1
|
Farzi R, Pirbonyeh N, Kadivar MR, Moattari A. Prevalence of Influenza Viruses A and B, Adenovirus, Respiratory Syncytial Virus, and Human Metapneumonia Viruses among Children with Acute Respiratory Tract Infection. Adv Virol 2024; 2024:7613948. [PMID: 38292215 PMCID: PMC10824580 DOI: 10.1155/2024/7613948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/04/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
Background Acute respiratory tract infection (ARTI) is a significant cause of morbidity and mortality among children worldwide. The majority of acute respiratory infections in children are caused by viruses, with respiratory syncytial virus (RSV) being the most frequently encountered. Other important viral pathogens include human metapneumovirus, human coronaviruses, adenovirus, and influenza. These infections can lead to complications such as bronchitis and pneumonia. So, this study aimed to evaluate the prevalence of influenza viruses A and B, adenovirus, respiratory syncytial virus (RSV), and human metapneumovirus (HMPV) in children with ARTI. Methods The molecular diagnostic of polymerase chain reaction approach was used to detect influenza (A and B), metapneumovirus, respiratory syncytial virus (RSV), and adenovirus in respiratory samples of children with acute respiratory infection hospitalization in a teaching hospital of the Shiraz University of Medical Sciences in January 2016-March 2017. Results Of the 340 patients examined, 208 (61.20%) were male and the median age was 3.13 ± 2.38 years. Respiratory viruses were found in 179 (52.64%) patients. The male-to-female ratio was 1.63 : 1 in patients who were viral positive. Detection rates for influenza A, adenovirus, influenza B, RSV, and HMPV were 28.23%, 24.70%, 8.52%, 3.23%, and 2.64%, respectively, and coinfections were detected in 24.02%. The most common combination of two-virus coinfections was IFVA/AdV, followed by IFVB/AdV, AdV, IFVB/IFVA, RSV/IFVA, HMPV/AdV, RSV/AdV, and HMPV/IFVA. Conclusion The high prevalence of respiratory viruses in children hospitalized with ARTI suggests that viral infection may play a role in disease pathogenesis. This should be confirmed through the conduct of case-control studies and may inform the role of vaccination to prevent respiratory viral infections.
Collapse
Affiliation(s)
- Rana Farzi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Pirbonyeh
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Burn and Wound Healing Research Center, Microbiology Department, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Rahim Kadivar
- Department of Pediatrics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- Professor Alborzi Clinical Microbiology Research Center, Namazi Hospital, Shiraz Medical University, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
2
|
Kawase M, Suwa R, Sugimoto S, Kakizaki M, Kume Y, Chishiki M, Ono T, Okabe H, Norito S, Ujike M, Hosoya M, Hashimoto K, Shirato K. Evidence of the simultaneous replications of active viruses in specimens positive for multiple respiratory viruses. Microbiol Spectr 2024; 12:e0192023. [PMID: 38051050 PMCID: PMC10783086 DOI: 10.1128/spectrum.01920-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/04/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Since the pandemic of coronavirus diseases 2019, the use of real-time PCR assay has become widespread among people who were not familiar with it in virus detection. As a result, whether a high real-time PCR value in one time test indicates virus transmissibly became a complicated social problem, regardless of the difference in assays and/or amplification conditions, the time and number of diagnostic test during the time course of infection. In addition, the multiple positives in the test of respiratory viruses further add to the confusion in the interpretation of the infection. To address this issue, we performed virus isolation using pediatric SARI (severe acute respiratory infections) specimens on air-liquid interface culture of human bronchial/tracheal epithelial cell culture. The result of this study can be a strong evidence that the specimens showing positivity for multiple agents in real-time PCR tests possibly contain infectious viruses.
Collapse
Affiliation(s)
- Miyuki Kawase
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| | - Reiko Suwa
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| | - Satoko Sugimoto
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| | - Masatoshi Kakizaki
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| | - Yohei Kume
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Mina Chishiki
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Takashi Ono
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Hisao Okabe
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Sakurako Norito
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Makoto Ujike
- Faculty of Veterinary Medicine, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Mitsuaki Hosoya
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Koichi Hashimoto
- Department of Pediatrics, School of Medicine, Fukushima Medical University, Hikarigaoka, Fukushima, Japan
| | - Kazuya Shirato
- Department of Virology III, National Institute of Infectious Disease, Gakuen, Musashimurayama, Tokyo, Japan
| |
Collapse
|
3
|
Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [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: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
Collapse
Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| |
Collapse
|
4
|
Barahimi E, Azad MH, Hesarooeyeh ZG, Hafshejani NH, Defaee S, Seddighi N. Late diagnosis of respiratory syncytial virus and influenza co-infection during coronavirus disease 2019 pandemic: a case report. J Med Case Rep 2023; 17:437. [PMID: 37864237 PMCID: PMC10589917 DOI: 10.1186/s13256-023-04187-3] [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: 01/04/2023] [Accepted: 09/20/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV)-induced disease is one of the important causes of flu-like illness in older adults and can cause serious disease in those who are at high-risk medical conditions. During coronavirus disease 2019 (COVID-19) pandemic, because of overlapping symptoms of severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) infection with other respiratory infections, diagnosing diseases based on clinical and radiological findings was challenging and could cause misdiagnosis. CASE PRESENTATION An 87-year-old Persian man was admitted to the hospital due to loss of consciousness, respiratory distress, tachypnea, and oliguria. He had previously hospitalized because of cough, fever, loss of appetite, and fatigue. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) polymerase chain reaction (PCR) test was performed which was negative; however, based on ground glass opacity on his chest computed tomography (CT) scan and being on the outbreak of COVID-19, he fulfilled case definition of COVID-19; therefore, he received protocol's treatment (remdesivir) for COVID-19 and relatively recovered and discharged. In our center, we requested brain and chest CT scans, blood tests, and multiplex PCR. Multiplex PCR revealed co-infection of influenza virus and RSV. Although we had started pneumonia and sepsis treatment, old age, weak immune system and the delay in initiation of right antibiotic and antivirus therapy altogether led him to die. CONCLUSION As a takeaway lesson of this case report, it is necessary to pay attention to viruses that show similar symptoms during future specific virus pandemics, especially in patients with old age and weak immune systems.
Collapse
Affiliation(s)
- Elham Barahimi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mehdi Hassani Azad
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Zahra Ghaeini Hesarooeyeh
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | | | - Sahar Defaee
- Internal Medicine Department, Shahid Mohammadi Hospital, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Narjes Seddighi
- Student Research Committee, Faculty of Para-Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| |
Collapse
|
5
|
Pinky L, DeAguero JR, Remien CH, Smith AM. How Interactions During Viral-Viral Coinfection Can Shape Infection Kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.05.535744. [PMID: 37066297 PMCID: PMC10104040 DOI: 10.1101/2023.04.05.535744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Respiratory virus infections are a leading cause of disease worldwide with multiple viruses detected in 20-30% of cases and several viruses simultaneously circulating. Some infections with viral copathogens have been shown to result in reduced pathogenicity while other virus pairings can worsen disease. The mechanisms driving these dichotomous outcomes are likely variable and have only begun to be examined in the laboratory and clinic. To better understand viral-viral coinfections and predict potential mechanisms that result in distinct disease outcomes, we first systematically fit mathematical models to viral load data from ferrets infected with respiratory syncytial virus (RSV) followed by influenza A virus (IAV) after 3 days. The results suggested that IAV reduced the rate of RSV production while RSV reduced the rate of IAV infected cell clearance. We then explored the realm of possible dynamics for scenarios not examined experimentally, including different infection order, coinfection timing, interaction mechanisms, and viral pairings. IAV coinfection with rhinovirus (RV) or SARS-CoV-2 (CoV2) was examined by using human viral load data from single infections together with murine weight loss data from IAV-RV, RV-IAV, and IAV-CoV2 coinfections to guide the interpretation of the model results. Similar to the results with RSV-IAV coinfection, this analysis showed that the increased disease severity observed during murine IAV-RV or IAV-CoV2 coinfection was likely due to slower clearance of IAV infected cells by the other viruses. On the contrary, the improved outcome when IAV followed RV could be replicated when the rate of RV infected cell clearance was reduced by IAV. Simulating viral-viral coinfections in this way provides new insights about how viral-viral interactions can regulate disease severity during coinfection and yields testable hypotheses ripe for experimental evaluation.
Collapse
|
6
|
Bhar A, Gierse LC, Meene A, Wang H, Karte C, Schwaiger T, Schröder C, Mettenleiter TC, Urich T, Riedel K, Kaderali L. Application of a maximal-clique based community detection algorithm to gut microbiome data reveals driver microbes during influenza A virus infection. Front Microbiol 2022; 13:979320. [PMID: 36338082 PMCID: PMC9630851 DOI: 10.3389/fmicb.2022.979320] [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: 06/27/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022] Open
Abstract
Influenza A Virus (IAV) infection followed by bacterial pneumonia often leads to hospitalization and death in individuals from high risk groups. Following infection, IAV triggers the process of viral RNA replication which in turn disrupts healthy gut microbial community, while the gut microbiota plays an instrumental role in protecting the host by evolving colonization resistance. Although the underlying mechanisms of IAV infection have been unraveled, the underlying complex mechanisms evolved by gut microbiota in order to induce host immune response following IAV infection remain evasive. In this work, we developed a novel Maximal-Clique based Community Detection algorithm for Weighted undirected Networks (MCCD-WN) and compared its performance with other existing algorithms using three sets of benchmark networks. Moreover, we applied our algorithm to gut microbiome data derived from fecal samples of both healthy and IAV-infected pigs over a sequence of time-points. The results we obtained from the real-life IAV dataset unveil the role of the microbial families Ruminococcaceae, Lachnospiraceae, Spirochaetaceae and Prevotellaceae in the gut microbiome of the IAV-infected cohort. Furthermore, the additional integration of metaproteomic data enabled not only the identification of microbial biomarkers, but also the elucidation of their functional roles in protecting the host following IAV infection. Our network analysis reveals a fast recovery of the infected cohort after the second IAV infection and provides insights into crucial roles of Desulfovibrionaceae and Lactobacillaceae families in combating Influenza A Virus infection. Source code of the community detection algorithm can be downloaded from https://github.com/AniBhar84/MCCD-WN.
