clinical detection techniques that reduce the financial expenditure of the society, accelerate the examination process, increase the accuracy of diagnosis, and eventually suppress the worldwide pandemic.
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Affiliation(s)
- Hsuan-Yu Mu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yu-Lun Lu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | | | - Jen-Huang Huang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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29
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McKay B, Ebell M, Billings WZ, Dale AP, Shen Y, Handel A. Associations Between Relative Viral Load at Diagnosis and Influenza A Symptoms and Recovery. Open Forum Infect Dis 2020; 7:ofaa494. [PMID: 33376754 PMCID: PMC7751133 DOI: 10.1093/ofid/ofaa494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/13/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Rapid point-of-care polymerase chain reaction (PCR) diagnostic tests generally provide a qualitative result of positive or negative only. Additional information about the relative viral load could be calculated. Such quantitative information might be useful for making treatment decisions. METHODS We enrolled students at a university health center who presented with cough and 1 additional flu-like symptom from December 2016 to February 2017. Data were collected before, during, and 5 days after the clinic visit. All those enrolled in the study received a point-of-care PCR test (cobas Liat). For those patients that tested positive for influenza A, we investigated correlations between the relative viral load and measures of disease severity and recovery. RESULTS One hundred thirty-five students tested positive for influenza A. We found a positive correlation between viral load and body temperature. Time since symptom onset seemed to have a negative correlation but was not statistically significant. We did not find any correlations between viral load and overall symptom severity or outcomes related to recovery. CONCLUSIONS Although we found a correlation between relative viral load and body temperature, for our study population of young, overall healthy adults, we did not find that relative viral load provided additional information that could help in determining treatment and disease outcomes. It could be that viral load does provide useful additional information for other groups of patients, such as young children or older adults. Further studies on those populations are warranted.
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Affiliation(s)
- Brian McKay
- Department of Epidemiology and Biostatistics, The University of Georgia, Athens, Georgia, USA
| | - Mark Ebell
- Department of Epidemiology and Biostatistics, The University of Georgia, Athens, Georgia, USA
| | - Wesley Zane Billings
- Department of Mathematics and Computer Science, Western Carolina University, Cullowhee, North Carolina, USA
| | - Ariella Perry Dale
- Colorado Department of Public Health and Environment, Denver, Colorado, USA
| | - Ye Shen
- Department of Epidemiology and Biostatistics, The University of Georgia, Athens, Georgia, USA
| | - Andreas Handel
- Department of Epidemiology and Biostatistics and Health Informatics Institute and Center for the Ecology of Infectious Diseases, The University of Georgia, Athens, Georgia, USA
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30
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Bénézit F, Loubet P, Galtier F, Pronier C, Lenzi N, Lesieur Z, Jouneau S, Lagathu G, L'Honneur AS, Foulongne V, Vallejo C, Alain S, Duval X, Houhou N, Costa Y, Vanhems P, Amour S, Carrat F, Lina B, Launay O, Tattevin P. Non-influenza respiratory viruses in adult patients admitted with influenza-like illness: a 3-year prospective multicenter study. Infection 2020; 48:489-495. [PMID: 32056143 PMCID: PMC7095392 DOI: 10.1007/s15010-019-01388-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 12/24/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE To describe the burden, and characteristics, of influenza-like illness (ILI) associated with non-influenza respiratory viruses (NIRV). METHODS We performed a prospective, multicenter, observational study of adults admitted with ILI during three influenza seasons (2012-2015). Patients were screened for picornavirus, respiratory syncytial virus (RSV), coronavirus, human metapneumovirus, adenovirus, bocavirus, parainfluenza virus, and influenza, by PCR on nasopharyngeal samples. We excluded patients coinfected with NIRV and influenza. RESULTS Among 1421 patients enrolled, influenza virus was detected in 535 (38%), and NIRV in 215 (15%), mostly picornavirus (n = 61), RSV (n = 53), coronavirus 229E (n = 48), and human metapneumovirus (n = 40). In-hospital mortality was 5% (NIRV), 4% (influenza), and 5% (no respiratory virus). As compared to influenza, NIRV were associated with age (median, 73 years vs. 68, P = 0.026), chronic respiratory diseases (53% vs. 45%, P = 0.034), cancer (14% vs. 9%, P = 0.029), and immunosuppressive drugs (21% vs. 14%, P = 0.028), and inversely associated with diabetes (18% vs. 25%, P = 0.038). On multivariable analysis, only chronic respiratory diseases (OR 1.5 [1.1-2.0], P = 0.008), and diabetes (OR 0.5 [0.4-0.8], P = 0.01) were associated with NIRV detection. CONCLUSIONS NIRV are common in adults admitted with ILI during influenza seasons. Outcomes are similar in patients with NIRV, influenza, or no respiratory virus.
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Affiliation(s)
- François Bénézit
- Université Rennes-I, Service Des Maladies Infectieuses et de Réanimation Médicale, Hôpital Pontchaillou, CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033, Rennes Cedex, France
| | - Paul Loubet
- Université Paris Descartes, Sorbonne Paris Cité; Inserm, CIC Cochin Pasteur, Innovative Clinical Research Network in VACcinology (I-REIVAC), Assistance Publique Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Florence Galtier
- Inserm, F-CRIN, Innovative Clinical Research Network in Vaccinology (I-REIVAC), Paris, France
- CIC1411, CHU Montpellier, Hôpital Saint Eloi, 34295, Montpellier, France
| | - Charlotte Pronier
- Université Rennes-I, Virologie, Hôpital Pontchaillou, Rennes, France
| | - Nezha Lenzi
- Université Paris Descartes, Sorbonne Paris Cité; Inserm, CIC Cochin Pasteur, Innovative Clinical Research Network in VACcinology (I-REIVAC), Assistance Publique Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Zineb Lesieur
- Université Paris Descartes, Sorbonne Paris Cité; Inserm, CIC Cochin Pasteur, Innovative Clinical Research Network in VACcinology (I-REIVAC), Assistance Publique Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Stéphane Jouneau
- Université Rennes-I, Pneumologie, Hôpital Pontchaillou, Rennes, France
- Inserm, CIC 1414, Université Rennes-I, Hôpital Pontchaillou, Rennes, France
| | - Gisèle Lagathu
- Université Rennes-I, Virologie, Hôpital Pontchaillou, Rennes, France
| | | | - Vincent Foulongne
- Service de Virologie, CHU Montpellier, Hôpital Saint Eloi, 34295, Montpellier, France
| | | | - Sophie Alain
- Univ. Limoges, INSERM, CHU Limoges, RESINFIT, U1092, 87000, Limoges, France
| | - Xavier Duval
- CIC1125, Hôpital Bichat Claude Bernard, APHP, Inserm, F-CRIN, Innovative Clinical Research Network in Vaccinology (I-REIVAC), Paris, France
| | - Nawal Houhou
- Laboratoire de Virologie, Hôpital Bichat Claude Bernard, Paris, France
| | - Yolande Costa
- CIC1125, Hôpital Bichat Claude Bernard, APHP, Inserm, F-CRIN, Innovative Clinical Research Network in Vaccinology (I-REIVAC), Paris, France
| | - Philippe Vanhems
- Service D'Hygiène, Epidémiologie et Prévention, Hospices Civils de Lyon, 69437, Lyon, France
- Laboratoire des Pathogènes Emergents-Fondation Mérieux, Centre International de Recherche en Infectiologie, Institut National de la Santé et de la Recherche Médicale U1111, Centre National de La Recherche Scientifique, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon, Lyon, France
| | - Sélilah Amour
- Service D'Hygiène, Epidémiologie et Prévention, Hospices Civils de Lyon, 69437, Lyon, France
| | - Fabrice Carrat
- Sorbonne Université, INSERM, Institut Pierre Louis D'Epidémiologie et de Santé Publique IPLESP, AP-HP, Hôpital Saint Antoine, 75013, Paris, France
| | - Bruno Lina
- Hospices Civils de Lyon, Laboratoire de Virologie, Institut Des Agents Infectieux (IAI), Centre National de Référence Des Virus Respiratoires France Sud, Hôpital de La Croix-Rousse, 69317, Lyon Cedex 04, France
| | - Odile Launay
- Université Paris Descartes, Sorbonne Paris Cité; Inserm, CIC Cochin Pasteur, Innovative Clinical Research Network in VACcinology (I-REIVAC), Assistance Publique Hôpitaux de Paris, Hôpital Cochin, Paris, France
| | - Pierre Tattevin
- Université Rennes-I, Service Des Maladies Infectieuses et de Réanimation Médicale, Hôpital Pontchaillou, CHU Pontchaillou, 2 rue Henri Le Guilloux, 35033, Rennes Cedex, France.
