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Berginc N, Sočan M, Prosenc Trilar K, Petrovec M. Seasonality and Genotype Diversity of Human Rhinoviruses during an Eight-Year Period in Slovenia. Microorganisms 2024; 12:341. [PMID: 38399745 PMCID: PMC10893136 DOI: 10.3390/microorganisms12020341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Due to the high socioeconomic burden of rhinoviruses, the development of prevention and treatment strategies is of high importance. Understanding the epidemiological and clinical features of rhinoviruses is essential in order to address these issues. Our study aimed to define the seasonality and molecular epidemiology of rhinoviruses in Slovenia. Over a period of eight years, a total of 20,425 patients from sentinel primary healthcare settings and sentinel hospitals were examined for a panel of respiratory viruses in the national programme for the surveillance of influenza-like illnesses and acute respiratory infections. The patients were from all age groups and had respiratory infections of various severity. Infection with a rhinovirus was confirmed using an RT-rPCR in 1834 patients, and 1480 rhinoviruses were genotyped. The molecular analysis was linked to demographical and meteorological data. We confirmed the year-round circulation of rhinoviruses with clear seasonal cycles, resulting in two seasonal waves with peaks in spring and autumn. High levels of genotype variability and co-circulation were confirmed between and within seasons and were analysed in terms of patient age, the patient source reflecting disease severity, and meteorological factors. Our study provides missing scientific information on the genotype diversity of rhinoviruses in Slovenia. As most previous investigations focused on exclusive segments of the population, such as children or hospitalised patients, and for shorter study periods, our study, with its design, size and length, contributes complementary aspects and new evidence-based knowledge to the regional and global understanding of rhinovirus seasonality and molecular epidemiology.
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Affiliation(s)
- Nataša Berginc
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Maja Sočan
- Centre for Infectious Diseases, National Institute of Public Health, 1000 Ljubljana, Slovenia
| | - Katarina Prosenc Trilar
- Department of Public Health Microbiology, National Laboratory of Health, Environment and Food, 1000 Ljubljana, Slovenia;
| | - Miroslav Petrovec
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
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Bergallo M, Daprà V, Rassu M, Calvi C, Montanari P, Galliano I. Human Bocavirus in children with acute gastroenteritis in Piedmont, Italy. Minerva Pediatr (Torino) 2023; 75:528-535. [PMID: 30605997 DOI: 10.23736/s2724-5276.18.05365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
BACKGROUND Gastroenteritis is a common disease in children, characterized by diarrhea, vomiting, abdominal pain, and fever. Co-detection of human Bocavirus (HBoV) with other gastroenteric viruses was reported a lot in patients with acute gastroenteritis. METHODS This paper presents the real-time RT-PCR Taqman assay for the detection and quantification of HBoV for clinical fecal samples collected from hospitalized children with acute gastroenteritis in Piedmont. RESULTS All fecal specimens were tested for the presence of HBoV with specific primers and probe. A total of 17 out of 123 (13.92%) episodes of acute gastroenteritis were associated with HBoV genomic detection with median viral load 6864.75±19784.79 genomes/mg fecal specimens. Among the 17 HBoV-positive cases, 11 were also positive for other viral pathogens, including Rotavirus (N.=2), astrovirus (N.=1), norovirus GII (N.=6), norovirus GI (N.=2). Two cases were positive for more than one virus including norovirus GII and norovirus GI (N.=1) and Rotavirus, sapovirus and astrovirus (N.=1). A higher detection of HBoV infections was observed in winter, and peaking in February. CONCLUSIONS Although HBoV is suspected to be responsible for gastroenteritis in children, our data showed that this association was uncertain since no difference was observed in term of viral load in the group with single infection of HBoV and group of coinfections with other viral agent.
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Affiliation(s)
- Massimiliano Bergallo
- Medical School, Department of Public Health and Pediatric Sciences, Citoimmunodiagnostics Laboratory, University of Turin, Turin, Italy -
- Unit of Infectious Diseases, Department of Pediatrics, Regina Margherita Children's Hospital, University of Turin, Turin, Italy -
| | - Valentina Daprà
- Medical School, Department of Public Health and Pediatric Sciences, Citoimmunodiagnostics Laboratory, University of Turin, Turin, Italy
| | - Marco Rassu
- Unit of Infectious Diseases, Department of Pediatrics, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Cristina Calvi
- Unit of Infectious Diseases, Department of Pediatrics, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Paola Montanari
- Medical School, Department of Public Health and Pediatric Sciences, Citoimmunodiagnostics Laboratory, University of Turin, Turin, Italy
- Unit of Infectious Diseases, Department of Pediatrics, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
| | - Ilaria Galliano
- Medical School, Department of Public Health and Pediatric Sciences, Citoimmunodiagnostics Laboratory, University of Turin, Turin, Italy
- Unit of Infectious Diseases, Department of Pediatrics, Regina Margherita Children's Hospital, University of Turin, Turin, Italy
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Gandhi L, Maisnam D, Rathore D, Chauhan P, Bonagiri A, Venkataramana M. Respiratory illness virus infections with special emphasis on COVID-19. Eur J Med Res 2022; 27:236. [PMID: 36348452 PMCID: PMC9641310 DOI: 10.1186/s40001-022-00874-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 10/26/2022] [Indexed: 11/10/2022] Open
Abstract
Viruses that emerge pose challenges for treatment options as their uniqueness would not know completely. Hence, many viruses are causing high morbidity and mortality for a long time. Despite large diversity, viruses share common characteristics for infection. At least 12 different respiratory-borne viruses are reported belonging to various virus taxonomic families. Many of these viruses multiply and cause damage to the upper and lower respiratory tracts. The description of these viruses in comparison with each other concerning their epidemiology, molecular characteristics, disease manifestations, diagnosis and treatment is lacking. Such information helps diagnose, differentiate, and formulate the control measures faster. The leading cause of acute illness worldwide is acute respiratory infections (ARIs) and are responsible for nearly 4 million deaths every year, mostly in young children and infants. Lower respiratory tract infections are the fourth most common cause of death globally, after non-infectious chronic conditions. This review aims to present the characteristics of different viruses causing respiratory infections, highlighting the uniqueness of SARS-CoV-2. We expect this review to help understand the similarities and differences among the closely related viruses causing respiratory infections and formulate specific preventive or control measures.