Collapse
Affiliation(s)
- Anirban Bhar
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | | | - Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Claudia Karte
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Theresa Schwaiger
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Charlotte Schröder
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | | | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| |
Collapse
|
7
|
Hwang JK, Na JY, Kim J, Oh JW, Kim YJ, Choi YJ. Age-Specific Characteristics of Adult and Pediatric Respiratory Viral Infections: A Retrospective Single-Center Study. J Clin Med 2022; 11:jcm11113197. [PMID: 35683584 PMCID: PMC9181129 DOI: 10.3390/jcm11113197] [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: 04/30/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 11/16/2022] Open
Abstract
This study aimed to identify age-specific characteristics of respiratory viral infections. Hospitalized patients with confirmed viral respiratory infections were included in the sample. The patients were divided into the pediatric group (<19 years old) and the adult group (≥19 years old). The groups were then subdivided based on age: 0−6, 7−12, 13−18, 19−49, 50−64, and ≥65 years old. These groups were compared to evaluate the differences in the pattern of respiratory viral infections. Among a total of 4058 pediatric patients (mean age 3.0 ± 2.9 years, n = 1793 females), 2829 (48.9%) had mono-infections, while 1229 (51.1%) had co-infections. Co-infections were the most common in the 0−6-year-old group (31.6%). Among 1550 adult patients (mean age 70.2 ± 15.3 years, n = 710 females), 1307 (85.6%) had mono-infections and 243 (14.4%) had co-infections. Co-infections were most common in the ≥65-year-old group (16.8%). Viral infection and co-infection rates decreased with age in pediatric patients but increased with increasing age in adults. In pediatric patients, the rates of viral infections and co-infections were high; the rate of co-infections was higher in younger patients. In adult patients, the rates of viral infections and co-infections were lower than those in pediatric patients; the rate of co-infections was higher in older patients.
Collapse
Affiliation(s)
- Jae Kyoon Hwang
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
| | - Jae Yoon Na
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
| | - Jihye Kim
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
| | - Jae-Won Oh
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Yong Joo Kim
- Department of Pediatrics, Hanyang University Seoul Hospital, Seoul 04763, Korea; (J.Y.N.); (J.K.); (Y.J.K.)
- Department of Pediatrics, College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Young-Jin Choi
- Department of Pediatrics, Hanyang University Guri Hospital, Guri 11923, Korea; (J.K.H.); (J.-W.O.)
- Correspondence:
| |
Collapse
|
8
|
Hamamoto I, Takahashi H, Shimazaki N, Nakamura K, Mizuta K, Sato K, Nishimura H, Yamamoto N, Hasegawa H, Odagiri T, Tashiro M, Nobusawa E. Suitability of NIID-MDCK cells as a substrate for cell-based influenza vaccine development from the perspective of adventitious virus susceptibility. Microbiol Immunol 2022; 66:361-370. [PMID: 35545856 DOI: 10.1111/1348-0421.12985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/27/2022] [Accepted: 05/08/2022] [Indexed: 11/30/2022]
Abstract
The practical use of cell-based seasonal influenza vaccines is currently being considered in Japan. From the perspective of adventitious virus contamination, we assessed the suitability of NIID-MDCK cells (NIID-MDCK-Cs) as a safe substrate for the isolation of influenza viruses from clinical specimens. We first established a sensitive multiplex real-time PCR system to screen for 27 respiratory viruses and used it on 34 virus samples that were isolated by passaging influenza-positive clinical specimens in NIID-MDCK-Cs. Incidentally, the limit of detection of the system was 100 or fewer genome copies per reaction. In addition to influenza viruses, human enterovirus 68 (HEV-D68) genomes were detected in two samples after two or three passages in NIID-MDCK-Cs. To further investigate the susceptibility of NIID-MDCK-Cs to adventitious viruses, eight common respiratory viruses were subjected to passages in NIID-MDCK-Cs. The genome copy numbers of seven viruses other than parainfluenza 3 decreased below the limit of detection (LOD) by passage 4. By passaging in NIID-MDCK-Cs, the genome numbers of the input HEV-D68, 1 x 108 copies, declined to 102 at passage 3 and to under the LOD at passage 4, whereas those of the other six viruses were under the LOD by passage 3. These results implied that during the process of isolating influenza viruses with NIID-MDCK-Cs, contaminating viruses other than parainfluenza 3 can be efficiently removed by passages in NIID-MDCK-Cs. NIID-MDCK-Cs could be a safe substrate for isolating influenza viruses that can be used to develop cell-based influenza vaccine candidate viruses. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Itsuki Hamamoto
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Hitoshi Takahashi
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Noriko Shimazaki
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Kazuya Nakamura
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Katsumi Mizuta
- Yamagata Prefectural Institute of Public Health, Yamagata, Japan
| | - Ko Sato
- Virus Research Center, Sendai Medical Center, National Hospital Organization, Sendai, Japan
| | - Hidekazu Nishimura
- Virus Research Center, Sendai Medical Center, National Hospital Organization, Sendai, Japan
| | - Norio Yamamoto
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan.,Department of Microbiology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Hideki Hasegawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Takato Odagiri
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Masato Tashiro
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| | - Eri Nobusawa
- Center for Influenza and Respiratory Virus Research, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo, 208-0011, Japan
| |
Collapse
|
9
|
Dai Y, Zhong J, Lan Y. Virus-virus interactions of febrile respiratory syndrome among patients in China based on surveillance data from February 2011 to December 2020. J Med Virol 2022; 94:4369-4377. [PMID: 35514049 DOI: 10.1002/jmv.27833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND The burden of acute respiratory infections is still considerable, and virus-virus interactions may affect their epidemics, but previous evidence is inconclusive. OBJECTIVE To quantitatively investigate the interactions among respiratory viruses at both the population and individual levels. METHODS Cases tested for influenza virus (IV), respiratory syncytial virus (RSV), human parainfluenza virus (PIV), human Adenovirus (AdV), human coronavirus (CoV), human bocavirus (BoV) and rhinoviruses (RV) were collected from the pathogen surveillance for febrile respiratory syndrome (FRS) in China from February 2011 to December 2020. We used spearman's rank correlation coefficients and binary logistic regression models to analyze the interactions between any two of the viruses at the population and individual levels, respectively. RESULTS Among 120,237 cases, 4.5% were co-infected with two or more viruses. Correlation coefficients showed 7 virus pairs were positively correlated, namely: IV and RSV, PIV and AdV, PIV and CoV, PIV and BoV, PIV and RV, AdV and BoV, CoV and RV. Regression models showed except for the negative interaction between IV and RV (OR=0.70, 95%CI: 0.61-0.81), all other virus pairs had positive interactions. CONCLUSION Most of the respiratory viruses interact positively, while IV and RV interact negatively. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Yucen Dai
- Department of Epidemiology and Health Statistics, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Jiao Zhong
- Department of Occupational and Environmental Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041.,Department of Osteoporosis, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Yajia Lan
- Department of Occupational and Environmental Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041
| |
Collapse
|
10
|
Sanz I, Perez D, Rojo S, Domínguez-Gil M, de Lejarazu RO, Eiros JM. Coinfections of influenza and other respiratory viruses are associated to children. An Pediatr (Barc) 2022; 96:334-341. [DOI: 10.1016/j.anpede.2021.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/11/2020] [Indexed: 11/29/2022] Open
|
11
|
Coinfection of SARS-CoV-2 and Influenza A virus increased disease severity, impaired neutralizing antibody, and CD4+ T cell responses. J Virol 2022; 96:e0187321. [PMID: 35107382 PMCID: PMC8941868 DOI: 10.1128/jvi.01873-21] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Given the current coronavirus disease 2019 (COVID-19) pandemic, coinfection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV) is a major concern for public health. However, the immunopathogenic events occurring with coinfections of SARS-CoV-2 and IAV remain unclear. Here, we report the pathogenic and immunological consequences of SARS-CoV-2 and IAV H1N1 coinfection in the K18-hACE2 transgenic mouse model. Compared with a single infection with SARS-CoV-2 or IAV, coinfections not only prolonged the primary virus infection period but also increased immune cell infiltration and inflammatory cytokine levels in bronchoalveolar lavage fluid leading to severe pneumonia and lung damage. Moreover, coinfections caused severe lymphopenia in peripheral blood, resulting in reduced total IgG, neutralizing antibody titers, and CD4+ T cell responses against each virus. This study sheds light on the immunopathogenesis of SARS-CoV-2 and IAV coinfection, which may guide the development of effective therapeutic strategies for the treatment of patients coinfected with these viruses. IMPORTANCE The cocirculation of influenza virus merging with the COVID-19 pandemic raises a potentially severe threat to public health. Recently, increasing numbers of SARS-CoV-2 and influenza virus coinfection have been reported from many countries. It is a worrisome issue that SARS-CoV-2 coinfection with other pathogens may worsen the clinical outcome and severity of COVID-19 and increase fatality. Here, we evaluated SARS-CoV-2 and IAV coinfection using the K18-hACE2 mouse model. Coinfected mice exhibited increased mortality with prolonged IAV shedding. Furthermore, coinfected mice showed a higher level of cytokines and chemokines than a single infection condition. Interestingly, our data show that coinfected mice showed significantly fewer virus-specific and neutralizing antibodies than the mice with a single infection. Overall, this study suggests that coinfection aggravates viral pathology by impaired neutralizing antibody response.
Collapse
|
12
|
Chekuri S, Szymczak WA, Goldstein DY, Nori P, Marrero Rolon R, Spund B, Singh-Tan S, Mohrmann L, Assa A, Southern WN, Baron SW. SARS-CoV-2 coinfection with additional respiratory virus does not predict severe disease: a retrospective cohort study. J Antimicrob Chemother 2021; 76:iii12-iii19. [PMID: 34555160 PMCID: PMC8460099 DOI: 10.1093/jac/dkab244] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) claimed over 4 million lives by July 2021 and continues to pose a serious public health threat. Objectives Our retrospective study utilized respiratory pathogen panel (RPP) results in patients with SARS-CoV-2 to determine if coinfection (i.e. SARS-CoV-2 positivity with an additional respiratory virus) was associated with more severe presentation and outcomes. Methods All patients with negative influenza/respiratory syncytial virus testing who underwent RPP testing within 7 days of a positive SARS-CoV-2 test at a large, academic medical centre in New York were examined. Patients positive for SARS-CoV-2 with a negative RPP were compared with patients positive for SARS-CoV-2 and positive for a virus by RPP in terms of biomarkers, oxygen requirements and severe COVID-19 outcome, as defined by mechanical ventilation or death within 30 days. Results Of the 306 SARS-CoV-2-positive patients with RPP testing, 14 (4.6%) were positive for a non-influenza virus (coinfected). Compared with the coinfected group, patients positive for SARS-CoV-2 with a negative RPP had higher inflammatory markers and were significantly more likely to be admitted (P = 0.01). Severe COVID-19 outcome occurred in 111 (36.3%) patients in the SARS-CoV-2-only group and 3 (21.4%) patients in the coinfected group (P = 0.24). Conclusions Patients infected with SARS-CoV-2 along with a non-influenza respiratory virus had less severe disease on presentation and were more likely to be admitted—but did not have more severe outcomes—than those infected with SARS-CoV-2 alone.