- Inserm, CIC 1414, Université Rennes-I, Hôpital Pontchaillou, Rennes, France.
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Rodrigues Guimarães Alves V, Perosa AH, de Souza Luna LK, Cruz JS, Conte DD, Bellei N. Influenza A(H1N1)pdm09 infection and viral load analysis in patients with different clinical presentations. Mem Inst Oswaldo Cruz 2020; 115:e200009. [PMID: 32428082 PMCID: PMC7233266 DOI: 10.1590/0074-02760200009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/27/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Influenza viral load (VL) can be a decisive factor in determining the antiviral efficacy in viral clearance. OBJECTIVE This study aimed to evaluate the rate of infection and the role of influenza VL on the clinical spectrum of illnesses among different patient groups attended at a tertiary hospital in Brazil. METHODS Samples were collected from patients presenting acute respiratory infection from 2009 to 2013. Overall, 2262 samples were analysed and distributed into three groups: (i) asymptomatic (AS); (ii) symptomatic outpatients (OP); and (iii) hospitalised patients (HP). VL (expressed in Log10 RNA copies/mL) was calculated through a quantitative real-time one-step reverse transcription-polymerase chain reaction (RT-PCR) assay aimed at the M gene, with human RNAseP target as internal control and normalising gene of threshold cycle values. FINDINGS A total of 162 (7.16%) H1N1pdm09 positive samples were analysed. Patients aged from 0.08 to 77 years old [median ± standard deviation (SD): 12.5 ± 20.54]. Children with 5 to 11 years old presented the highest detection (p < 0.0001). AS patients had the lowest VL, with a significant difference when compared with symptomatic patients (p = 0.0003). A higher VL was observed within two days of disease onset. Ten patients (HP group) received antiviral treatment and were followed up and presented a mean initial VL of 6.64 ± 1.82. A complete viral clearance for 50% of these patients was reached after 12 days of treatment. MAIN CONCLUSIONS It is important to evaluate AS patients as potential spreaders, as viral shedding was still present, even at lower VL. Our results suggest that patients with underlying diseases and severe clinical symptoms may be considered for prolonged viral treatment.
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Affiliation(s)
- Vitória Rodrigues Guimarães Alves
- Disciplina de Infectologia, Laboratório de Virologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | | | - Luciano Kleber de Souza Luna
- Disciplina de Infectologia, Laboratório de Virologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Jessica Santiago Cruz
- Disciplina de Infectologia, Laboratório de Virologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Danielle Dias Conte
- Disciplina de Infectologia, Laboratório de Virologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Nancy Bellei
- Disciplina de Infectologia, Laboratório de Virologia Clínica, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
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32
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Liu X, Yang J, Li Q, Wang Y, Wang Y, Li G, Shi J, Ding P, Guo J, Deng R, Zhang G. A strip test for the optical determination of influenza virus H3 subtype using gold nanoparticle coated polystyrene latex microspheres. Mikrochim Acta 2020; 187:306. [PMID: 32356232 DOI: 10.1007/s00604-020-04255-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/31/2020] [Indexed: 12/12/2022]
Abstract
A strip test is described for the optical determination of influenza virus H3 subtype. It utilizes gold nanoparticle (AuNP) coated polystyrene latex microspheres (PS) as the label and a sandwich format. The AuNP and PS particles were linked using monoclonal antibodies against influenza virus as the bridge. Under the optimal conditions, the visual detection limit of the AuNP-PS-based strip test was as low as 1/16 hemagglutination unit (HAU). It was 64 times higher than that of 10 nm (4 HAU) AuNP-based strip tests. Quantitative analysis showed that the detection limit of the AuNP-PS-based strip is 0.016 HAU. The AuNP-PS-based strip test showed no cross-reactivity to the other subtypes (H1, H5, H7, or H9) of influenza viruses. Graphical abstract .
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Affiliation(s)
- Xiao Liu
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
- Department of Medicine, Henan Medical College, Zhengzhou, 451191, China
| | - Jifei Yang
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Qingmei Li
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Yinbiao Wang
- School of Public Health, Xinxiang Medical University, Xinxiang, 453003, China
| | - Yanhong Wang
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Ge Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jianzhou Shi
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Peiyang Ding
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Junqing Guo
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Ruiguang Deng
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Gaiping Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.
- Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
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Inter- Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes. Microorganisms 2020; 8:microorganisms8010133. [PMID: 31963512 PMCID: PMC7022955 DOI: 10.3390/microorganisms8010133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015-2017) and its implications on disease severity. A total of 90 nasal samples positive for the pH1N1 virus were deep-sequenced and analyzed to detect low-frequency variants (LFVs) and haplotypes. Parallel evolution of LFVs was seen in the hemagglutinin (HA) gene across three scales: among patients (33%), across years (22%), and at global scale. Remarkably, investigating the emergence of LFVs at the consensus level demonstrated that within-host virus evolution recapitulates evolutionary dynamics seen at the global scale. Analysis of virus diversity at the HA haplotype level revealed the clustering of low-frequency haplotypes from early 2015 with dominant strains of 2016, indicating rapid haplotype evolution. Haplotype sharing was also noticed in all years, strongly suggesting haplotype transmission among patients infected during a specific influenza season. Finally, more than half of patients with severe symptoms harbored a larger number of haplotypes, mostly in patients under the age of five. Therefore, patient age, haplotype diversity, and the presence of certain LFVs should be considered when interpreting illness severity. In addition to its importance in understanding virus evolution, sub-consensus virus diversity together with whole genome sequencing is essential to explain variabilities in clinical outcomes that cannot be explained by either analysis alone.