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Affiliation(s)
- Lekha Gandhi
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Deepti Maisnam
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Deepika Rathore
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Preeti Chauhan
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Anvesh Bonagiri
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Musturi Venkataramana
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India.
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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.
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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
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5
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Respiratory viral infections other than SARS CoV-2 among the North Indian patients presenting with acute respiratory illness during the first COVID-19 wave. Virusdisease 2022; 33:57-64. [PMID: 35411310 PMCID: PMC8985743 DOI: 10.1007/s13337-022-00761-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 02/22/2022] [Indexed: 11/19/2022] Open
Abstract
Acute respiratory infections due to viral or bacterial etiology can cause 60 deaths per one lakh population. Viral etiology is more common as compared to bacterial, but lack of definite diagnosis leads to increased usage of empirical antibiotics. During the first wave of the COVID-19 pandemic, there was a need to identify co-infections especially in severe acute respiratory illness (SARI) patients to identify it as one of the cofactors for increased severity of illness and to identify the causative agents in COVID-19 negative individuals. The SARS CoV-2 real time PCR was carried out using ICMR approved kits and the other respiratory viruses were detected using the multiplex commercially available real time kit. A total of 186 patients presenting with either SARI (89.8%) or influenza like illness (10.2%) were included in the study. Out of these, 43 (23.1%) were positive for SARS CoV-2 RNA and 2 (4.6%) patients with SARI showed concomitant infection with either human rhinovirus or human respiratory syncytial virus . Out of 143 patients negative for SARS CoV-2, 35 (24.5%) were positive for one or more microbial infections and 28 (19.6%) infected with other respiratory viral infection most common being human rhinovirus. The results suggest that viral coinfections are significantly higher among COVID-19 negative individuals (24.5% vs 4.6%) presenting with respiratory illness as compared to COVID-19 positive individuals possibly due to viral interference and competitive advantage of SARS-CoV-2 in modulating the host immunity. Further detailed research is required for the understanding of mechanisms of viral co-infection.
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Ahmed A, Alsenaidy AM, Mobaireek KF, AlSaadi MM. Viral etiology of acute respiratory infections during 2014–16 in Riyadh, Saudi Arabia. Future Virol 2022. [DOI: 10.2217/fvl-2020-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Viral etiology of respiratory infections is not well understood in Saudi Arabia. This study was conceptualized to understand viral etiology in children with acute respiratory tract infections (ARTI) from Riyadh. Patients and methods: Respiratory viruses were detected by real-time PCR in nasopharyngeal aspirates or swab from 580 children aged ≤5 years. Results: Respiratory viruses were detected in 64% of the samples with 6% mixed viral infections. Respiratory syncytial virus, adenovirus, influenza, parainfluenza and human metapneumovirus infections accounted for 42, 20, 16, 12 and 10%, respectively. Maximum prevalence (37%) was among the lowest age group followed by 30% among the 7- to 12-month age group. Conclusion: The prevalence and determinants of viral etiology are in line with the previous report from the region. No major shift in the viral etiologies was observed in the 2-year study period.