Collapse
Affiliation(s)
- Sweta Chekuri
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Wendy A Szymczak
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - D Yitzchak Goldstein
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Priya Nori
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Infectious Disease, Montefiore Medical Center, Bronx, NY, USA
| | - Rebecca Marrero Rolon
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Pathology, Montefiore Medical Center, Bronx, NY, USA
| | - Brian Spund
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Sumeet Singh-Tan
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Laurel Mohrmann
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Andrei Assa
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - William N Southern
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| | - Sarah W Baron
- Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Department of Medicine, Montefiore Medical Center, Bronx, NY, USA.,Division of Hospital Medicine, Montefiore Medical Center, Bronx, NY, USA
| |
Collapse
|
13
|
Zapf AJ, Hardick J, McBryde B, Sauer LM, Fenstermacher KZJ, Ricketts EP, Lin YC, Chen KF, Hsieh YH, Dugas A, Shaw-Saliba K, Pekosz A, Gaydos CA, Rothman RE. Impact of coinfection status and comorbidity on disease severity in adult emergency department patients with influenza B. Influenza Other Respir Viruses 2021; 16:236-246. [PMID: 34533270 PMCID: PMC8818819 DOI: 10.1111/irv.12907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022] Open
Abstract
Background Influenza B accounts for approximately one fourth of the seasonal influenza burden. However, research on the importance of influenza B has received less attention compared to influenza A. We sought to describe the association of both coinfections and comorbidities with disease severity among adults presenting to emergency departments (ED) with influenza B. Methods Nasopharyngeal samples from patients found to be influenza B positive in four US and three Taiwanese ED over four consecutive influenza seasons (2014–2018) were tested for coinfections with the ePlex RP RUO panel. Multivariable logistic regressions were fitted to model adjusted odds ratios (aOR) for two severity outcomes separately: hospitalization and pneumonia diagnosis. Adjusting for demographic factors, underlying health conditions, and the National Early Warning Score (NEWS), we estimated the association of upper respiratory coinfections and comorbidity with disease severity (including hospitalization or pneumonia). Results Amongst all influenza B positive individuals (n = 446), presence of another upper respiratory pathogen was associated with an increased likelihood of hospitalization (aOR = 2.99 [95% confidence interval (95% CI): 1.14–7.85, p = 0.026]) and pneumonia (aOR = 2.27 [95% CI: 1.25–4.09, p = 0.007]). Chronic lung diseases (CLD) were the strongest predictor for hospitalization (aOR = 3.43 [95% CI: 2.98–3.95, p < 0.001]), but not for pneumonia (aOR = 1.73 [95% CI: 0.80–3.78, p = 0.166]). Conclusion Amongst ED patients infected with influenza B, the presence of other upper respiratory pathogens was independently associated with both hospitalization and pneumonia; presence of CLD was also associated with hospitalization. These findings may be informative for ED clinician's in managing patients infected with influenza B.
Collapse
Affiliation(s)
- Alexander J Zapf
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Justin Hardick
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Breana McBryde
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Lauren M Sauer
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Erin P Ricketts
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yi-Chin Lin
- Department of Emergency Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Kuan-Fu Chen
- Department of Emergency Medicine, Chang Gung Memorial Hospital, Keelung, Taiwan.,Clinical Informatics and Medical Statistics Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Hsiang Hsieh
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrea Dugas
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kathryn Shaw-Saliba
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Charlotte A Gaydos
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard E Rothman
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | |
Collapse
|
14
|
Rais Y, Fu Z, Drabovich AP. Mass spectrometry-based proteomics in basic and translational research of SARS-CoV-2 coronavirus and its emerging mutants. Clin Proteomics 2021; 18:19. [PMID: 34384361 PMCID: PMC8358260 DOI: 10.1186/s12014-021-09325-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 08/07/2021] [Indexed: 01/08/2023] Open
Abstract
Molecular diagnostics of the coronavirus disease of 2019 (COVID-19) now mainly relies on the measurements of viral RNA by RT-PCR, or detection of anti-viral antibodies by immunoassays. In this review, we discussed the perspectives of mass spectrometry-based proteomics as an analytical technique to identify and quantify proteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and to enable basic research and clinical studies on COVID-19. While RT-PCR and RNA sequencing are indisputably powerful techniques for the detection of SARS-CoV-2 and identification of the emerging mutations, proteomics may provide confirmatory diagnostic information and complimentary biological knowledge on protein abundance, post-translational modifications, protein-protein interactions, and the functional impact of the emerging mutations. Pending advances in sensitivity and throughput of mass spectrometry and liquid chromatography, shotgun and targeted proteomic assays may find their niche for the differential quantification of viral proteins in clinical and environmental samples. Targeted proteomic assays in combination with immunoaffinity enrichments also provide orthogonal tools to evaluate cross-reactivity of serology tests and facilitate development of tests with the nearly perfect diagnostic specificity, this enabling reliable testing of broader populations for the acquired immunity. The coronavirus pandemic of 2019-2021 is another reminder that the future global pandemics may be inevitable, but their impact could be mitigated with the novel tools and assays, such as mass spectrometry-based proteomics, to enable continuous monitoring of emerging viruses, and to facilitate rapid response to novel infectious diseases.
Collapse
Affiliation(s)
- Yasmine Rais
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Zhiqiang Fu
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
15
|
Pacheco GA, Gálvez NMS, Soto JA, Andrade CA, Kalergis AM. Bacterial and Viral Coinfections with the Human Respiratory Syncytial Virus. Microorganisms 2021; 9:microorganisms9061293. [PMID: 34199284 PMCID: PMC8231868 DOI: 10.3390/microorganisms9061293] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 02/07/2023] Open
Abstract
The human respiratory syncytial virus (hRSV) is one of the leading causes of acute lower respiratory tract infections in children under five years old. Notably, hRSV infections can give way to pneumonia and predispose to other respiratory complications later in life, such as asthma. Even though the social and economic burden associated with hRSV infections is tremendous, there are no approved vaccines to date to prevent the disease caused by this pathogen. Recently, coinfections and superinfections have turned into an active field of study, and interactions between many viral and bacterial pathogens have been studied. hRSV is not an exception since polymicrobial infections involving this virus are common, especially when illness has evolved into pneumonia. Here, we review the epidemiology and recent findings regarding the main polymicrobial infections involving hRSV and several prevalent bacterial and viral respiratory pathogens, such as Staphylococcus aureus, Pseudomonas aeruginosa, Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Klebsiella pneumoniae, human rhinoviruses, influenza A virus, human metapneumovirus, and human parainfluenza viruses. As reports of most polymicrobial infections involving hRSV lack a molecular basis explaining the interaction between hRSV and these pathogens, we believe this review article can serve as a starting point to interesting and very much needed research in this area.
Collapse
Affiliation(s)
- Gaspar A. Pacheco
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
| | - Nicolás M. S. Gálvez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
| | - Jorge A. Soto
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
| | - Catalina A. Andrade
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
| | - Alexis M. Kalergis
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute of Immunology and Immunotherapy, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile; (G.A.P.); (N.M.S.G.); (J.A.S.); (C.A.A.)
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
- Correspondence: ; Tel.: +56-2-686-2842; Fax: +56-2-222-5515
| |
Collapse
|
16
|
Sanz I, Perez D, Rojo S, Domínguez-Gil M, Lejarazu ROD, Eiros JM. [Coinfections of influenza and other respiratory viruses are associated to children]. An Pediatr (Barc) 2021; 96:S1695-4033(21)00143-0. [PMID: 33745837 DOI: 10.1016/j.anpedi.2020.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Coinfections of influenza and other respiratory viruses (ORVs) are frequent in the epidemic season. The aim of this study was to examine the demographic and virological variables associated with coinfections by influenza and ORVs. MATERIALS AND METHODS We analysed respiratory samples of patients with laboratory-confirmed influenza using molecular diagnostic methods obtained in 8 consecutive influenza seasons (2011-2012 to 2018-2019). We analysed data focusing on different variables: age, sex, type of patient (hospitalized/sentinel) and detected type/subtype of influenza. RESULTS Coinfections of influenza and ORVs were detected in 17.8% of influenza-positive samples. The probability of detecting coinfection was significantly higher in young children (0-4 years; OR: 2.7; 95% CI: 2.2-3.4), children (5-14 years; OR: 1.6; 95% CI: 1.2-2.1) and patients infected with the A(H3N2) subtype (OR: 1.4; 95% CI: 1.14-1.79). Also, we found a significantly higher frequency of coinfections involving influenza and 2 or more other respiratory viruses in young children (0-4 years; OR: 0.5; 95% CI: 0.32-0.8), adults (40-64 years; OR: 0.5; 95% CI: 0.3-0.9) and women (OR: 0.7; 95% CI: 0.5-0.9). DISCUSSION These results show that coinfections of influenza and ORVs are more frequent in young children and children, and in cases involving the A(H3N2) influenza subtype. Our findings can be useful to guide the use of multiplex diagnostic methods in laboratories with limited resources.