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Arias-Bravo G, Valderrama G, Inostroza J, Reyes-Farías M, Garcia-Diaz DF, Zorondo-Rodríguez F, Fuenzalida LF. Overnutrition in Infants Is Associated With High Level of Leptin, Viral Coinfection and Increased Severity of Respiratory Infections: A Cross-Sectional Study. Front Pediatr 2020; 8:44. [PMID: 32133330 PMCID: PMC7041426 DOI: 10.3389/fped.2020.00044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/28/2020] [Indexed: 01/01/2023] Open
Abstract
Objective: To investigate the relationship of overnutrition (obese and overweight) with severity of illness in children hospitalized with acute lower respiratory infections (ALRIs), frequency of viral coinfections and leptin levels. Methods: We studied 124 children <2 years old that were hospitalized for ALRI. Nutritional status was calculated by z-scores according to weight-for-age z-scores, length or height-for-age z-scores, and weight-for-height z-scores. Nasopharyngeal aspirates (NPAs) were obtained and viral respiratory pathogens were identified using reverse transcription polymerase chain reactions (RT-PCR). Respiratory syncytial virus (RSV) load was assessed using quantitative RT-PCR. NPA and plasma leptin level were measured. Clinical data and nutritional status were recorded, and patients were followed up until hospital discharge. Viral coinfection was defined as the presence of two or more viruses detected in the same respiratory sample. Severity of illness was determined by length of hospitalization and duration of oxygen therapy. Results: Children with overnutrition showed a greater frequency of viral coinfection than those with normal weight (71% obese vs. 37% normal weight p = 0.013; 68% overweight vs. 37% normal weight p = 0.004). A lower RSV load was found in obese (5.91 log10 copies/mL) and overweight children (6.49 log10 copies/mL) compared to normal weight children (8.06 log10 copies/mL; p = 0.021 in both cases). In multivariate analysis, obese, and overweight infants <6 months old were associated with longer hospital stays (RR = 1.68; CI: 1.30-2.15 and obese: RR = 1.68; CI: 1.01-2.71, respectively) as well as a greater duration of oxygen therapy (RR = 1.80; IC: 1.41-2.29 and obese: RR = 1.91; CI: 1.15-3.15, respectively). Obese children <6 months showed higher plasma leptin level than normal weight children (7.58 vs. 5.12 ng/μl; p <0.046). Conclusions: In infants younger than 6 months, overnutrition condition was related to increased severity of infections and high plasma leptin level. Also, children with overnutrition showed a greater frequency of viral coinfection and low RSV viral load compared to normal weights children. These findings further contribute to the already existent evidence supporting the importance of overnutrition prevention in pediatric populations.
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Affiliation(s)
- Guisselle Arias-Bravo
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile.,Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile
| | | | - Jaime Inostroza
- Jeffrey Modell Centre for Diagnosis and Research in Primary Immunodeficiencies, Facultad de Medicina, Universidad de La Frontera, Temuco, Chile
| | - Marjorie Reyes-Farías
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Diego F Garcia-Diaz
- Laboratorio de Nutrigenomica, Departamento de Nutricion, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Loreto F Fuenzalida
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
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Rodrigues Guimarães Alves V, Kleber de Souza Luna L, Santiago Cruz J, Helena Perosa A, Bellei N. Influenza B viral load analysis in patients with acute respiratory infection from a tertiary hospital in Brazil. J Med Virol 2019; 92:1350-1354. [PMID: 31803951 PMCID: PMC7228353 DOI: 10.1002/jmv.25648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/29/2019] [Indexed: 11/05/2022]
Abstract
Currently, 2 genotypes of Influenza B viruses (IFB) are cocirculating in humans: Victoria (VIC) and Yamagata (YAM). Infection and viral load (VL) were analyzed in 105 genotyped IFB (59 VIC and 46 YAM) out of 3452 respiratory samples from immunodepressed (ID), immunocompetent (IC) including outpatients (OP) and hospitalized patients (HP) attended during 2001-2013 at São Paulo Hospital. VL (Log10 RNA copies/mL) calculation was possible in 78 samples (47 VIC, 31 YAM). The age group of 12 to 18 years presented the highest detection (14.13%). Rates of infection among groups were of 3.67% (IC), 1.68% (ID), 3.50% (OP), 0.6% (HP), and VLs varied from 2.8 to 10.13 with no difference regarding age, immune status, and disease severity. From 10 OP vaccinated against influenza, 8 (7 children, 1 ID) received a matching strain shot (VIC), and 2 a monovalent influenza A H1N1pdm09. Those patients presented a VL of 6.31 ± 1.62 (mean ± SD). IFB infection rates follow an age pattern, but VL seems not to be related to frequency or clinical outcome. IFB patients with previous immunization could point to some protection for VIC infections since there was no HP. Other immunological aspects, such as lineage infection immune priming, previous infections, and vaccinations, should be further investigated.
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Affiliation(s)
- Vitória Rodrigues Guimarães Alves
- Clinical Virology Laboratory, Infectious Diseases Unit, Medicine Department, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | - Luciano Kleber de Souza Luna
- Clinical Virology Laboratory, Infectious Diseases Unit, Medicine Department, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | - Jessica Santiago Cruz
- Clinical Virology Laboratory, Infectious Diseases Unit, Medicine Department, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
| | | | - Nancy Bellei
- Clinical Virology Laboratory, Infectious Diseases Unit, Medicine Department, Universidade Federal de São Paulo, Escola Paulista de Medicina, São Paulo, Brazil
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36
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Clinique et diagnostic de la grippe saisonnière. ACTUALITES PHARMACEUTIQUES 2019. [DOI: 10.1016/j.actpha.2019.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Gaspard P, Mosnier A, Simon L, Ali-Brandmeyer O, Rabaud C, Larocca S, Heck B, Aho-Glélé S, Pothier P, Ambert-Balay K. Gastroenteritis and respiratory infection outbreaks in French nursing homes from 2007 to 2018: Morbidity and all-cause lethality according to the individual characteristics of residents. PLoS One 2019; 14:e0222321. [PMID: 31550261 PMCID: PMC6759171 DOI: 10.1371/journal.pone.0222321] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 08/27/2019] [Indexed: 01/09/2023] Open
Abstract
Background Gastroenteritis (GE) and respiratory tract infection (RTI) outbreaks are a significant issue in nursing homes. This study aimed to describe GE and RTI outbreaks with infection and all-cause lethality rates according to the individual characteristics of nursing home residents. Methods Clinical and virological surveillance were conducted (2007 to 2018). Virus stratifications for the analysis were: outbreaks with positive norovirus or influenza identifications (respectively NoV+ or Flu+), episodes with no NoV or influenza identification or testing (respectively NoV- or Flu-). Associations between individual variables (sex, age, length of stay (LOS), autonomy status) and infection and lethality rates were tested with univariate and Mantel-Haenszel (MH) methods. Results 61 GE outbreaks and 76 RTI oubreaks (total 137 outbreaks) were recorded involving respectively 4309 and 5862 residents. In univariate analysis, higher infection rates and age were associated in NoV+, NoV-, and Flu+ contexts, and lower infection rates were associated with longer stays (NoV+ and NoV-). In MH stratified analysis (virus, sex (female/male)) adjusted for LOS (<4 or ≥4 years), the odds of being infected remained significant among older residents (≥86 years): NoV+/male (Odds ratio (ORMH): 1.64, 95% confidence interval (CI): 1.16–2.30) and Flu+/female and male (respectively ORMH: 1.50, CI: 1.27–1.79 and 1.73, CI: 1.28–2.33). In univariate analysis, lower autonomy status (NoV+, Flu+ and Flu-) and increased age (Flu+) were associated with higher lethality. In MH adjusted analysis, significant ORage adjusted for autonomy was: Flu+/ ≥86 years compared with <86 years, 1.97 (1.19–3.25) and ORautonomy adjusted for age for the more autonomous group (compared with the less autonomous group) was: Flu+, 0.41 (0.24–0.69); Flu-, 0.42 (0.20, 0.90). Conclusion The residents of nursing homes are increasingly elderly and dependent. The specific infection and lethality risks according to these two factors indicate that surveillance and infection control measures are essential and of high priority.