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Affiliation(s)
- Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman M Alsenaidy
- Department of Biochemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Khalid Fahad Mobaireek
- Pediatric Emergency Department, Children’s Hospital, King Fahad Medical City, Riyadh, 12231, Saudi Arabia
| | - Muslim Mohammed AlSaadi
- Department of Pediatrics, College of Medicine, King Khalid University Hospital, King Saud University, Riyadh, 11533, Saudi Arabia
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SARS-CoV-2 and Influenza Virus Co-Infection Cases Identified through ILI/SARI Sentinel Surveillance: A Pan-India Report. Viruses 2022; 14:v14030627. [PMID: 35337033 PMCID: PMC8954151 DOI: 10.3390/v14030627] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2/influenza virus co-infection studies have focused on hospitalized patients who usually had grave sequelae. Here, we report SARS-CoV-2/influenza virus co-infection cases from both community and hospital settings reported through integrated ILI/SARI (Influenza Like Illness/Severe Acute Respiratory Infection) sentinel surveillance established by the Indian Council of Medical Research. We describe the disease progression and outcomes in these cases. Out of 13,467 samples tested from 4 July 2021–31 January 2022, only 5 (0.04%) were of SARS-CoV-2/influenza virus co-infection from 3 different sites in distinct geographic regions. Of these, three patients with extremes of age required hospital admission, but none required ICU admission or mechanical ventilation. No mortality was reported. The other two co-infection cases from community settings were managed at home. This is the first report on SARS-CoV-2/Influenza virus co-infection from community as well as hospital settings in India and shows that influenza viruses are circulating in the community even during COVID-19. The results emphasize the need for continuous surveillance for multiple respiratory pathogens for effective public health management of ILI/SARI cases in line with the WHO (World Health Organization) recommendations.
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8
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Lapa SA, Miftakhov RA, Klochikhina ES, Ammur YI, Blagodatskikh SA, Shershov VE, Zasedatelev AS, Chudinov AV. Development of Multiplex RT-PCR with Immobilized Primers for Identification of Infectious Human Pneumonia Pathogens. Mol Biol 2021; 55:828-838. [PMID: 34955557 PMCID: PMC8682033 DOI: 10.1134/s0026893321040063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/23/2022]
Abstract
A prototype of a system for the detection of infectious human pneumonia pathogens based on multiplex solid-phase reverse transcription PCR (RT-PCR) was developed. Primers were designed to identify the DNA of six bacterial pneumonia pathogen strains, and the RNA of two viral pathogens of pneumonia: influenza A and SARS-CoV-2. The signal accumulation of elongated immobilized primers occurs due to the incorporation of fluorescently labeled nucleotides in the chain. The signal is detected after all the components of the mixture are removed, which significantly reduces the background signal and increases the sensitivity of the analysis. The use of a specialized detector makes it possible to read the signals of elongated primers directly through the transparent cover film of the reaction chamber. This solution is designed to prevent cross-contamination and is suitable for simultaneous testing of a large number of test samples. The proposed platform is able to detect the presence of several pathogens of pneumonia in a sample and has an open architecture that allows expansion of the range of pathogenic bacteria and viruses that can be detected.
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Affiliation(s)
- S A Lapa
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - R A Miftakhov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - E S Klochikhina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Yu I Ammur
- Mechnikov Institute of Vaccines and Serums, 105064 Moscow, Russia
| | - S A Blagodatskikh
- Scientific Center of Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - V E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A S Zasedatelev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - A V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Keshavarz Valian N, Pourakbari B, Asna Ashari K, Hosseinpour Sadeghi R, Mahmoudi S. Evaluation of human coronavirus OC43 and SARS-COV-2 in children with respiratory tract infection during the COVID-19 pandemic. J Med Virol 2021; 94:1450-1456. [PMID: 34786736 PMCID: PMC8661600 DOI: 10.1002/jmv.27460] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 09/06/2021] [Accepted: 11/15/2021] [Indexed: 12/23/2022]
Abstract
The coronavirus disease 2019 (COVID‐19) pandemic is an overwhelming crisis across the world. Human Coronavirus OC43 (HCoV‐OC43) is a Betacoronavirus responsible mostly for mild respiratory symptoms. Since the presentations of HCoV‐OC43 and severe acute respiratory syndrome coronavirus 2 (SARS‐COV‐2) are believed to resemble a lot, the aim of this study was to evaluate the frequency and characteristics of HCoV‐OC43 in the current pandemic and the rate of coinfection for the two viruses. One hundred and seventeen patients referred to Children's Medical Center, Tehran, Iran with respiratory symptoms were included. Real‐time reverse transcription‐polymerase chain reaction (RT‐PCR) methods were performed for the detection of HCoV‐OC43 and SARS‐COV‐2. Totally, 23 (20%) had a positive RT‐PCR for HCoV‐OC43 and 25 (21%) were positive for SARS‐COV‐2. Two patients (2%) had a positive PCR for both HCoV‐OC43 and SARS‐COV‐2. The two groups showed significant differences in having contact with family members with suspected or confirmed COVID‐19 (p = 0.017), fever (p = 0.02), edema (p = 0.036), vomiting (p < 0.001), abdominal complaints (p = 0.005), and myalgia (p = 0.02). The median level of lymphocyte count in patients with HCoV‐OC43 was significantly lower than patients with SARS‐COV‐2 infection (p = 0.039). The same frequency of SARS‐COV‐2 and HCoV‐OC43 was found in children with respiratory symptoms during the COVID‐19 pandemic. The rate of coinfection of SARS‐COV‐2 with HCoV‐OC43 in our study was 0.08. Further research into the cocirculation of endemic coronaviruses, such as HCoV‐OC43 and SARS‐CoV2, in different regions, is highly recommended. Attempts to determine the geographic distribution and recruit more flexible test panel designs are also highly recommended. The same frequency of SARS‐COV‐2 and HCoV‐OC43 was found in children with respiratory symptoms during the COVID‐19 pandemic. The rate of co‐infection of SARS‐COV‐2 with HCoV‐OC43 was 0.08. The frequency of fever, headache, edema, vomiting, abdominal complaints and myalgia was significantly higher in the HCoV‐OC43 group compared with the SARS‐COV‐2 group.