Collapse
Affiliation(s)
- Ivan Sanz
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España.
| | - Diana Perez
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España
| | - Silvia Rojo
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España; Unidad de Virología, Servicio de Microbiología e Inmunología, Hospital Clínico Universitario de Valladolid, Valladolid, España
| | - Marta Domínguez-Gil
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España; Servicio de Microbiología, Hospital Universitario Río Hortega, Valladolid, España
| | - Raúl Ortiz de Lejarazu
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España
| | - José María Eiros
- Centro Nacional de Gripe de Valladolid, Edifico Rondilla, Hospital Clínico Universitario de Valladolid, Valladolid, España; Unidad de Virología, Servicio de Microbiología e Inmunología, Hospital Clínico Universitario de Valladolid, Valladolid, España; Servicio de Microbiología, Hospital Universitario Río Hortega, Valladolid, España
| |
Collapse
|
17
|
Lopez-Acevo CA, Arrendondo-Loza E, Salinas-Carmona MC, Rendon A, Martinez-Castilla AM, Vázquez-Marmolejo AV, Munoz-Maldonado G, Rosas-Taraco AG. Cortisol and perceived stress are associated with cytokines levels in patients infected with influenza B virus. Cytokine 2020; 138:155400. [PMID: 33338918 DOI: 10.1016/j.cyto.2020.155400] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/27/2022]
Abstract
Influenza B virus (IBV) causes respiratory infectious disease. Cytokines are important immune mediators during infectious diseases. Cortisol and stress have been related to respiratory infection susceptibility and cytokine regulation. Little is known about systemic cytokines, cortisol, and perceived stress in the early stages of IBV infection. We researched the systemic cytokines and cortisol, as well as the perceived stress and blood cell count in patients infected with IBV. The diagnosis was established using the Luminex xTAG RVP kit and confirmed with qRT-PCR for IBV viral load. The perceived stress was evaluated using the perceived stress scale (PSS-10). Twenty-five plasma cytokines were determined using multiplex immunoassay and cortisol by ELISA. The leukocyte differential count was measured with a standard laboratory protocol. Th1, Th17, and IL-10 cytokines were higher in IBV infected patients (P < 0.05). Leukocytes and neutrophil count negatively correlated with viral load (P < 0.05). Perceived stress had a negative effect on monocyte and systemic cytokines in IBV infected patients (P < 0.05). Cortisol was higher in patients infected with IBV and correlated positively with CCL20 (P < 0.05). Cortisol showed a positive effect on most of the systemic cytokines (P < 0.05). In conclusion, a cytokine pattern was found in IBV infected patients, as well as the possible role of leukocyte counts in the control of IBV. Our results suggest the importance of cortisol and perceived stress on systemic cytokines in patients infected with IBV, but more studies are needed to understand their role in cytokine production in respiratory infectious disease.
Collapse
Affiliation(s)
- Carlos A Lopez-Acevo
- Universidad Autonoma de Nuevo Leon, Faculty of Medicine, Department of Psichiatry, Monterrey, Nuevo Leon, Mexico
| | - Erick Arrendondo-Loza
- Universidad Autonoma de Nuevo Leon, Faculty of Medicine, Department of Immunology, Monterrey, Nuevo Leon, Mexico
| | - Mario C Salinas-Carmona
- Universidad Autonoma de Nuevo Leon, Faculty of Medicine, Department of Immunology, Monterrey, Nuevo Leon, Mexico
| | - Adrian Rendon
- Universidad Autonoma de Nuevo Leon, University Hospital, Centro de Investigacion Prevencion y Tratamiento de Infecciones Respiratorias (CIPTIR)
| | - Azalia M Martinez-Castilla
- Universidad Autonoma de Nuevo Leon, Faculty of Medicine, Department of Immunology, Monterrey, Nuevo Leon, Mexico
| | - Anna V Vázquez-Marmolejo
- Universidad Autonoma de Nuevo Leon, Faculty of Medicine, Department of Immunology, Monterrey, Nuevo Leon, Mexico
| | - Gerardo Munoz-Maldonado
- Universidad Autonoma de Nuevo Leon, University Hospital, Service of General Surgery, Monterrey, Nuevo Leon, Mexico
| | - Adrian G Rosas-Taraco
- Universidad Autonoma de Nuevo Leon, Faculty of Medicine, Department of Immunology, Monterrey, Nuevo Leon, Mexico.
| |
Collapse
|
18
|
Lew S, Manes P, Smith B. Coinfection with SARS-CoV-2 and Influenza A Virus in a 32-Year-Old Man. AMERICAN JOURNAL OF CASE REPORTS 2020; 21:e926092. [PMID: 33188162 PMCID: PMC7672510 DOI: 10.12659/ajcr.926092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND There was a growing presumption that coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and another viral respiratory illness was nonexistent. Although there has been an increasing number of coinfection cases since the beginning of the SARS-CoV-2 pandemic, there is still a significant lack of information regarding the symptomatology, treatment, prognosis, and reasoning behind coinfection. This raises concern of the possibility of misdiagnosis or delay in treatment. CASE REPORT This case report discusses a coinfection of SARS-CoV-2 and Influenza A in a 32-year-old man to highlight that these viruses can coexist within the same patient. This patient unfortunately died of persistent respiratory failure after several days in the ICU. CONCLUSIONS Coinfection of SARS-CoV-2 and Influenza A can occur and lead to a poor prognosis.
Collapse
Affiliation(s)
- Sungyub Lew
- Department of Family Medicine, Brooklyn Hospital Center, Brooklyn, NY, USA
| | - Prabhjot Manes
- Department of Family Medicine, Brooklyn Hospital Center, Brooklyn, NY, USA
| | - Brittany Smith
- Department of Family Medicine, Brooklyn Hospital Center, Brooklyn, Grenada.,Saint George's University School of Medicine, True Blue, Grenada
| |
Collapse
|
19
|
Friedler A. Sociocultural, behavioural and political factors shaping the COVID-19 pandemic: the need for a biocultural approach to understanding pandemics and (re)emerging pathogens. Glob Public Health 2020; 16:17-35. [PMID: 33019889 DOI: 10.1080/17441692.2020.1828982] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although there has been increasing focus in recent years on interdisciplinary approaches to health and disease, and in particular the dimension of social inequalities in epidemics, infectious diseases have been much less focused on. This is especially true in the area of cultural dynamics and their effects on pathogen behaviours, although there is evidence to suggest that this relationship is central to shaping our interactions with infectious disease agents on a variety of levels. This paper makes a case for a biocultural approach to pandemics such as COVID-19. It then uses this biocultural framework to examine the anthropogenic dynamics that influenced and continue to shape the COVID-19 pandemic, both during its initial phase and during critical intersections of the pandemic. Through this understanding of biocultural interactions between people, animals and pathogens, a broader societal and political dimension is drawn as a function of population level and international cultures, to reflect on the culturally mediated differential burden of the pandemic. Ultimately, it is argued that a biocultural perspective on infectious disease pandemics will allow for critical reflection on how culture shapes our behaviours at all levels, and how the effects of these behaviours are ultimately foundational to pathogen ecology and evolution.
Collapse
Affiliation(s)
- Anna Friedler
- Département des sciences humaines et sociales, École des Hautes Études en Santé Publique - Campus de Paris, Saint-Denis, France.,l'Unité des Virus Emergents, Aix-Marseille Université, Marseille, France
| |
Collapse
|
20
|
Ozaras R, Cirpin R, Duran A, Duman H, Arslan O, Bakcan Y, Kaya M, Mutlu H, Isayeva L, Kebanlı F, Deger BA, Bekeshev E, Kaya F, Bilir S. Influenza and COVID-19 coinfection: Report of six cases and review of the literature. J Med Virol 2020; 92:2657-2665. [PMID: 32497283 DOI: 10.1002/jmv.26125] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) pandemic caused infection in a season when influenza is still prevalent. Both viruses have similar transmission characteristics and common clinical manifestations. Influenza has been described to cause respiratory infection with some other respiratory pathogens. However, the information of COVID-19 and influenza coinfection is limited. In this study, we reported our coinfected cases and reviewed the literature. We included all COVID-19 diagnosed patients. All patients with a presumed diagnosis of COVID-19 were routinely screened for influenza. Their thorax radiology was reviewed for COVID-19-influenza differentiation. During the study period, 1103 patients have been diagnosed with COVID-19. Among them, six patients (0.54%) were diagnosed coinfected with influenza. There have been 28 more coinfected patients reported. Laboratory-based screening studies reported more patients. Thorax radiology findings were compatible with COVID-19 in five and with influenza in one of our patients. Our cases were mild to moderate in severity. The reported cases in the literature included patients died (n = 2) and those living ventilator dependent or under mechanical ventilation. COVID-19 and influenza coinfection is rare. Screening studies report more cases, suggesting that unless screening patients with COVID-19, the coinfection remains undiagnosed and underestimated. Increasing experience in thoracic radiology may contribute to diagnose the responsible virus(es) from the clinical illness. Influenza vaccine for larger population groups can be recommended to simplify clinicians' work.
Collapse
Affiliation(s)
- Resat Ozaras
- Infectious Diseases Department, Medilife Health Group, Istanbul, Turkey
| | - Rasim Cirpin
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Arif Duran
- Emergency Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Habibe Duman
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Ozgur Arslan
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Yasin Bakcan
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Metin Kaya
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Huseyin Mutlu
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Leyla Isayeva
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Fatih Kebanlı
- Chest Diseases Department, Medilife Health Group, Istanbul, Turkey
| | - Bekir A Deger
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Eldar Bekeshev
- Radiology Department, Medilife Health Group, Istanbul, Turkey
| | - Fatma Kaya
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| | - Suat Bilir
- Internal Medicine Department, Medilife Health Group, Istanbul, Turkey
| |
Collapse
|
21
|
Le YH, Nguyen KC, Coleman KK, Nguyen TT, Than ST, Phan HH, Nguyen MD, Ngu ND, Phan DT, Hoang PVM, Trieu LP, Bailey ES, Warkentien TE, Gray GC. Virus detections among patients with severe acute respiratory illness, Northern Vietnam. PLoS One 2020; 15:e0233117. [PMID: 32396550 PMCID: PMC7217455 DOI: 10.1371/journal.pone.0233117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/28/2020] [Indexed: 01/02/2023] Open
Abstract
Severe acute respiratory illness (SARI) is a major cause of death and morbidity in low- and middle-income countries, however, the etiologic agents are often undetermined due to the lack of molecular diagnostics in hospitals and clinics. To examine evidence for select viral infections among patients with SARI in northern Vietnam, we studied 348 nasopharyngeal samples from military and civilian patients admitted to 4 hospitals in the greater Hanoi area from 2017–2019. Initial screening for human respiratory viral pathogens was performed in Hanoi, Vietnam at the National Institute of Hygiene and Epidemiology (NIHE) or the Military Institute of Preventative Medicine (MIPM), and an aliquot was shipped to Duke-NUS Medical School in Singapore for validation. Patient demographics were recorded and used to epidemiologically describe the infections. Among military and civilian cases of SARI, 184 (52.9%) tested positive for one or more respiratory viruses. Influenza A virus was the most prevalent virus detected (64.7%), followed by influenza B virus (29.3%), enterovirus (3.8%), adenovirus (1.1%), and coronavirus (1.1%). Risk factor analyses demonstrated an increased risk of influenza A virus detection among military hospital patients (adjusted OR, 2.0; 95% CI, 1.2–3.2), and an increased risk of influenza B virus detection among patients enrolled in year 2017 (adjusted OR, 7.9; 95% CI, 2.7–22.9). As influenza A and B viruses were commonly associated with SARI and are treatable, SARI patients entering these hospitals would benefit if the hospitals were able to adapt onsite molecular diagnostics.