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Affiliation(s)
- Philippe Gaspard
- Hospital Hygiene Service, Rouffach Hospital Center, Rouffach, France
- UMR 6249 Chrono-Environnement, University of Franche-Comté, Besançon, France
- * E-mail:
| | | | - Loic Simon
- Coordination Centre for Nosocomial Infection Control, Eastern Regions, Nancy University Hospital, Nancy, France
| | - Olivia Ali-Brandmeyer
- Coordination Centre for Nosocomial Infection Control, Eastern Regions, Nancy University Hospital, Nancy, France
| | - Christian Rabaud
- Coordination Centre for Nosocomial Infection Control, Eastern Regions, Nancy University Hospital, Nancy, France
| | - Sabrina Larocca
- Hospital Hygiene Service, Rouffach Hospital Center, Rouffach, France
| | - Béatrice Heck
- Hospital Hygiene Service, Rouffach Hospital Center, Rouffach, France
| | - Serge Aho-Glélé
- Department of Epidemiology and Infection Control, Dijon University Hospital, Dijon, France
| | - Pierre Pothier
- University Burgundy Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
- National Reference Center for Gastroenteritis Viruses, Laboratory of Biology and Pathology, University Hospital, Dijon, France
| | - Katia Ambert-Balay
- University Burgundy Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
- National Reference Center for Gastroenteritis Viruses, Laboratory of Biology and Pathology, University Hospital, Dijon, France
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Clinical correlation of influenza and respiratory syncytial virus load measured by digital PCR. PLoS One 2019; 14:e0220908. [PMID: 31479459 PMCID: PMC6720028 DOI: 10.1371/journal.pone.0220908] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/25/2019] [Indexed: 02/07/2023] Open
Abstract
Acute respiratory tract infections are a major cause of respiratory morbidity and mortality in pediatric patients worldwide. However, accurate viral and immunologic markers to predict clinical outcomes of this patient population are still lacking. Droplet digital PCR assays for influenza and respiratory syncytial virus (RSV) were designed and performed in 64 respiratory samples from 23 patients with influenza virus infection and 73 samples from 19 patients with RSV infection. Samples of patients with hematologic malignancies, solid tumors, or sickle cell disease were included. Clinical information from institutional medical records was reviewed to assess disease severity. Samples from patients with fever or respiratory symptoms had a significantly higher viral loads than those from asymptomatic patients. Samples from patients with influenza virus and RSV infection collected at presentation had significantly higher viral loads than those collected from patients after completing a course of oseltamivir or ribavirin, respectively. RSV loads correlated positively with clinical symptoms in patients ≤5 years of age, whereas influenza viral loads were associated with clinical symptoms, irrespective of age. Patients receiving antivirals for influenza and RSV had a significant reduction in viral loads after completing therapy. Digital PCR offers an effective method to monitor the efficacy of antiviral treatment for respiratory tract infections in immunocompromised hosts.
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Lalueza A, Folgueira D, Muñoz-Gallego I, Trujillo H, Laureiro J, Hernández-Jiménez P, Moral-Jiménez N, Castillo C, Ayuso B, Díaz-Pedroche C, Torres M, Arrieta E, Arévalo-Cañas C, Madrid O, Lumbreras C. Influence of viral load in the outcome of hospitalized patients with influenza virus infection. Eur J Clin Microbiol Infect Dis 2019; 38:667-673. [PMID: 30820840 PMCID: PMC7102091 DOI: 10.1007/s10096-019-03514-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 02/14/2019] [Indexed: 01/30/2023]
Abstract
The role of viral load in the outcome of patients requiring hospital admission due to influenza is not well established. We aim to assess if there is an association between the viral load and the outcome in hospitalized patients with a confirmed influenza virus infection. A retrospective observational study including all adult patients who were hospitalized in our center with a confirmed influenza virus infection from January to May 2016. Viral load was measured by real-time reverse-transcriptase–polymerase chain reaction (rRT-PCR) cycle threshold (Ct) value on upper respiratory tract samples. Its value was categorized into three groups (low Ct, ≤ 20; intermediate Ct, > 20–30; and high Ct, > 30). Two hundred thirty-nine patients were included. Influenza A/H1N1pdm09 was isolated in 207 cases (86.6%). The mean Ct value was 26.69 ± 5.81. The viral load was higher in the unvaccinated group when compared with the vaccinated patients (Ct 25.17 ± 5.55 vs. 27.58 ± 4.97, p = 0.004). Only 27 patients (11.29%) presented a high viral load. Patients with a high viral load more often showed abnormal findings on chest X-ray (p = 0.015) and lymphopenia (p = 0.097). By contrast, there were no differences between the three groups (according to viral load), in associated pneumonia, respiratory failure, need for mechanical ventilation, sepsis, or in-hospital mortality. Our findings suggest that in patients admitted to the hospital with confirmed influenza virus infection (mostly A/H1N1pdm09), a high viral load is associated with a higher presence of abnormal findings on chest X-ray but not with a significant worse prognosis. In these cases, standardized quantitative PCR could be useful.
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Affiliation(s)
- Antonio Lalueza
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain. .,Department of Medicine, School of Medicine, Complutense University, Madrid, Spain. .,Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.
| | - Dolores Folgueira
- Department of Medicine, School of Medicine, Complutense University, Madrid, Spain.,Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.,Department of Microbiology, University Hospital 12 de Octubre, Madrid, Spain
| | - Irene Muñoz-Gallego
- Department of Microbiology, University Hospital 12 de Octubre, Madrid, Spain
| | - Hernando Trujillo
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | - Jaime Laureiro
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | - Pilar Hernández-Jiménez
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | | | - Cristina Castillo
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | - Blanca Ayuso
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | - Carmen Díaz-Pedroche
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain.,Department of Medicine, School of Medicine, Complutense University, Madrid, Spain
| | - Marta Torres
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | - Estibaliz Arrieta
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | - Coral Arévalo-Cañas
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | - Olaya Madrid
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain
| | - Carlos Lumbreras
- Department of Internal Medicine, University Hospital 12 de Octubre, Av. Córdoba km 5400, 28041, Madrid, Spain.,Department of Medicine, School of Medicine, Complutense University, Madrid, Spain.,Instituto de Investigación Hospital 12 de Octubre (i+12), Madrid, Spain.,Infectious Diseases Unit, University Hospital 12 de Octubre, Madrid, Spain
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Single-Step Detection of the Influenza Virus Hemagglutinin Using Bacterially-Produced Quenchbodies. SENSORS 2018; 19:s19010052. [PMID: 30583603 PMCID: PMC6338965 DOI: 10.3390/s19010052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/05/2018] [Accepted: 12/20/2018] [Indexed: 01/07/2023]
Abstract
We have successfully generated a Quenchbody that enables the detection of the influenza virus hemagglutinin (HA), in a simple and convenient manner. By two-site labeling of the bacterially-produced anti-HA Fab with ATTO520, its fluorescence intensity was increased to 4.4-fold, in the presence of a nanomolar concentration of H1N1 HA. Our results indicate the potential use of this Quenchbody, as a sensor for the simple in situ detection of influenza A virus.