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Affiliation(s)
- Nasrin Keshavarz Valian
- Department of Periodontics, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Babak Pourakbari
- Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Kosar Asna Ashari
- Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Shima Mahmoudi
- Pediatric Infectious Disease Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
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Wondrak GT, Jandova J, Williams SJ, Schenten D. Solar simulated ultraviolet radiation inactivates HCoV-NL63 and SARS-CoV-2 coronaviruses at environmentally relevant doses. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2021; 224:112319. [PMID: 34598020 PMCID: PMC8463283 DOI: 10.1016/j.jphotobiol.2021.112319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/18/2021] [Indexed: 12/23/2022]
Abstract
The germicidal properties of short wavelength ultraviolet C (UVC) light are well established and used to inactivate many viruses and other microbes. However, much less is known about germicidal effects of terrestrial solar UV light, confined exclusively to wavelengths in the UVA and UVB regions. Here, we have explored the sensitivity of the human coronaviruses HCoV-NL63 and SARS-CoV-2 to solar-simulated full spectrum ultraviolet light (sUV) delivered at environmentally relevant doses. First, HCoV-NL63 coronavirus inactivation by sUV-exposure was confirmed employing (i) viral plaque assays, (ii) RT-qPCR detection of viral genome replication, and (iii) infection-induced stress response gene expression array analysis. Next, a detailed dose-response relationship of SARS-CoV-2 coronavirus inactivation by sUV was elucidated, suggesting a half maximal suppression of viral infectivity at low sUV doses. Likewise, extended sUV exposure of SARS-CoV-2 blocked cellular infection as revealed by plaque assay and stress response gene expression array analysis. Moreover, comparative (HCoV-NL63 versus SARS-CoV-2) single gene expression analysis by RT-qPCR confirmed that sUV exposure blocks coronavirus-induced redox, inflammatory, and proteotoxic stress responses. Based on our findings, we estimate that solar ground level full spectrum UV light impairs coronavirus infectivity at environmentally relevant doses. Given the urgency and global scale of the unfolding SARS-CoV-2 pandemic, these prototype data suggest feasibility of solar UV-induced viral inactivation, an observation deserving further molecular exploration in more relevant exposure models.
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Affiliation(s)
- Georg T Wondrak
- Department of Pharmacology and Toxicology, College of Pharmacy and UA Cancer Center, University of Arizona, Tucson, AZ, United States of America.
| | - Jana Jandova
- Department of Pharmacology and Toxicology, College of Pharmacy and UA Cancer Center, University of Arizona, Tucson, AZ, United States of America
| | - Spencer J Williams
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ, United States of America
| | - Dominik Schenten
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ, United States of America.
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Design and Evaluation of Multiplex One-Step Reverse Transcription PCR-Dipstick Chromatography Method for the Analysis of Seven Respiratory Pathogens. Curr Microbiol 2021; 78:3656-3666. [PMID: 34338833 PMCID: PMC8326646 DOI: 10.1007/s00284-021-02621-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022]
Abstract
Influenza A, influenza B, severe acute respiratory syndrome coronavirus 2, adenovirus, respiratory syncytial virus, Mycoplasma pneumoniae, and Chlamydophila pneumoniae are common pathogens that can cause severe pneumonia and other symptoms, resulting in acute lower respiratory tract infections. The objective of this study was to design and evaluate a sensitive and specific multiplex one-step reverse transcription PCR (RT-PCR)–dipstick chromatography method for simultaneous rapid detection of these seven pathogens. Streptavidin-coated blue latex particles were used to read out a positive signal. Based on the DNA–DNA hybridization of oligonucleotide sequences (Tag) for forward primer with the complementary oligonucleotide sequence (cTag) on the dipstick and biotin–streptavidin interactions, PCR products were able to be illuminated visually on the dipstick. The specificity and the limit of detection (LOD) were also evaluated. Moreover, the clinical performance of this method was compared with Sanger sequencing for 896 samples. No cross reaction with other pathogens was found, confirming the high specificity of this method. The LOD was 10 copies/µL for each of the tested pathogens, and the whole procedure took less than 40 min. Using 896 samples, the sensitivity and specificity were shown to be no lower than 94.5%. The positive predictive value was higher than 82.1%, and the negative predictive value was higher than 99.5%. The kappa value between the PCR–dipstick chromatography method and Sanger sequencing ranged from 0.869 to 0.940. In summary, our one-step RT-PCR–dipstick chromatography method is a sensitive and specific tool for rapidly detecting multiplex respiratory pathogens.