Collapse
Affiliation(s)
- Yen H. Le
- Military Institute of Preventive Medicine, Hanoi, Vietnam
| | - Khanh C. Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Kristen K. Coleman
- Emerging Infectious Diseases Programme, Duke-National University of Singapore, Singapore
| | - Tham T. Nguyen
- Emerging Infectious Diseases Programme, Duke-National University of Singapore, Singapore
| | - Son T. Than
- Emerging Infectious Diseases Programme, Duke-National University of Singapore, Singapore
| | - Hai H. Phan
- Hai Phong Provincial Preventive Medicine Center, Hai Phong, Vietnam
| | - Manh D. Nguyen
- Military Institute of Preventive Medicine, Hanoi, Vietnam
| | - Nghia D. Ngu
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Dan T. Phan
- Military Institute of Preventive Medicine, Hanoi, Vietnam
| | | | - Long P. Trieu
- Military Institute of Preventive Medicine, Hanoi, Vietnam
| | - Emily S. Bailey
- Division of Infectious Diseases, Global Health Institute, Duke University, Durham, North Carolina, United States of America
| | | | - Gregory C. Gray
- Emerging Infectious Diseases Programme, Duke-National University of Singapore, Singapore
- Division of Infectious Diseases, Global Health Institute, Duke University, Durham, North Carolina, United States of America
- Global Health Center, Duke Kunshan University, Kunshan, China
- * E-mail:
| |
Collapse
|
22
|
LeBlanc JJ, ElSherif M, Mulpuru S, Warhuus M, Ambrose A, Andrew M, Boivin G, Bowie W, Chit A, Dos Santos G, Green K, Halperin SA, Hatchette TF, Ibarguchi B, Johnstone J, Katz K, Langley JM, Lagacé-Wiens P, Loeb M, Lund A, MacKinnon-Cameron D, McCarthy A, McElhaney JE, McGeer A, Poirier A, Powis J, Richardson D, Semret M, Shinde V, Smyth D, Trottier S, Valiquette L, Webster D, Ye L, McNeil S. Validation of the Seegene RV15 multiplex PCR for the detection of influenza A subtypes and influenza B lineages during national influenza surveillance in hospitalized adults. J Med Microbiol 2020; 69:256-264. [PMID: 31264957 PMCID: PMC7431100 DOI: 10.1099/jmm.0.001032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/16/2019] [Indexed: 01/04/2023] Open
Abstract
Background. The Serious Outcomes Surveillance Network of the Canadian Immunization Research Network (CIRN SOS) has been performing active influenza surveillance since 2009 (ClinicalTrials.gov identifier: NCT01517191). Influenza A and B viruses are identified and characterized using real-time reverse-transcriptase polymerase chain reaction (RT-PCR), and multiplex testing has been performed on a subset of patients to identify other respiratory virus aetiologies. Since both methods can identify influenza A and B, a direct comparison was performed.Methods. Validated real-time RT-PCRs from the World Health Organization (WHO) to identify influenza A and B viruses, characterize influenza A viruses into the H1N1 or H3N2 subtypes and describe influenza B viruses belonging to the Yamagata or Victoria lineages. In a subset of patients, the Seeplex RV15 One-Step ACE Detection assay (RV15) kit was also used for the detection of other respiratory viruses.Results. In total, 1111 nasopharyngeal swabs were tested by RV15 and real-time RT-PCRs for influenza A and B identification and characterization. For influenza A, RV15 showed 98.0 % sensitivity, 100 % specificity and 99.7 % accuracy. The performance characteristics of RV15 were similar for influenza A subtypes H1N1 and H3N2. For influenza B, RV15 had 99.2 % sensitivity, 100 % specificity and 99.8 % accuracy, with similar assay performance being shown for both the Yamagata and Victoria lineages.Conclusions. Overall, the detection of circulating subtypes of influenza A and lineages of influenza B by RV15 was similar to detection by real-time RT-PCR. Multiplex testing with RV15 allows for a more comprehensive respiratory virus surveillance in hospitalized adults, without significantly compromising the reliability of influenza A or B virus detection.
Collapse
Affiliation(s)
- J. J. LeBlanc
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - M. ElSherif
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - S. Mulpuru
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - M. Warhuus
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - A. Ambrose
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - M. Andrew
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - G. Boivin
- Centre Hospitalier Universitaire de Québec, QC, Canada
| | - W. Bowie
- University of British Columbia, Vancouver, BC, Canada
| | - A. Chit
- Sanofi Pasteur, Swiftwater, PA, USA
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - G. Dos Santos
- Business & Decision Life Sciences (on behalf of GSK), Bruxelles, Belgium
- Present address: GSK, Wavre, Belgium
| | - K. Green
- Mount Sinai Hospital, Toronto, ON, Canada
| | - S. A. Halperin
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - T. F. Hatchette
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - B. Ibarguchi
- GSK, Mississauga, ON, Canada
- Present address: Bayer, Inc., Mississauga, Ontario, Canada
| | - J. Johnstone
- Public Health Ontario and University of Toronto, Toronto, ON, Canada
| | - K. Katz
- North York General Hospital, Toronto, ON, Canada
| | - J. M. Langley
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | | | - M. Loeb
- Public Health Ontario and University of Toronto, Toronto, ON, Canada
| | - A. Lund
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - D. MacKinnon-Cameron
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - A. McCarthy
- Ottawa Hospital General, Ottawa, Ontario, Canada
| | - J. E. McElhaney
- Health Sciences North Research Institute, Sudbury, ON, Canada
| | - A. McGeer
- Mount Sinai Hospital, Toronto, ON, Canada
| | - A. Poirier
- Centre Intégré Universitaire de Santé et Services Sociaux, Quebec, QC, Canada
| | - J. Powis
- Toronto East General Hospital, Toronto, ON, Canada
| | | | - M. Semret
- McGill University, Montreal, QC, Canada
| | - V. Shinde
- GSK, King of Prussia, PA, USA
- Present address: Novavax Vaccines, Washington, DC, USA
| | - D. Smyth
- The Moncton Hospital, Moncton, NB, Canada
| | - S. Trottier
- Centre Hospitalier Universitaire de Québec, QC, Canada
| | | | | | - L. Ye
- Canadian Center for Vaccinology, Dalhousie University, IWK Health Centre, and Nova Scotia Health Authority, Halifax, NS, Canada
| | - S. A. McNeil
- Ottawa Hospital Research Institute, University of Ottawa, Ottawa, ON, Canada
| |
Collapse
|
23
|
Increased Detection of Viruses in Children with Respiratory Tract Infection Using PCR. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17020564. [PMID: 31952364 PMCID: PMC7013517 DOI: 10.3390/ijerph17020564] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/06/2020] [Accepted: 01/12/2020] [Indexed: 01/06/2023]
Abstract
Respiratory viruses are a common cause of respiratory tract infection (RTI), particularly in neonates and children. Rapid and accurate diagnosis of viral infections could improve clinical outcomes and reduce the use of antibiotics and treatment sessions. Advances in diagnostic technology contribute to the accurate detection of viruses. We performed a multiplex real-time polymerase chain reaction (PCR) to investigate the viral etiology in pediatric patients and compared the detection rates with those determined using traditional antigen tests and virus cultures. Fifteen respiratory viruses were included in our investigation: respiratory syncytial virus A/B (RSV), influenza virus A (FluA) and influenza virus B (FluB), human metapneumovirus (MPV), enterovirus (EV), human parainfluenza virus (PIV) types 1-4, human rhinovirus (RV), human coronavirus OC43, NL63, and 229E, human adenovirus (ADV), and human bocavirus (Boca). In total, 474 specimens were collected and tested. Respiratory viruses were detected more frequently by PCR (357, 75.3%) than they were by traditional tests (229, 49.3%). The leading pathogens were RSV (113, 23.8%), RV (72, 15.2%), PIV3 (53, 11.2%), FluA (51, 10.8%), and ADV (48, 10.1%). For children younger than 5 years, RSV and RV were most prevalent; for children older than 5 years, FluA and ADV were the most frequently detected. Of the specimens, 25.8% (92/357) were coinfected with two or more viruses. RV, Boca, PIV2, FluB, and PIV4 had higher rates of coinfection; MPV and PIV1 had the lowest rates of coinfection (9.1% and 5.3%). To conclude, the detection power of PCR was better than that of traditional antigen tests and virus cultures when considering the detection of respiratory viruses. RSV and RV were the leading viral pathogens identified in the respiratory specimens. One-quarter of the positive specimens were coinfected with two or more viruses. In the future, further application of PCR may contribute to the rapid and accurate diagnosis of respiratory viruses and could improve patient outcomes.
Collapse
|
24
|
A 3-Year Retrospective Study of the Epidemiology of Acute Respiratory Viral Infections in Pediatric Patients With Cancer Undergoing Chemotherapy. J Pediatr Hematol Oncol 2019; 41:e242-e246. [PMID: 30688827 DOI: 10.1097/mph.0000000000001418] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Acute viral respiratory infections are common causes of febrile episodes in children. There are still limited data about distribution of acute viral respiratory infections in children with cancer. OBJECTIVE The first aim of this study was to evaluate the viral etiology and seasonality of acute viral respiratory infection in pediatric patients with cancer in a 3-year study. Our second aim was to evaluate the impact of viral infections on delaying the patients' chemotherapy or radiotherapy. MATERIALS AND METHODS This cross-sectional study was conducted from January 2014 to July 2017. Nasopharyngeal aspirates were analyzed in patients younger than 21 years with acute respiratory infections. Patients were treated in the Pediatric Hematology and Oncology Department of Dr. Behçet Uz Children's Hospital with real-time multiplex polymerase chain reaction. Data were analyzed to determine the frequency and seasonality of infections. The χ or the Fisher exact tests were used. RESULTS A total of 219 samples of nasopharyngeal aspirates and blood were analyzed. The mean patient age was 76.8±59.3 months, with 46.3% female and 53.7% male children in a total of 108 patients. Of this total, 55% (60/108 cases) had multiple acute respiratory infections. Acute lymphoblastic leukemia (48.1%) was the most prevalent disease. The 3 most prevalent viruses were human rhinovirus (HRV) (33.1%), parainfluenza (PI) (18.7%), and coronavirus (CoV) (14.8%). In terms of the seasonal distribution of viruses, PI was most common in winter 2014, HRV in spring 2014, HRV in fall 2014, PI in winter 2015 and summer 2015, CoV in spring 2015, HRV in fall 2015, both influenza and HRV in winter 2016, both human metapneumovirus and bocavirus in spring 2016, HRV in summer 2016, both HRV and PI in fall 2016, both respiratory syncytial virus and influenza in winter 2017, HRV in spring 2017, and both HRV and adenovirus in summer 2017. The mean duration of neutropenia for patients with viral respiratory infection was 17.1±13.8 (range: 2 to 90) days. The mean duration of symptoms of viral respiratory infection was 6.8±4.2 (range: 2 to 31) days. A delay in chemotherapy treatment owing to viral respiratory infection was detected in 73 (33.3%) patients. The mean duration of delay in chemotherapy treatment was 9.6±5.4 (range: 3 to 31) days. CONCLUSIONS In conclusion, we report our 3-year experience about the frequency and seasonality of respiratory viruses in children with cancer.