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Tunheim G, Laake I, Robertson AH, Waalen K, Hungnes O, Naess LM, Cox RJ, Mjaaland S, Trogstad L. Antibody levels in a cohort of pregnant women after the 2009 influenza A(H1N1) pandemic: Waning and association with self-reported severity and duration of illness. Influenza Other Respir Viruses 2018; 13:191-200. [PMID: 30536590 PMCID: PMC6379636 DOI: 10.1111/irv.12623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/05/2018] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND A population-based pregnancy cohort was established in Norway to study potential effects of exposure to the 2009 influenza pandemic or pandemic vaccination during pregnancy. OBJECTIVES We studied maternal A(H1N1)pdm09-specific hemagglutination inhibition (HI)-titer levels and waning in women with influenza-like illness (ILI) in pregnancy compared to vaccinated women. Moreover, we studied the association between HI-titers and self-reported severity and duration of ILI. METHODS HI-titers against the pandemic virus were measured in maternal blood samples obtained at birth, 3-9 months after exposure, and linked with information about pregnancy, influenza and vaccination from national registries and a cohort questionnaire. RESULTS Among 1821 pregnant women included, 43.7% were unvaccinated and 19.3% of these had ILI. HI-titers were low (geometric mean titer (GMT) 11.3) in the unvaccinated women with ILI. Higher HI-titers (GMT 37.8) were measured in the vaccinated women. Estimated HI-titer waning was similar for vaccinated women and women with ILI. Most ILI episodes were moderate and lasted 3-5 days. Women with ILI reporting specific influenza symptoms such as fever or cough had higher HI-titers than women without these symptoms. Women who reported being "very ill" or illness duration of >5 days had higher HI-titers than women reporting less severe illness or illness of shorter duration, respectively. CONCLUSIONS Antibody waning was similar in vaccinated women and women with ILI. More severe ILI or longer duration of illness was associated with higher HI-titers. Most unvaccinated pregnant women with ILI had low HI-titers, probably due to moderate illness and HI-titer waning between exposure and sampling.
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Affiliation(s)
- Gro Tunheim
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,K. G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway
| | - Ida Laake
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Anna Hayman Robertson
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristian Waalen
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Olav Hungnes
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Lisbeth M Naess
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Rebecca J Cox
- K. G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway.,The Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Research and Development, Haukeland University Hospital, Bergen, Norway
| | - Siri Mjaaland
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,K. G. Jebsen Centre for Influenza Vaccine Research, University of Oslo, Oslo, Norway
| | - Lill Trogstad
- Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway
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42
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Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections. Clin Microbiol Rev 2018; 32:32/1/e00042-18. [PMID: 30541871 DOI: 10.1128/cmr.00042-18] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.
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43
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Ye S, Cowled CJ, Yap CH, Stambas J. Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1. Sci Rep 2018; 8:15468. [PMID: 30341336 PMCID: PMC6195505 DOI: 10.1038/s41598-018-33605-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
Current prophylactic and therapeutic strategies targeting human influenza viruses include vaccines and antivirals. Given variable rates of vaccine efficacy and antiviral resistance, alternative strategies are urgently required to improve disease outcomes. Here we describe the use of HiSeq deep sequencing to analyze host gene expression in primary human alveolar epithelial type II cells infected with highly pathogenic avian influenza H5N1 virus. At 24 hours post-infection, 623 host genes were significantly upregulated, including the cell adhesion molecule CEACAM1. H5N1 virus infection stimulated significantly higher CEACAM1 protein expression when compared to influenza A PR8 (H1N1) virus, suggesting a key role for CEACAM1 in influenza virus pathogenicity. Furthermore, silencing of endogenous CEACAM1 resulted in reduced levels of proinflammatory cytokine/chemokine production, as well as reduced levels of virus replication following H5N1 infection. Our study provides evidence for the involvement of CEACAM1 in a clinically relevant model of H5N1 infection and may assist in the development of host-oriented antiviral strategies.
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Affiliation(s)
- Siying Ye
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia. .,AAHL CSIRO Deakin Collaborative Biosecurity Laboratory, East Geelong, Victoria, Australia.
| | | | - Cheng-Hon Yap
- University Hospital Geelong, Barwon Health, Geelong, Victoria, Australia
| | - John Stambas
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia.,AAHL CSIRO Deakin Collaborative Biosecurity Laboratory, East Geelong, Victoria, Australia
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44
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Ferraris O, Casalegno JS, Frobert E, Bouscambert Duchamp M, Valette M, Jacquot F, Raoul H, Lina B, Ottmann M. The NS Segment of H1N1pdm09 Enhances H5N1 Pathogenicity in a Mouse Model of Influenza Virus Infections. Viruses 2018; 10:v10090504. [PMID: 30227598 PMCID: PMC6164720 DOI: 10.3390/v10090504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 11/17/2022] Open
Abstract
In 2009, the co-circulation of H5N1 and H1N1pdm09 raised concerns that a reassortment event may lead to highly pathogenic influenza strains. H1N1pdm09 and H5N1 are able to infect the same target cells of the lower respiratory tract. To investigate the capacity of the emergence of reassortant viruses, we characterized viruses obtained from the co-infection of cells with H5N1 (A/Turkey/13/2006) and H1N1pdm09 (A/Lyon/969/2009 H1N1). In our analysis, all the screened reassortants possessed the PB2, HA, and NP segments from H5N1 and acquired one or two of the H1N1pdm09 segments. Moreover, the in vivo infections showed that the acquisition of the NS segment from H1N1pdm09 increased the virulence of H5N1 in mice. We conclude, therefore, that reassortment can occur between these two viruses, even if this process has never been detected in nature.
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Affiliation(s)
- Olivier Ferraris
- Laboratoire de Virologie et Pathologies Humaines Virpath, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69372 CEDEX 08 Lyon, France.
| | - Jean-Sébastien Casalegno
- Laboratoire de Virologie et Pathologies Humaines Virpath, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69372 CEDEX 08 Lyon, France.
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord des Hospices Civils de Lyon, 69317 CEDEX 04 Lyon, France.
| | - Emilie Frobert
- Laboratoire de Virologie et Pathologies Humaines Virpath, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69372 CEDEX 08 Lyon, France.