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Wondrak GT, Jandova J, Williams SJ, Schenten D. Solar simulated ultraviolet radiation inactivates HCoV-NL63 and SARS-CoV-2 coronaviruses at environmentally relevant doses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.06.25.449831. [PMID: 34282415 PMCID: PMC8288145 DOI: 10.1101/2021.06.25.449831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The germicidal properties of short wavelength ultraviolet C (UVC) light are well established and used to inactivate many viruses and other microbes. However, much less is known about germicidal effects of terrestrial solar UV light, confined exclusively to wavelengths in the UVA and UVB regions. Here, we have explored the sensitivity of the human coronaviruses HCoV-NL63 and SARS-CoV-2 to solar-simulated full spectrum ultraviolet light (sUV) delivered at environmentally relevant doses. First, HCoV-NL63 coronavirus inactivation by sUV-exposure was confirmed employing (i) viral plaque assays, (ii) RT-qPCR detection of viral genome replication, and (iii) infection-induced stress response gene expression array analysis. Next, a detailed dose-response relationship of SARS-CoV-2 coronavirus inactivation by sUV was elucidated, suggesting a half maximal suppression of viral infectivity at low sUV doses. Likewise, extended sUV exposure of SARS-CoV-2 blocked cellular infection as revealed by plaque assay and stress response gene expression array analysis. Moreover, comparative (HCoV-NL63 versus SARS-CoV-2) single gene expression analysis by RT-qPCR confirmed that sUV exposure blocks coronavirus-induced redox, inflammatory, and proteotoxic stress responses. Based on our findings, we estimate that solar ground level full spectrum UV light impairs coronavirus infectivity at environmentally relevant doses. Given the urgency and global scale of the unfolding SARS-CoV-2 pandemic, these prototype data suggest feasibility of solar UV-induced viral inactivation, an observation deserving further molecular exploration in more relevant exposure models.
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Affiliation(s)
- Georg T. Wondrak
- Department of Pharmacology and Toxicology, College of Pharmacy and UA Cancer Center, University of Arizona, Tucson, Arizona
| | - Jana Jandova
- Department of Pharmacology and Toxicology, College of Pharmacy and UA Cancer Center, University of Arizona, Tucson, Arizona
| | - Spencer J. Williams
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, Arizona
| | - Dominik Schenten
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, Arizona
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Yu L, Wang J, Li X, Mao L, Sui Y, Chen W, Pelechano V, Guo X, Yin X. Simultaneous detection of SARS-CoV-2 and pandemic (H1N1) 2009 virus with real-time isothermal platform. Heliyon 2021; 7:e07584. [PMID: 34307953 PMCID: PMC8280398 DOI: 10.1016/j.heliyon.2021.e07584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/14/2021] [Accepted: 07/12/2021] [Indexed: 12/24/2022] Open
Abstract
The recent ongoing outbreak of novel coronavirus SARS-CoV-2 (known as COVID-19) is a severe threat to human health worldwide. By press time, more than 3.3 million people have died from COVID-19, with many countries experiencing peaks in infections and hospitalizations. The main symptoms of infection with SARS-CoV-2 include fever, chills, coughing, shortness of breath or difficulty breathing, fatigue, muscle or body aches and pains. While the symptoms of the pandemic (H1N1) 2009 virus have many similarities to the signs and transmission routes of the novel coronavirus, e.g., fever, cough, sore throat, body aches, headache, chills and fatigue. And a few cases of serious illness, rapid progress, can appear viral pneumonia, combined with respiratory failure, multiple organ function damage, serious people can die. Therefore, there is an urgent need to develop a rapid and accurate field diagnostic method to effectively identify the two viruses and treat these early infections on time, thus helping to control the spread of the disease. Among molecular detection methods, RT-LAMP (real-time reverse transcription-loop-mediated isothermal amplification) has some advantages in pathogen detection due to its rapid, accurate and effective detection characteristics. Here, we combined the primers of the two viruses with the fluorescent probes on the RT-LAMP detection platform to detect the two viruses simultaneously. Firstly, RT-LAMP method was used respectively to detect the two viruses at different concentrations to determine the effectiveness and sensitivity of probe primers to the RNA samples. And then, the two virus samples were detected simultaneously in the same reaction tube to validate if testing for the two viruses together had an impact on the results compared to detecting alone. We verified the detection efficiency of three highly active BST variants during RT-LAMP assay. We expect that this assay can effectively and accurately distinguish COVID-19 from the pandemic (H1N1) 2009, so that these two diseases with similar symptoms can be appropriately differentiated and treated.