Collapse
|
25
|
Vasileiou S, Turney AM, Kuvalekar M, Mukhi SS, Watanabe A, Lulla P, Ramos CA, Naik S, Vera JF, Tzannou I, Leen AM. Rapid generation of multivirus-specific T lymphocytes for the prevention and treatment of respiratory viral infections. Haematologica 2019; 105:235-243. [PMID: 31004020 PMCID: PMC6939529 DOI: 10.3324/haematol.2018.206896] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/16/2019] [Indexed: 11/29/2022] Open
Affiliation(s)
- Spyridoula Vasileiou
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Anne M Turney
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Manik Kuvalekar
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Shivani S Mukhi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Ayumi Watanabe
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Premal Lulla
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Carlos A Ramos
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Swati Naik
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Juan F Vera
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Ifigeneia Tzannou
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| | - Ann M Leen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, USA
| |
Collapse
|
26
|
Price OH, Sullivan SG, Sutterby C, Druce J, Carville KS. Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia. Epidemiol Infect 2019; 147:e221. [PMID: 31364539 PMCID: PMC6625191 DOI: 10.1017/s0950268819001055] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/18/2019] [Accepted: 03/27/2019] [Indexed: 12/29/2022] Open
Abstract
Several studies have reported evidence of interference between respiratory viruses: respiratory viruses rarely reach their epidemic peak concurrently and there appears to be a negative association between infection with one respiratory virus and co-infection with another. We used results spanning 16 years (2002-2017) of a routine diagnostic multiplex panel that tests for nine respiratory viruses to further investigate these interactions in Victoria, Australia. Time series analyses were used to plot the proportion positive for each virus. The seasonality of all viruses included was compared with respiratory syncytial virus (RSV) and influenza A virus using cross-correlations. Logistic regression was used to explore the likelihood of co-infection with one virus given infection with another. Seasonal peaks were observed each year for influenza A and RSV and less frequently for influenza B, coronavirus and parainfluenza virus. RSV circulated an average of 6 weeks before influenza A. Co-infection with another respiratory virus was less common with picornavirus, RSV or influenza A infection. Our findings provide further evidence of a temporal relationship in the circulation of respiratory viruses. A greater understanding of the interaction between respiratory viruses may enable better prediction of the timing and magnitude of respiratory virus epidemics.
Collapse
Affiliation(s)
- O. H. Price
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
| | - S. G. Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - C. Sutterby
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - J. Druce
- Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
| | - K. S. Carville
- Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
| |
Collapse
|
27
|
Neumann F, Hernández-Neuta I, Grabbe M, Madaboosi N, Albert J, Nilsson M. Padlock Probe Assay for Detection and Subtyping of Seasonal Influenza. Clin Chem 2018; 64:1704-1712. [PMID: 30257827 DOI: 10.1373/clinchem.2018.292979] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/31/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Influenza remains a constant threat worldwide, and WHO estimates that it affects 5% to 15% of the global population each season, with an associated 3 to 5 million severe cases and up to 500000 deaths. To limit the morbidity and the economic burden of influenza, improved diagnostic assays are needed. METHODS We developed a multiplexed assay for the detection and subtyping of seasonal influenza based on padlock probes and rolling circle amplification. The assay simultaneously targets all 8 genome segments of the 4 circulating influenza variants-A(H1N1), A(H3N2), B/Yamagata, and B/Victoria-and was combined with a prototype cartridge for inexpensive digital quantification. Characterized virus isolates and patient nasopharyngeal swabs were used for assay design and analytical validation. The diagnostic performance was assessed by blinded testing of 50 clinical samples analyzed in parallel with a commercial influenza assay, Simplexa™ Flu A/B & RSV Direct. RESULTS The assay had a detection limit of 18 viral RNA copies and achieved 100% analytical and clinical specificity for differential detection and subtyping of seasonal circulating influenza variants. The diagnostic sensitivity on the 50 clinical samples was 77.5% for detecting influenza and up to 73% for subtyping seasonal variants. CONCLUSIONS We have presented a proof-of-concept padlock probe assay combined with an inexpensive digital readout for the detection and subtyping of seasonal influenza strains A and B. The demonstrated high specificity and multiplexing capability, together with the digital quantification, established the assay as a promising diagnostic tool for seasonal influenza.
Collapse
Affiliation(s)
- Felix Neumann
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Iván Hernández-Neuta
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Malin Grabbe
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Narayanan Madaboosi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Jan Albert
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden;
| |
Collapse
|
28
|
Ramírez-Palacios LR, Reséndez-Pérez D, Rodríguez-Padilla MC, Saavedra-Alonso S, Real-Najarro O, Fernández-Santos NA, Rodriguez Perez MA. Molecular diagnosis of microbial copathogens with influenza A(H1N1)pdm09 in Oaxaca, Mexico. Res Rep Trop Med 2018; 9:49-62. [PMID: 30050355 PMCID: PMC6047622 DOI: 10.2147/rrtm.s144075] [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] [Indexed: 11/23/2022] Open
Abstract
Background Multiple factors have been associated with the severity of infection by influenza A(H1N1)pdm09. These include H1N1 cases with proven coinfections showing clinical association with bacterial contagions. Purpose The objective was to identify H1N1 and copathogens in the Oaxaca (Mexico) population. A cross-sectional survey was conducted from 2009 to 2012. A total of 88 study patients with confirmed H1N1 by quantitative RT-PCR were recruited. Methods Total nucleic acid from clinical samples of study patients was analyzed using a TessArray RPM-Flu microarray assay to identify other respiratory pathogens. Results High prevalence of copathogens (77.3%; 68 patients harbored one to three pathogens), predominantly from Streptococcus, Haemophilus, Neisseria, and Pseudomonas, were detected. Three patients (3.4%) had four or five respiratory copathogens, whereas others (19.3%) had no copathogens. Copathogenic occurrence with Staphylococcus aureus was 5.7%, Coxsackie virus 2.3%, Moraxella catarrhalis 1.1%, Klebsiella pneumoniae 1.1%, and parainfluenza virus 3 1.1%. The number of patients with copathogens was four times higher to those with H1N1 alone (80.68% and 19.32%, respectively). Four individuals (4.5%; two males, one female, and one infant) who died due to H1N1 were observed to have harbored such copathogens as Streptococcus, Staphylococcus, Haemophilus, and Neisseria. Conclusion In summary, copathogens were found in a significant number (>50%) of cases of influenza in Oaxaca. Timely detection of coinfections producing increased acuity or severity of disease and treatment of affected patients is urgently needed.
Collapse
Affiliation(s)
| | - Diana Reséndez-Pérez
- Departamento de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Maria Cristina Rodríguez-Padilla
- Departamento de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Santiago Saavedra-Alonso
- Departamento de Inmunología y Virología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | | | | | | |
Collapse
|
29
|
Abstract
Coinfections involving viruses are being recognized to influence the disease pattern that occurs relative to that with single infection. Classically, we usually think of a clinical syndrome as the consequence of infection by a single virus that is isolated from clinical specimens. However, this biased laboratory approach omits detection of additional agents that could be contributing to the clinical outcome, including novel agents not usually considered pathogens. The presence of an additional agent may also interfere with the targeted isolation of a known virus. Viral interference, a phenomenon where one virus competitively suppresses replication of other coinfecting viruses, is the most common outcome of viral coinfections. In addition, coinfections can modulate virus virulence and cell death, thereby altering disease severity and epidemiology. Immunity to primary virus infection can also modulate immune responses to subsequent secondary infections. In this review, various virological mechanisms that determine viral persistence/exclusion during coinfections are discussed, and insights into the isolation/detection of multiple viruses are provided. We also discuss features of heterologous infections that impact the pattern of immune responsiveness that develops.
Collapse
|
30
|
Lima MT, Oliveira GP, Assis FL, Bretas de Oliveira D, Vaz SM, Trindade GDS, Abrahão JS, Kroon EG. Ocular Vaccinia Infection in Dairy Worker, Brazil. Emerg Infect Dis 2018; 24:161-162. [PMID: 29260673 PMCID: PMC5749457 DOI: 10.3201/eid2401.170430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We studied a clinical case of vaccinia virus that caused an ocular manifestation in a dairy worker in Brazil. Biologic and molecular analyses identified a co-infection with 2 isolates from different Brazilian vaccinia virus phylogenetic groups.
Collapse
|
31
|
Tang JW, Lam TT, Zaraket H, Lipkin WI, Drews SJ, Hatchette TF, Heraud JM, Koopmans MP. Global epidemiology of non-influenza RNA respiratory viruses: data gaps and a growing need for surveillance. THE LANCET. INFECTIOUS DISEASES 2017; 17:e320-e326. [PMID: 28457597 PMCID: PMC7164797 DOI: 10.1016/s1473-3099(17)30238-4] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 01/06/2017] [Accepted: 02/07/2017] [Indexed: 01/13/2023]
Abstract
Together with influenza, the non-influenza RNA respiratory viruses (NIRVs), which include respiratory syncytial virus, parainfluenza viruses, coronavirus, rhinovirus, and human metapneumovirus, represent a considerable global health burden, as recognised by WHO's Battle against Respiratory Viruses initiative. By contrast with influenza viruses, little is known about the contemporaneous global diversity of these viruses, and the relevance of such for development of pharmaceutical interventions. Although far less advanced than for influenza, antiviral drugs and vaccines are in different stages of development for several of these viruses, but no interventions have been licensed. This scarcity of global genetic data represents a substantial knowledge gap and impediment to the eventual licensing of new antiviral drugs and vaccines for NIRVs. Enhanced genetic surveillance will assist and boost research and development into new antiviral drugs and vaccines for these viruses. Additionally, understanding the global diversity of respiratory viruses is also part of emerging disease preparedness, because non-human coronaviruses and paramyxoviruses have been listed as priority concerns in a recent WHO research and development blueprint initiative for emerging infectious diseases. In this Personal View, we explain further the rationale for expanding the genetic database of NIRVs and emphasise the need for greater investment in this area of research.