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord des Hospices Civils de Lyon, 69317 CEDEX 04 Lyon, France.
| | - Maude Bouscambert Duchamp
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord des Hospices Civils de Lyon, 69317 CEDEX 04 Lyon, France.
| | - Martine Valette
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord des Hospices Civils de Lyon, 69317 CEDEX 04 Lyon, France.
- Laboratoire de Virologie, Centre National de Référence Virus des Infections Respiratoires, Groupement Hospitalier Nord des Hospices Civils de Lyon, 69317 CEDEX 04 Lyon, France.
| | - Frédéric Jacquot
- Laboratoire P4 Jean Mérieux Inserm US003, 69365 CEDEX 07 Lyon, France.
| | - Hervé Raoul
- Laboratoire P4 Jean Mérieux Inserm US003, 69365 CEDEX 07 Lyon, France.
| | - Bruno Lina
- Laboratoire de Virologie et Pathologies Humaines Virpath, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69372 CEDEX 08 Lyon, France.
- Laboratoire de Virologie, Institut des Agents Infectieux, Groupement Hospitalier Nord des Hospices Civils de Lyon, 69317 CEDEX 04 Lyon, France.
- Laboratoire de Virologie, Centre National de Référence Virus des Infections Respiratoires, Groupement Hospitalier Nord des Hospices Civils de Lyon, 69317 CEDEX 04 Lyon, France.
| | - Michèle Ottmann
- Laboratoire de Virologie et Pathologies Humaines Virpath, CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, CNRS UMR5308, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 69372 CEDEX 08 Lyon, France.
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45
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Feikin DR, Fu W, Park DE, Shi Q, Higdon MM, Baggett HC, Brooks WA, Deloria Knoll M, Hammitt LL, Howie SRC, Kotloff KL, Levine OS, Madhi SA, Scott JAG, Thea DM, Adrian PV, Antonio M, Awori JO, Baillie VL, DeLuca AN, Driscoll AJ, Ebruke BE, Goswami D, Karron RA, Li M, Morpeth SC, Mwaba J, Mwansa J, Prosperi C, Sawatwong P, Sow SO, Tapia MD, Whistler T, Zaman K, Zeger SL, O' Brien KL, Murdoch DR. Is Higher Viral Load in the Upper Respiratory Tract Associated With Severe Pneumonia? Findings From the PERCH Study. Clin Infect Dis 2018; 64:S337-S346. [PMID: 28575373 PMCID: PMC5447843 DOI: 10.1093/cid/cix148] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background. The etiologic inference of identifying a pathogen in the upper respiratory tract (URT) of children with pneumonia is unclear. To determine if viral load could provide evidence of causality of pneumonia, we compared viral load in the URT of children with World Health Organization–defined severe and very severe pneumonia and age-matched community controls. Methods. In the 9 developing country sites, nasopharyngeal/oropharyngeal swabs from children with and without pneumonia were tested using quantitative real-time polymerase chain reaction for 17 viruses. The association of viral load with case status was evaluated using logistic regression. Receiver operating characteristic (ROC) curves were constructed to determine optimal discriminatory viral load cutoffs. Viral load density distributions were plotted. Results. The mean viral load was higher in cases than controls for 7 viruses. However, there was substantial overlap in viral load distribution of cases and controls for all viruses. ROC curves to determine the optimal viral load cutoff produced an area under the curve of <0.80 for all viruses, suggesting poor to fair discrimination between cases and controls. Fatal and very severe pneumonia cases did not have higher viral load than less severe cases for most viruses. Conclusions. Although we found higher viral loads among pneumonia cases than controls for some viruses, the utility in using viral load of URT specimens to define viral pneumonia was equivocal. Our analysis was limited by lack of a gold standard for viral pneumonia.
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Affiliation(s)
- Daniel R Feikin
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Wei Fu
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Rheumatology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Daniel E Park
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Milken Institute School of Public Health, Department of Epidemiology and Biostatistics, George Washington University, District of Columbia
| | - Qiyuan Shi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Melissa M Higdon
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Henry C Baggett
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi.,Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - W Abdullah Brooks
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Maria Deloria Knoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Laura L Hammitt
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Stephen R C Howie
- Medical Research Council Unit, Basse, The Gambia.,Department of Paediatrics, University of Auckland, and.,Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Karen L Kotloff
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Orin S Levine
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Bill & Melinda Gates Foundation, Seattle, Washington
| | - Shabir A Madhi
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - J Anthony G Scott
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Donald M Thea
- Center for Global Health and Development, Boston University School of Public Health, Massachusetts
| | - Peter V Adrian
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Martin Antonio
- Medical Research Council Unit, Basse, The Gambia.,Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, and.,Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Juliet O Awori
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi
| | - Vicky L Baillie
- Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, and.,Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrea N DeLuca
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Epidemiology
| | - Amanda J Driscoll
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Doli Goswami
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Ruth A Karron
- Department of International Health, Center for Immunization Research, and
| | - Mengying Li
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Susan C Morpeth
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom.,Microbiology Laboratory, Middlemore Hospital, Counties Manukau District Health Board, Auckland, New Zealand
| | - John Mwaba
- Department of Pathology and Microbiology, University Teaching Hospital, and.,Zambia Center for Applied Health Research and Development, Lusaka
| | - James Mwansa
- Department of Pathology and Microbiology, University Teaching Hospital, and.,Zambia Center for Applied Health Research and Development, Lusaka
| | - Christine Prosperi
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Pongpun Sawatwong
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi
| | - Samba O Sow
- Centre pour le Développement des Vaccins (CVD-Mali), Bamako
| | - Milagritos D Tapia
- Division of Infectious Disease and Tropical Pediatrics, Department of Pediatrics, Center for Vaccine Development, Institute of Global Health, University of Maryland School of Medicine, Baltimore
| | - Toni Whistler
- Global Disease Detection Center, Thailand Ministry of Public Health-US Centers for Disease Control and Prevention Collaboration, Nonthaburi.,Division of Global Health Protection, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Khalequ Zaman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka and Matlab
| | - Scott L Zeger
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Katherine L O' Brien
- Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David R Murdoch
- Department of Pathology, University of Otago, and.,Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand
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46
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Moreira LP, Watanabe ASA, Camargo CN, Melchior TB, Granato C, Bellei N. Respiratory syncytial virus evaluation among asymptomatic and symptomatic subjects in a university hospital in Sao Paulo, Brazil, in the period of 2009-2013. Influenza Other Respir Viruses 2018; 12:326-330. [PMID: 29078028 PMCID: PMC5907818 DOI: 10.1111/irv.12518] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2017] [Indexed: 12/27/2022] Open
Abstract
Background The respiratory syncytial virus (RSV) is recognized as an important cause of respiratory tract infections. Immunocompromised patients, healthcare workers (HCWs) and children contacts are at increased risk of acquiring the infection. However, the impact of asymptomatic infection in transmission has not been well studied. Objectives: this study evaluated the frequency and viral load (VL) of RSV in nasal swab samples of individuals with different risk factors for acquiring infection in a university hospital in Sao Paulo, Brazil. Methods We included 196 symptomatic children and their 192 asymptomatic caregivers, 70 symptomatic and 95 asymptomatic HCWs, 43 samples from symptomatic HIV‐positive outpatients, and 100 samples of asymptomatic HIV patients in the period of 2009‐2013. Results RSV infection was detected in 10.1% (70/696) of samples, 4.4% (17/387) of asymptomatic patients, and 17.1% (53/309) from symptomatic patients. (P < .0001). The VL of symptomatic patients (4.7 log copies/mL) was significantly higher compared to asymptomatic patients (2.3 log copies/mL). RSV detection among asymptomatic caregivers (6.8%; 13/192) was significantly higher compared to other asymptomatic adults, HIV and HCWs (2.0%; 4/195; P = .0252). A close contact with an infected child at home was an important risk to RSV acquisition [OR 22.6 (95% CI 4.8‐106.7)]. Children who possibly transmitted the virus to their asymptomatic contacts had significantly higher viral load than children who probably did not transmit (P < .0001). Conclusions According to our results, it is important to know if people circulating inside the hospital have close contact with acute respiratory infected children.