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Affiliation(s)
- Lin Yu
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Jingyao Wang
- Biotech & Biomedicine (Shenyang) Group Ltd., Shenyang, 110000, China
| | - Xuelong Li
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Lingling Mao
- Liaoning Center for Disease Control and Prevention, 110005, Shenyang, Liaoning, China
| | - Yi Sui
- Department of Neurology, Shenyang First People's Hospital (Shenyang Brain Hospital), Shenyang, 110041, China
| | - Weihua Chen
- Biotech & Biomedicine (Shenyang) Group Ltd., Shenyang, 110000, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
- College of Life Science, HeNan Normal University, 453007 Xinxiang, Henan, China
- Pluri Biotech Co.Ltd, Xuzhou, 221001, China
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna 17165, Sweden
| | - Xing Guo
- Department of Neurobiology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Nanjing Medical University, Nanjing 211166, Jiangsu, China
| | - Xiushan Yin
- Applied Biology Laboratory, Shenyang University of Chemical Technology, 110142, Shenyang, China
- Biotech & Biomedicine (Shenyang) Group Ltd., Shenyang, 110000, China
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna 17165, Sweden
- Pluri Biotech Co.Ltd, Xuzhou, 221001, China
- Nanog Biotech Co.Ltd, Shanghai, 200000, China
- Biotech & Biomedicine Science (Jiangxi) Co. Ltd, Ganzhou, 341000, China
- Department of Respiratory and Critical Care Medicine, Central Hospital Affiliated to Shenyang Medical College, Shenyang 110024, China
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Sawada S, Matsubara S. Microbiology of Acute Maxillary Sinusitis in Children. Laryngoscope 2021; 131:E2705-E2711. [PMID: 33939189 PMCID: PMC8519026 DOI: 10.1002/lary.29564] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVES/HYPOTHESIS Acute rhinosinusitis is a frequent common cold-related complication in children. Despite the need for appropriate treatment, its underlying microbiology remains unclear. This study aimed to investigate the microbiology of acute rhinosinusitis in children. STUDY DESIGN Prospective non controlled study. METHODS Thirty-one pediatric acute maxillary sinusitis patients with severe symptoms were assessed. The subjects were 17 males and 14 females aged 5 to 14 years (mean age, 9.1 years). Maxillary sinus aspirates were collected and cultured, with subsequent viral and bacterial polymerase chain reaction (PCR) analysis. Bacteria were analyzed using culturing and PCR, and viruses were analyzed using PCR. The PCR kits used identify 18 types of respiratory viruses and 13 types of bacteria. RESULTS At least one pathogen was detected in 30 of 31 aspirates (97%) using PCR, and none of the aspirates contained respiratory viruses alone. Ten aspirates (32%) contained both viruses and bacteria. The most common viruses detected were rhinovirus (13%) and influenza virus (10%). The most common bacteria were Haemophilus influenzae (45%), Streptococcus pneumoniae (32%), Moraxella catarrhalis (16%), and Chlamydophila pneumoniae (13%). Bacteria were found in 21 of 31 cases (68%) via bacterial culturing. Culturing revealed that H influenzae was the most common pathogen (42%). CONCLUSIONS In pediatric acute maxillary sinusitis, respiratory bacteria were detected in 65% of the sinus aspirates and both bacteria and viruses in 32%. The most common viruses were rhinovirus and influenza virus, and the most common bacteria were H influenzae and S pneumoniae. Viral and bacterial PCR is useful for accurately investigating the microbiology in pediatric sinusitis. LEVEL OF EVIDENCE Level 3. Laryngoscope, 2021.
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Affiliation(s)
- Shoichi Sawada
- Department of Otolaryngology, Sawada Eye and Ear Clinic, Fukuicho, Kochi City, Kochi, Japan
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Cissé A, Milucky J, Ilboudo AK, Waller JL, Bicaba B, Medah I, Mirza S, Whitney CG, Tarnagda Z. Comparison of performance between Fast Track Diagnostics Respiratory Kit and the CDC global reference laboratory for influenza rRT-PCR panel for detection of influenza A and influenza B. Influenza Other Respir Viruses 2021; 15:381-388. [PMID: 33638312 PMCID: PMC8051705 DOI: 10.1111/irv.12830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 11/30/2022] Open
Abstract
Background Reliable diagnostics are a key to identifying influenza infections. Objectives Our objectives were to describe the detection of influenza among severe acute respiratory infection (SARI) cases, to compare test results from the Fast Track Diagnostics (FTD) Kit for influenza detection to the Centers for Disease Control (CDC) human influenza virus detection and characterization panel, and to assess seasonality of influenza in Burkina Faso. Methods Nasopharyngeal and oropharyngeal specimens from SARI cases (hospitalized patients with fever, cough, and onset in the previous 10 days) were tested using the FTD‐33 Kit and the CDC rRT‐PCR influenza assays. We assessed sensitivity and specificity of the FTD‐33 Kit for detecting influenza A, influenza B, and the influenza A(H1N1)pdm09 strain using the CDC human influenza rRT‐PCR panel as the gold standard. Results From December 2016 to February 2019, 1706 SARI cases were identified, 1511 specimens were tested, and 211 were positive for influenza A (14.0%) and 100 for influenza B (6.6%) by either assay. Higher influenza circulation occurred between November and April with varying peaks of influenza A and influenza B. Sensitivity of the FTD‐33 assay was 91.9% for influenza A, 95.7% for influenza B, and 93.8% for A(H1N1)pdm09 subtype. Specificity was over 99% for all three tests. Conclusions Our study indicates that Burkina Faso has one peak of influenza each year which is similar to the Northern Hemisphere and differs from other countries in West Africa. We found high concordance of influenza results between the two assays indicating FTD‐33 can be used to reliably detect influenza among SARI cases.