Collapse
Affiliation(s)
- Julian W Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary, Leicester, UK; Department of Infection, Inflammation and Immunity, University of Leicester, Leicester, UK.
| | - Tommy T Lam
- School of Public Health, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology, and Microbiology, American University of Beirut, Beirut, Lebanon
| | - W Ian Lipkin
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Steven J Drews
- Alberta Provincial Laboratory for Public Health, University of Alberta, Edmonton, AB, Canada
| | - Todd F Hatchette
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | | | - Marion P Koopmans
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, Netherlands
| |
Collapse
|
32
|
Szymański K, Cieślak K, Kowalczyk D, Brydak LB. Co-infection with Influenza Viruses and Influenza-Like Virus During the 2015/2016 Epidemic Season. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 968:7-12. [PMID: 28181195 PMCID: PMC7122344 DOI: 10.1007/5584_2016_182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
Concerning viral infection of the respiratory system, a single virus can cause a variety of clinical symptoms and the same set of symptoms can be caused by different viruses. Moreover, infection is often caused by a combination of viruses acting at the same time. The present study demonstrates, using multiplex RT-PCR and real-time qRT-PCR, that in the 2015/2016 influenza season, co-infections were confirmed in patients aged 1 month to 90 years. We found 73 co-infections involving influenza viruses, 17 involving influenza viruses and influenza-like viruses, and six involving influenza-like viruses. The first type of co-infections above mentioned was the most common, amounting to 51 cases, with type A and B viruses occurring simultaneously. There also were four cases of co-infections with influenza virus A/H1N1/pdm09 and A/H1N1/ subtypes and two cases with A/H1N1/pdm09 and A/H3N2/ subtypes. The 2015/2016 epidemic season was characterized by a higher number of confirmed co-infections compared with the previous seasons. Infections by more than one respiratory virus were most often found in children and in individuals aged over 65.
Collapse
Affiliation(s)
- K Szymański
- Department of Influenza Research, National Influenza Center, National Institute of Public Health - National Institute of Hygiene, 24 Chocimska Street, 00-791, Warsaw, Poland.
| | - K Cieślak
- Department of Influenza Research, National Influenza Center, National Institute of Public Health - National Institute of Hygiene, 24 Chocimska Street, 00-791, Warsaw, Poland
| | - D Kowalczyk
- Department of Influenza Research, National Influenza Center, National Institute of Public Health - National Institute of Hygiene, 24 Chocimska Street, 00-791, Warsaw, Poland
| | - L B Brydak
- Department of Influenza Research, National Influenza Center, National Institute of Public Health - National Institute of Hygiene, 24 Chocimska Street, 00-791, Warsaw, Poland
| |
Collapse
|
33
|
Utilization Management in a Large Community Hospital. UTILIZATION MANAGEMENT IN THE CLINICAL LABORATORY AND OTHER ANCILLARY SERVICES 2017. [PMCID: PMC7123185 DOI: 10.1007/978-3-319-34199-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The utilization management of laboratory tests in a large community hospital is similar to academic and smaller community hospitals. There are numerous factors that influence laboratory utilization. Outside influences like hospitals buying physician practices, increasing numbers of hospitalists, and hospital consolidation will influence the number and complexity of the test menu that will need to be monitored for over and/or under utilization in the central laboratory and reference laboratory. CLIA’88 outlines the four test categories including point-of-care testing (waived) and provider-performed microscopy that need laboratory test utilization management. Incremental cost analysis is the most efficient method for evaluating utilization reduction cost savings. Economies of scale define reduced unit cost per test as test volume increases. Outreach programs in large community hospitals provide additional laboratory tests from non-patients in physician offices, nursing homes, and other hospitals. Disruptive innovations are changing the present paradigms in clinical diagnostics, like wearable sensors, MALDI-TOF, multiplex infectious disease panels, cell-free DNA, and others. Obsolete tests need to be universally defined and accepted by manufacturers, physicians, laboratories, and hospitals, to eliminate access to their reagents and testing platforms.
Collapse
|
34
|
Arbefeville S, Ferrieri P. Epidemiologic Analysis of Respiratory Viral Infections Mainly in Hospitalized Children and Adults in a Midwest University Medical Center After the Implementation of a 14-Virus Multiplex Nucleic Acid Amplification Test. Am J Clin Pathol 2017; 147:43-49. [PMID: 28028115 PMCID: PMC7109917 DOI: 10.1093/ajcp/aqw185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To investigate the etiology of viral respiratory tract infections mainly in hospitalized children and adults over a 12-month consecutive period after implementation of a 14-virus multiplex nucleic acid amplification test. METHODS From January 2014 to January 2015, a total of 2,237 respiratory samples were analyzed with the US Food and Drug Administration-cleared eSensor Respiratory Viral Panel (GenMark Diagnostics, Carlsbad, CA). RESULTS Of the 2,237 specimens tested, 788 specimens were positive for at least one virus, giving a positivity rate of 35.2%, and because of viral codetection, a total of 862 viral targets were identified. The age groups with the highest positivity rates were the 0- to 1-year (73.5%) and 2- to 6-year (78.4%) age groups. The overall viral codetection rate was 9.1%. Human rhinovirus (HRV) was the most prevalent respiratory virus found in children and adults. The peak of HRV seen in September 2014 represented a combination of HRV and enterovirus D68, 2014 epidemic respiratory infections. CONCLUSION The ability to detect a wider range of respiratory viruses gave us a better understanding of the etiology of respiratory infections in our population, particularly for HRV and enhanced our ability to detect viral coinfection.
Collapse
Affiliation(s)
- Sophie Arbefeville
- From the Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
- Corresponding author: Sophie Arbefeville, MD, Dept of Laboratory Medicine and Pathology, University of Minnesota Medical School, B203-3 Mayo Building, MMC 609 Mayo, 420 Delaware St SE, Minneapolis, MN 55455; . Presented in part at the 115th General Meeting, American Society for Microbiology; May 30 to June 2, 2015; New Orleans, LA
| | - Patricia Ferrieri
- From the Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis
| |
Collapse
|
35
|
Shafagati N, Fite K, Patanarut A, Baer A, Pinkham C, An S, Foote B, Lepene B, Kehn-Hall K. Enhanced detection of respiratory pathogens with nanotrap particles. Virulence 2016; 7:756-69. [PMID: 27145085 PMCID: PMC5029303 DOI: 10.1080/21505594.2016.1185585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 04/15/2016] [Accepted: 04/27/2016] [Indexed: 10/21/2022] Open
Abstract
The Influenza virus is a leading cause of respiratory disease in the United States each year. While the virus normally causes mild to moderate disease, hospitalization and death can occur in many cases. There are several methodologies that are used for detection; however problems such as decreased sensitivity and high rates of false-negative results may arise. There is a crucial need for an effective sample preparation technology that concentrates viruses at low abundance while excluding resident analytes that may interfere with detection. Nanotrap particles are hydrogel particles that are coupled to chemical dye affinity baits that bind a broad range of proteins and virions. Within minutes (<30 minutes), Nanotrap particles concentrate low abundant proteins and viruses from clinically complex matrices. Nanotrap particles with reactive red baits concentrated numerous respiratory viruses including various strains and subtypes of Influenza virus, Coronavirus, and Respiratory Syncytial Virus from saliva, nasal fluid swab specimens, and nasal aspirates. Detection was enhanced more than 10-fold when coupled to plaque assays and qRT-PCR. Importantly, Nanotrap particle can efficiently capture and concentrate multiple viral pathogens during a coinfection scenario. These results collectively demonstrate that Nanotrap particles are an important tool that can easily be integrated into various detection methodologies.
Collapse
Affiliation(s)
- Nazly Shafagati
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Katherine Fite
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
| | | | - Alan Baer
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Chelsea Pinkham
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Soyeon An
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Benjamin Foote
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
| | | | - Kylene Kehn-Hall
- National Center for Biodefense and Infectious Diseases, School of Systems Biology, George Mason University, Manassas, VA, USA
| |
Collapse
|
36
|
Direct Comparison of Alere i and cobas Liat Influenza A and B Tests for Rapid Detection of Influenza Virus Infection. J Clin Microbiol 2016; 54:2763-2766. [PMID: 27582513 DOI: 10.1128/jcm.01586-16] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 08/24/2016] [Indexed: 02/04/2023] Open
Abstract
We compared two rapid, point-of care nucleic acid amplification tests for detection of influenza A and B viruses (Alere i [Alere] and cobas Liat [Roche Diagnostics]) with the influenza A and B virus test components of the FilmArray respiratory panel (BioFire Diagnostics) using 129 respiratory specimens collected in universal viral transport medium (80 influenza A virus and 16 influenza B virus positive) from both adult and pediatric patients. The sensitivities of the Alere test were 71.3% for influenza A virus and 93.3% for influenza B virus, with specificities of 100% for both viruses. The sensitivities and specificities of the Liat test were 100% for both influenza A and B viruses. The poor sensitivity of the Alere test for detection of influenza A virus was likely due to a study set that included many low-positive samples that were below its limit of detection.
Collapse
|
37
|
Abstract
Seasonal and pandemic influenza are the two faces of respiratory infections caused by influenza viruses in humans. As seasonal influenza occurs on an annual basis, the circulating virus strains are closely monitored and a yearly updated vaccination is provided, especially to identified risk populations. Nonetheless, influenza virus infection may result in pneumonia and acute respiratory failure, frequently complicated by bacterial coinfection. Pandemics are, in contrary, unexpected rare events related to the emergence of a reassorted human-pathogenic influenza A virus (IAV) strains that often causes increased morbidity and spreads extremely rapidly in the immunologically naive human population, with huge clinical and economic impact. Accordingly, particular efforts are made to advance our knowledge on the disease biology and pathology and recent studies have brought new insights into IAV adaptation mechanisms to the human host, as well as into the key players in disease pathogenesis on the host side. Current antiviral strategies are only efficient at the early stages of the disease and are challenged by the genomic instability of the virus, highlighting the need for novel antiviral therapies targeting the pulmonary host response to improve viral clearance, reduce the risk of bacterial coinfection, and prevent or attenuate acute lung injury. This review article summarizes our current knowledge on the molecular basis of influenza infection and disease progression, the key players in pathogenesis driving severe disease and progression to lung failure, as well as available and envisioned prevention and treatment strategies against influenza virus infection.