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Affiliation(s)
| | | | | | | | - Celso Granato
- Medicine Department, Sao Paulo Federal University, Sao Paulo, Brazil
| | - Nancy Bellei
- Medicine Department, Sao Paulo Federal University, Sao Paulo, Brazil
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47
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Casalegno JS, Eibach D, Valette M, Enouf V, Daviaud I, Behillil S, Vabret A, Soulary JC, Benchaib M, Cohen JM, van der Werf S, Mosnier A, Lina B. Performance of influenza case definitions for influenza community surveillance: based on the French influenza surveillance network GROG, 2009-2014. ACTA ACUST UNITED AC 2017; 22:30504. [PMID: 28422004 PMCID: PMC5388124 DOI: 10.2807/1560-7917.es.2017.22.14.30504] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/14/2016] [Indexed: 11/20/2022]
Abstract
International case definitions recommended by the Centers for Disease Control and Prevention (CDC), the European Centre for Disease Prevention and Control (ECDC), and the World Health Organization (WHO) are commonly used for influenza surveillance. We evaluated clinical factors associated with the laboratory-confirmed diagnosis of influenza and the performance of these influenza case definitions by using a complete dataset of 14,994 patients with acute respiratory infection (ARI) from whom a specimen was collected between August 2009 and April 2014 by the Groupes Régionaux d'Observation de la Grippe (GROG), a French national influenza surveillance network. Cough and fever ≥ 39 °C most accurately predicted an influenza infection in all age groups. Several other symptoms were associated with an increased risk of influenza (headache, weakness, myalgia, coryza) or decreased risk (adenopathy, pharyngitis, shortness of breath, otitis/otalgia, bronchitis/ bronchiolitis), but not throughout all age groups. The WHO case definition for influenza-like illness (ILI) had the highest specificity with 21.4%, while the ECDC ILI case definition had the highest sensitivity with 96.1%. The diagnosis among children younger than 5 years remains challenging. The study compared the performance of clinical influenza definitions based on outpatient surveillance and will contribute to improving the comparability of data shared at international level.
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Affiliation(s)
- Jean-Sebastien Casalegno
- Univ Lyon, Virpath, CIRI, INSERM U1111, CNRS, ENS, Université Claude Bernard Lyon 1, Lyon, France.,These authors contributed equally.,National Reference Center for influenza viruses, National Influenza Center (southern France), Laboratory of Virology, Hospices Civils de Lyon, Lyon, France
| | - Daniel Eibach
- These authors contributed equally.,Bernhard Nocht Institute for Tropical Medicine (BNITM), Hamburg, Germany
| | - Martine Valette
- National Reference Center for influenza viruses, National Influenza Center (southern France), Laboratory of Virology, Hospices Civils de Lyon, Lyon, France
| | - Vincent Enouf
- Coordinating Center of the National Reference Center for influenza viruses, National Influenza Center (northern France), Institut Pasteur, UMR 3569 CNRS, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Isabelle Daviaud
- Réseau des Groupes Régionaux d'Observation de la Grippe (GROG network).,OpenRome, Paris, France
| | - Sylvie Behillil
- Coordinating Center of the National Reference Center for influenza viruses, National Influenza Center (northern France), Institut Pasteur, UMR 3569 CNRS, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Astrid Vabret
- UNICAEN, EA4655 - U2RM, Normandie University, Caen, France.,Department of Virology, University Hospital, Caen, France
| | | | - Mehdi Benchaib
- Service de Médecine de la Reproduction, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Bron, France
| | - Jean Marie Cohen
- Réseau des Groupes Régionaux d'Observation de la Grippe (GROG network).,OpenRome, Paris, France
| | - Sylvie van der Werf
- Coordinating Center of the National Reference Center for influenza viruses, National Influenza Center (northern France), Institut Pasteur, UMR 3569 CNRS, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Anne Mosnier
- Réseau des Groupes Régionaux d'Observation de la Grippe (GROG network).,OpenRome, Paris, France
| | - Bruno Lina
- Univ Lyon, Virpath, CIRI, INSERM U1111, CNRS, ENS, Université Claude Bernard Lyon 1, Lyon, France.,National Reference Center for influenza viruses, National Influenza Center (southern France), Laboratory of Virology, Hospices Civils de Lyon, Lyon, France
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48
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Loubet P, Lenzi N, Valette M, Foulongne V, Krivine A, Houhou N, Lagathu G, Rogez S, Alain S, Duval X, Galtier F, Postil D, Tattevin P, Vanhems P, Carrat F, Lina B, Launay O. Clinical characteristics and outcome of respiratory syncytial virus infection among adults hospitalized with influenza-like illness in France. Clin Microbiol Infect 2016; 23:253-259. [PMID: 27903461 PMCID: PMC7128342 DOI: 10.1016/j.cmi.2016.11.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/20/2016] [Accepted: 11/22/2016] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The aim of this study was to analyse characteristics and outcome of respiratory syncytial virus (RSV) infection in adults hospitalized with influenza-like illness (ILI). METHODS Patients hospitalized with ILI were included in this prospective, multicentre study carried out in six French hospitals during three consecutive influenza seasons (2012-2015). RSV and other respiratory viruses were detected by multiplex PCR in nasopharyngeal swabs. Risk factors for RSV infection were identified by backward stepwise logistic regression analysis. RESULTS A total of 1452 patients hospitalized with ILI were included, of whom 59% (861/1452) were >65 years and 83% (1211/1452) had underlying chronic illnesses. RSV was detected in 4% (59/1452), and influenza virus in 39% (566/1452). Risk factors for RSV infection were cancer (adjusted OR 2.1, 95% CI 1.1-4.1, p 0.04), and immunosuppressive treatment (adjusted OR 2.0, 95% CI 1.1-3.8, p 0.03). Patients with RSV had a median length of stay of 9 days (6-25), and 57% of them (30/53) had complications, including pneumonia (23/53, 44%) and respiratory failure (15/53, 28%). Fifteen per cent (8/53) were admitted to an intensive care unit, and the in-hospital mortality rate was 8% (4/53). Pneumonia was more likely to occur in patients with RSV than in patients with RSV-negative ILI (44% (23/53) versus 26% (362/1393), p 0.006) or with influenza virus infection (44% versus 28% (157/560), p 0.02). CONCLUSION RSV is an infrequent cause of ILI during periods of influenza virus circulation but can cause severe complications in hospitalized adults. Risk factors for RSV detection in adults hospitalized with ILI include cancer and immunosuppressive treatment. Specific immunization and antiviral therapy might benefit patients at risk.