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Affiliation(s)
- Assana Cissé
- Laboratoire National de Référence-Grippes (LNR-G), Institut de Recherche en Sciences de la Santé (IRSS), Bobo Dioulasso, Burkina Faso
| | - Jennifer Milucky
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - Abdoul Kader Ilboudo
- Laboratoire National de Référence-Grippes (LNR-G), Institut de Recherche en Sciences de la Santé (IRSS), Bobo Dioulasso, Burkina Faso
| | - Jessica L Waller
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - Brice Bicaba
- Direction de la Protection de la Santé de la Population, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Isaïe Medah
- Direction de la Protection de la Santé de la Population, Ministère de la Santé, Ouagadougou, Burkina Faso
| | - Sara Mirza
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - Cynthia G Whitney
- Centers for Disease Control and Prevention, National Center for Immunization and Respiratory Diseases, Atlanta, GA, USA
| | - Zekiba Tarnagda
- Laboratoire National de Référence-Grippes (LNR-G), Institut de Recherche en Sciences de la Santé (IRSS), Bobo Dioulasso, Burkina Faso
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Abed Y, Schibler M, Checkmahomed L, Carbonneau J, Venable MC, Fage C, Giannotti F, Goncalves AR, Kaiser L, Boivin G. Molecular pathway of influenza pan-neuraminidase inhibitor resistance in an immunocompromised patient. Antivir Ther 2020; 24:581-587. [PMID: 32031540 DOI: 10.3851/imp3344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Neuraminidase (NA) inhibitors (NAIs), including oseltamivir and zanamivir, play an important therapeutic role against influenza infections in immunocompromised patients. In such settings, however, NAI therapy may lead to the emergence of resistance involving mutations within the influenza surface genes. The aim of this study was to investigate the evolution of NA and haemagglutinin (HA) genes of influenza A(H1N1)pdm09 virus in an immunocompromised patient receiving oseltamivir then zanamivir therapies. METHODS Nasopharyngeal swab (NPS) samples were collected between 27 January 2018 and 11 April 2018 from a haematopoietic stem cell transplant recipient. These include 10 samples collected either pre-therapy, during oseltamivir and zanamivir treatment as well as after therapy. The A(H1N1)pdm09 HA/NA genes were sequenced. The H275Y NA substitution was quantified by droplet digital RT-PCR assay. A(H1N1)pdm09 recombinant viruses containing HA mutations were tested by HA elution experiments to investigate in vitro binding properties. RESULTS Oseltamivir rapidly induced the H275Y NA mutation which constituted 98.33% of the viral population after 15 days of oseltamivir treatment. The related HA gene contained S135A and P183S substitutions within the receptor-binding site. After a switch to zanamivir, 275H/Y and 119E/G/D mixed populations were detected. In the last samples, the double H275Y-E119G NA variant dominated with S135A and P183S HA substitutions. CONCLUSIONS This report confirms that oseltamivir can rapidly induce the emergence of the H275Y substitution in A(H1N1)pdm09 viruses and subsequent switch to zanamivir can lead to additional substitutions at codon E119 resulting in multi-drug resistance. Such data additionally suggest a potential compensatory role for HA substitutions near the receptor binding site.
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Affiliation(s)
- Yacine Abed
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Manuel Schibler
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland
| | - Liva Checkmahomed
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Julie Carbonneau
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Marie-Christine Venable
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Clément Fage
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
| | - Federica Giannotti
- Division of Hematology, Geneva University Hospitals, Geneva, Switzerland
| | - Ana Rita Goncalves
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Geneva University Hospitals, Geneva, Switzerland
| | - Guy Boivin
- Research Center in Infectious Diseases of the CHUQ-CHUL and Laval University, Québec City, QC, Canada
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Emperador DM, Mazzola LT, Kelly-Cirino C. An open-source molecular diagnostic platform approach for outbreak and epidemic preparedness. Afr J Lab Med 2020; 9:1017. [PMID: 33102172 PMCID: PMC7564747 DOI: 10.4102/ajlm.v9i2.1017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Background Diagnostic development for outbreak pathogens has typically followed a disease-specific reactive rather than proactive response. Given the diversity of outbreak pathogens, particularly those prioritised by the World Health Organization Research and Development Blueprint, a more flexible and proactive approach to epidemic preparedness is needed to expand access to critical molecular diagnostic tests in peripheral and resource-constrained deployment settings. Objective New and more sustainable directives are needed to spur the development of high-quality products, particularly for epidemics more often found in low- and middle-income countries. To leverage and de-risk the development process, we present the benefits and challenges of an open-source business model for co-development of molecular diagnostic tests for decentralised settings. Methods We identify key outbreak pathogens that are available only for testing in high infrastructure laboratories and compare in-country installed base platforms that could be leveraged for menu expansion. Key strengths and challenges for development are highlighted for both platform and assay developers, with discussion of how to leverage and de-risk the process through an open-source development model. Results Depending on the specific partner strengths, options for partnership roles are presented. The proposed open-source business model addresses the particular challenges in the detection of outbreak- and epidemic-prone pathogens in low- and middle-income countries, reduces development and deployment risks to support outbreak response, strengthens diagnostic capacity and creates a viable market for product developers. Conclusion We hope this model for a collaborative and open-source approach for molecular diagnostics serves to encourage stakeholders to consider co-development partnerships to improve outbreak preparedness and epidemic/pandemic response.