Collapse
Affiliation(s)
- Christin Peteranderl
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Carole Schmoldt
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| |
Collapse
|
38
|
Abstract
Seasonal and pandemic influenza are the two faces of respiratory infections caused by influenza viruses in humans. As seasonal influenza occurs on an annual basis, the circulating virus strains are closely monitored and a yearly updated vaccination is provided, especially to identified risk populations. Nonetheless, influenza virus infection may result in pneumonia and acute respiratory failure, frequently complicated by bacterial coinfection. Pandemics are, in contrary, unexpected rare events related to the emergence of a reassorted human-pathogenic influenza A virus (IAV) strains that often causes increased morbidity and spreads extremely rapidly in the immunologically naive human population, with huge clinical and economic impact. Accordingly, particular efforts are made to advance our knowledge on the disease biology and pathology and recent studies have brought new insights into IAV adaptation mechanisms to the human host, as well as into the key players in disease pathogenesis on the host side. Current antiviral strategies are only efficient at the early stages of the disease and are challenged by the genomic instability of the virus, highlighting the need for novel antiviral therapies targeting the pulmonary host response to improve viral clearance, reduce the risk of bacterial coinfection, and prevent or attenuate acute lung injury. This review article summarizes our current knowledge on the molecular basis of influenza infection and disease progression, the key players in pathogenesis driving severe disease and progression to lung failure, as well as available and envisioned prevention and treatment strategies against influenza virus infection.
Collapse
Affiliation(s)
- Christin Peteranderl
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Susanne Herold
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| | - Carole Schmoldt
- Department of Internal Medicine II, University of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany
| |
Collapse
|
39
|
Evaluation of the Activity of Influenza and Influenza-Like Viruses in the Epidemic Season 2013/2014. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 857:1-7. [PMID: 25786402 PMCID: PMC7121991 DOI: 10.1007/5584_2015_116] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Infections caused by respiratory viruses can have different clinical symptoms, while specific set of symptoms can be induced by different viruses. Despite usually mild course of disease, some viruses causing certain disease entity can result in serious complications. Therefore, quick and appropriate diagnostic is crucial for administering proper treatment. In the epidemic season 2013/2014, 2,497 specimens were tested. Infections caused by influenza viruses were confirmed in 9.8%, while infections caused by influenza-like viruses (ILI) in 13.2%. The co-domination of A/H1N1/pdm09 (29.4%) with A/H3N2/ (30.6%) was observed among circulating subtypes of influenza virus type A. Analysis of positive specimens categorized into 7 age groups indicated that most of morbidity to influenza was noted in the age intervals: 26-44 (22.9%) and 45-64 years old (21.6%). Considering infections caused by influenza-like viruses, the highest amount of positive cases was registered in the age group 0-4 years old (92.7%) with the highest ratio of RSV (87.9%) and PIV-3 (10.5%). Judging by the epidemiological and virological indicators, the 2013/14 influenza season was mild and only low virus activity was reported in Poland as well as in most European countries. Still, 9,000 hospitalizations and 17 deaths were registered in Poland during this epidemic season.
Collapse
|
40
|
Cui B, Zhang D, Pan H, Zhang F, Farrar J, Law F, van Doorn HR, Wu B, Ba-Thein W. Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China. BMC Infect Dis 2015; 15:124. [PMID: 25884513 PMCID: PMC4365542 DOI: 10.1186/s12879-015-0863-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 03/02/2015] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Acute respiratory infections (ARIs) are common in children and mostly caused by viruses, but the significance of the detection of multiple viruses in ARIs is unclear. This study investigated 14 respiratory viruses in ARIs among children and associated meteorological factors in Shantou, southern China. METHODS Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses--influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV)--by multiplex real-time PCR. RESULTS We identified at least one virus in 82.3% (884/1,074) and multiple viruses in 38.6% (415/1,074) of patients. EV and HRV were the most frequently detected single viruses (42.3%, 374/884 and 39.9%, 353/884 respectively) and co-detected pair (23.1%, 96/415). Overlapping seasonal trends of viruses were recorded over the year, with dual peaks for EV and single peaks for the others. By logistic regression analysis, EV was positively associated with the average temperature and humidity, hCoV, and PIV4, but negatively with HRV, PIV3, and hBoV. HRV was inversely associated with EV and PIV3. CONCLUSIONS This study reports high viral detection and co-detection rates in pediatric ARI cases mainly due to EV and HRV. Many viruses circulated throughout the year with similar seasonal trends in association with temperature, humidity, and wind velocity. Statistically significant associations were present among the viruses. Understanding the polyviral etiology and viral interactions in the cases with multiple viruses warrants further studies.
Collapse
Affiliation(s)
- Binglin Cui
- Pediatric Department, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - Dangui Zhang
- The Research Center of Translational Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - Hui Pan
- Shantou-Oxford Clinical Research Unit, Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - Fan Zhang
- Oncology Research Laboratory, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Viet Nam.
| | - Frieda Law
- Consultant Office, Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Ho Chi Minh City, Viet Nam.
| | - Beiyan Wu
- Pediatric Department, the First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China.
| | - William Ba-Thein
- Shantou-Oxford Clinical Research Unit, Shantou University Medical College, Shantou, Guangdong, P.R. China.
- Department of Microbiology and Immunology, Shantou University Medical College, Shantou, Guangdong, 515041, P.R. China.
| |
Collapse
|
41
|
Seo YB, Song JY, Choi MJ, Kim IS, Yang TU, Hong KW, Cheong HJ, Kim WJ. Etiology and clinical outcomes of acute respiratory virus infection in hospitalized adults. Infect Chemother 2014; 46:67-76. [PMID: 25024868 PMCID: PMC4091371 DOI: 10.3947/ic.2014.46.2.67] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/24/2014] [Accepted: 03/17/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Etiologies and clinical profiles of acute respiratory viral infections need to be clarified to improve preventive and therapeutic strategies. MATERIALS AND METHODS A retrospective observational study at a single, university-affiliated center was performed to evaluate the respiratory viral infection etiologies in children compared to that in adults and to document the clinical features of common viral infections for adults from July 2009 to April 2012. RESULTS The common viruses detected from children (2,800 total patients) were human rhinovirus (hRV) (31.8%), adenovirus (AdV) (19.2%), respiratory syncytial virus (RSV) A (17.4%), RSV B (11.7%), and human metapneumovirus (hMPV) (9.8%). In comparison, influenza virus A (IFA) had the highest isolation rate (28.5%), followed by hRV (15.5%), influenza virus B (IFB) (15.0%), and hMPV (14.0%), in adults (763 total patients). Multiple viruses were detected in single specimens from 22.4% of children and 2.0% of adults. IFA/IFB, RSV A/B, and hMPV exhibited strong seasonal detection and similar circulating patterns in children and adults. Adult patients showed different clinical manifestations according to causative viruses; nasal congestion and rhinorrhea were more common in hRV and human coronavirus (hCoV) infection. Patients with RSV B, hRV, or AdV tended to be younger, and those infected with RSV A and hMPV were likely to be older. Those with RSV A infection tended to stay longer in hospital, enter the intensive care unit more frequently, and have a fatal outcome more often. The bacterial co-detection rate was 26.5%, and those cases were more likely to have lower respiratory tract involvement (P = 0.001), longer hospital stay (P = 0.001), and higher mortality (P = 0.001). CONCLUSIONS The etiologic virus of an acute respiratory infection can be cautiously inferred based on a patient's age and clinical features and concurrent epidemic data. Large-scale prospective surveillance studies are required to provide more accurate information about respiratory viral infection etiology, which could favorably influence clinical outcomes.
Collapse
Affiliation(s)
- Yu Bin Seo
- Division of Infectious Diseases, Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Joon Young Song
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Min Ju Choi
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - In Seon Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Tea Un Yang
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Kyung-Wook Hong
- Division of Infectious Diseases, Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, Korea
| | - Hee Jin Cheong
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Woo Joo Kim
- Division of Infectious Diseases, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| |
Collapse
|
42
|
He Y, Lin GY, Wang Q, Cai XY, Zhang YH, Lin CX, Lu CD, Lu XD. A 3-year prospective study of the epidemiology of acute respiratory viral infections in hospitalized children in Shenzhen, China. Influenza Other Respir Viruses 2014; 8:443-51. [PMID: 24828783 PMCID: PMC4181804 DOI: 10.1111/irv.12257] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2014] [Indexed: 12/22/2022] Open
Abstract
Background The epidemiology of local viral etiologies is essential for the management of viral respiratory tract infections. Limited data are available in China to describe the epidemiology of viral respiratory infections, especially in small–medium cities and rural areas. Objectives To determine the viral etiology and seasonality of acute respiratory infections in hospitalized children, a 3-year study was conducted in Shenzhen, China. Methods Nasopharyngeal aspirates from eligible children were collected. Influenza and other respiratory viruses were tested by molecular assays simultaneously. Data were analyzed to describe the frequency and seasonality. Results Of the 2025 children enrolled in the study, 971 (48·0%) were positive for at least one viral pathogen, in which 890 (91·7%) were <4 years of age. The three most prevalent viruses were influenza A (IAV; 35·8%), respiratory syncytial virus (RSV; 30·5%) and human rhinovirus (HRV; 21·5%). Co-infections were found in 302 cases (31·1%), and dual viral infection was dominant. RSV, HRV and IAV were the most frequent viral agents involved in co-infection. On the whole, the obvious seasonal peaks mainly from March to May were observed with peak strength varying from 1 year to another. Conclusions This study provides a basic profile of the epidemiology of acute respiratory viral infection in hospitalized children in Shenzhen. The spectrum of viruses in the study site is similar to that in other places, but the seasonality is closely related to geographic position, different from that in big cities in northern China and neighboring Hong Kong.
Collapse
Affiliation(s)
- Ying He
- Department of Laboratory Medicine, Affiliated Futian People's Hospital, Guangdong Medical College, Shenzhen, China; Institute of Clinical Microbiology, Affiliated Futian People's Hospital, Guangdong Medical College, Shenzhen, China
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Medical Management of Acute Rhinosinusitis in Children and Adults. DISEASES OF THE SINUSES 2014. [PMCID: PMC7122618 DOI: 10.1007/978-1-4939-0265-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
44
|
|