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Affiliation(s)
- P Loubet
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, France; Service de Maladies Infectieuses et Tropicales, Hôpital Bichat, AP-HP, Paris, France
| | - N Lenzi
- Inserm, F-CRIN, Innovative clinical research network in vaccinology (I-REIVAC), Paris, France
| | - M Valette
- CNR Virus Influenza, Institut des Agents Infectieux, GHN, Hospices Civils de Lyon, Lyon, France
| | - V Foulongne
- CHU de Montpellier, Laboratoire de Virologie, Hôpital Saint Eloi, Inserm U 1058, Montpellier, France
| | - A Krivine
- AP-HP, Hôpital Cochin Broca Hôtel-Dieu, Laboratoire de Virologie, Paris, France
| | - N Houhou
- AP-HP, Hôpital Bichat-Claude Bernard, Laboratoire de Virologie, Paris, France
| | - G Lagathu
- CHRU Pontchaillou, Laboratoire de Virologie, Rennes, France
| | - S Rogez
- CHU Dupuytren, Service Bactériologie, Virologie, Hygiène, Limoges Cedex, France
| | - S Alain
- CHU Dupuytren, Laboratoire de Virologie, Limoge Cedex, France
| | - X Duval
- IAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, France; Inserm CIC 1425, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - F Galtier
- Inserm, F-CRIN, Innovative clinical research network in vaccinology (I-REIVAC), Paris, France; CHU de Montpellier, Inserm CIC 1411, Hôpital Saint-Eloi, Montpellier, France
| | - D Postil
- CHU Dupuytren, CIC 1435, Limoge Cedex, France
| | - P Tattevin
- CHRU Pontchaillou, Maladies Infectieuses et Réanimation Médicale, CIC INSERM 1414, Rennes, France
| | - P Vanhems
- Service d'Hygiène, Epidémiologie et Prévention, Groupement Hospitalier Edouard Herriot, Lyon, France; Emerging Pathogens Laboratory - Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI) Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - F Carrat
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France; Public health department, Hopital Saint-Antoine, APHP, Paris, France
| | - B Lina
- CNR Virus Influenza, Institut des Agents Infectieux, GHN, Hospices Civils de Lyon, Lyon, France; CIRI, Centre International de Recherche en Infectiologie, Virpath, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Hospices Civils de Lyon, Univ Lyon, Lyon, France
| | - O Launay
- Inserm, F-CRIN, Innovative clinical research network in vaccinology (I-REIVAC), Paris, France; Inserm, CIC 1417, Paris, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Department of Infectious Diseases, CIC Cochin Pasteur, Cochin Broca Hôtel-Dieu hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.
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Bonizzoli M, Arvia R, di Valvasone S, Liotta F, Zakrzewska K, Azzi A, Peris A. Human herpesviruses respiratory infections in patients with acute respiratory distress (ARDS). Med Microbiol Immunol 2016; 205:371-9. [PMID: 27138606 PMCID: PMC7086591 DOI: 10.1007/s00430-016-0456-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 04/23/2016] [Indexed: 12/29/2022]
Abstract
Acute respiratory distress syndrome (ARDS) is today a leading cause of hospitalization in intensive care unit (ICU). ARDS and pneumonia are closely related to critically ill patients; however, the etiologic agent is not always identified. The presence of human herpes simplex virus 1, human cytomegalovirus and Epstein–Barr virus in respiratory samples of critically ill patients is increasingly reported even without canonical immunosuppression. The main aim of this study was to better understand the significance of herpesviruses finding in lower respiratory tract of ARDS patients hospitalized in ICU. The presence of this group of herpesviruses, in addition to the research of influenza viruses and other common respiratory viruses, was investigated in respiratory samples from 54 patients hospitalized in ICU, without a known microbiological causative agent. Moreover, the immunophenotype of each patient was analyzed. Herpesviruses DNA presence in the lower respiratory tract seemed not attributable to an impaired immunophenotype, whereas a significant correlation was observed between herpesviruses positivity and influenza virus infection. A higher ICU mortality was significantly related to the presence of herpesvirus infection in the lower respiratory tract as well as to impaired immunophenotype, as patients with poor outcome showed severe lymphopenia, affecting in particular T (CD3+) cells, since the first days of ICU hospitalization. In conclusion, these results indicate that herpesviruses lower respiratory tract infection, which occurs more frequently following influenza virus infection, can be a negative prognostic marker. An independent risk factor for ICU patients with ARDS is an impaired immunophenotype.
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Affiliation(s)
- Manuela Bonizzoli
- Intensive Care Unit and Regional ECMO Referral Center, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Rosaria Arvia
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Simona di Valvasone
- Intensive Care Unit and Regional ECMO Referral Center, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Francesco Liotta
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Krystyna Zakrzewska
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Alberta Azzi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
| | - Adriano Peris
- Intensive Care Unit and Regional ECMO Referral Center, Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
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50
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Thompson MG, Ferber JR, Odouli R, David D, Shifflett P, Meece JK, Naleway AL, Bozeman S, Spencer SM, Fry AM, Li DK. Results of a pilot study using self-collected mid-turbinate nasal swabs for detection of influenza virus infection among pregnant women. Influenza Other Respir Viruses 2016; 9:155-60. [PMID: 25711978 PMCID: PMC4415700 DOI: 10.1111/irv.12309] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2015] [Indexed: 11/30/2022] Open
Abstract
Background We evaluated the feasibility of asking pregnant women to self-collect and ship respiratory specimens. Methods In a preliminary laboratory study, we compared the RT-PCR cycle threshold (CT) values of influenza A and B viruses incubated at 4 storage temperatures (from 4 to 35°C) for 6 time periods (8, 24, 48, 72, and 168 hours and 30 days), resulting in 24 conditions that were compared to an aliquot tested after standard freezing (−20°C) (baseline condition). In a subsequent pilot study, during January–February, 2014, we delivered respiratory specimen collection kits to 53 pregnant women with a medically attended acute respiratory illness using three delivery methods. Results CT values were stable after storage at temperatures <27°C for up to 72 hours for influenza A viruses and 48 hours for influenza B viruses. Of 53 women who received kits during the pilot, 89% collected and shipped nasal swabs as requested. However, 30% (14/47) of the women took over 2 days to collect and ship their specimen. The human control gene, ribonuclease P (RNase P), was detected in 100% of nasal swab specimens. However, the mean CT values for RNase P (26·5, 95% confidence interval [CI] = 26·0–27·1) and for the 8 influenza A virus positives in our pilot (32·2, 95% CI = 28·9–35·5) were significantly higher than the CTs observed in our 2010–2012 study using staff-collected nasal pharyngeal swabs (P-values < 0·01). Discussion Self-collection of respiratory specimens is a promising research method, but further research is needed to quantify the sensitivity and specificity of the approach.
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Affiliation(s)
- Mark G Thompson
- Influenza Division, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
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