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Affiliation(s)
- Devy M Emperador
- Foundation for Innovative and New Diagnostics, Geneva, Switzerland
| | - Laura T Mazzola
- Foundation for Innovative and New Diagnostics, San Francisco, California, United States
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Li Y, Xu P, Wan Z, Du H, Jin X, Zhang C. Single-tube detection of nine bacterial antibiotic-resistance genes by a 2-dimensional multiplex qPCR assay based on fluorescence and melting temperature. Mol Biol Rep 2020; 47:7341-7348. [PMID: 32888129 DOI: 10.1007/s11033-020-05789-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/28/2020] [Indexed: 12/21/2022]
Abstract
Simple, multiplex qPCR methods are advantages for rapid molecular diagnosis of multiple antibiotics-resistant genes simultaneously. However, the number of genes can be detected in a single reaction tube is often limited by the fluorescence channels of a real-time PCR instrument. In this study, we developed a simple 2-D multiplex qPCR method by combining the probe colors and amplicon Tm values to overcome the mechanical limit of the machine. The principle of the novel assay was validated by detection of nine bacterial antibiotic-resistance genes (KPC, NDM, VIM, OXA-48, GES, CIT, EBC, ACC and DHA) in a single reaction tube. This assay is highly sensitive within a range of 30-3000 copies per reaction. The simplicity, rapidity, high sensitivity and specificity, and low cost of the novel method make it a promising tool for developing clinical diagnostic kits for monitoring resistance and other genetic determinants of infectious diseases.
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Affiliation(s)
- Yingxue Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
- Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China
- School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Ping Xu
- Department of Clinical Laboratory, The Fifth People's Hospital of Suzhou, Suzhou, 215000, China
| | - Zhenzhou Wan
- Medical Laboratory of Taizhou Fourth People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, 215000, China.
| | - Xia Jin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Chiyu Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.
- Pathogen Discovery and Evolution Unit, Institut Pasteur of Shanghai, Chinese Academy of Science, Shanghai, 200031, China.
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Duplex PCR for Detection of Aleutian Disease Virus from Biological and Environmental Samples. ACTA VET-BEOGRAD 2019. [DOI: 10.2478/acve-2019-0034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Aleutian disease is one of the most serious disease entities affecting mink farms. The disease causes significant economic losses in mink breeding countries. The aim of the study was to optimize a diagnostic test based on duplex PCR to enable detection of Aleutian disease virus in biological and environmental samples.
Blood (n = 40) and spleen (n = 40) samples from animals with suspected infection, and swabs from cages in which infected animals were kept (n = 20) were used for analysis. DNA was isolated from the samples, followed by optimization of the duplex PCR reaction targeting sequences coding NS1 and VP2 proteins. The qPCR method was used to determine the sensitivity of the reaction. The specificity of the analysis was confirmed by the sequencing results.
Optimized duplex PCR enabled detection of Aleutian Mink Disease Virus (AMDV) genetic material in biological and environmental samples. Testing of the sensitivity of the method indicated clear amplification for both primer pairs at 102 copies of viral DNA in a reaction. Sequencing confirmed the specificity of the reaction, which in the case of both primer pairs indicated an over 90% agreement between the isolates and the variants of the virus from the databases.
The use of duplex PCR to detect two regions of the AMDV genome may increase the sensitivity and specificity of the method and significantly expand the possibilities of further analysis based on sequencing.
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Kenmoe S, Tcharnenwa C, Monamele GC, Kengne CN, Ripa MN, Whitaker B, Alroy KA, Balajee SA, Njouom R. Comparison of FTD® respiratory pathogens 33 and a singleplex CDC assay for the detection of respiratory viruses: A study from Cameroon. Diagn Microbiol Infect Dis 2019; 94:236-242. [PMID: 30738690 PMCID: PMC7127211 DOI: 10.1016/j.diagmicrobio.2019.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/09/2019] [Accepted: 01/09/2019] [Indexed: 12/04/2022]
Abstract
Introduction: This study compares the detection of 14 common respiratory viruses by two different real-time reverse transcription polymerase chain reaction (rRT-PCR) methods: in house singleplex tests developed by the Centers for Disease Control and Prevention and the commercially available Fast Track Diagnostic (FTD®) Respiratory Pathogens 33 multiplex test. Methods: A total of 217 nasopharyngeal swabs were analyzed using CDC singleplex rRT-PCR and FTD® Respiratory Pathogens 33 multiplex assays, for the detection of 14 respiratory viruses. Results: The results showed that 179/217 (82.5%) samples were positive with the singleplex method and 183/217 (84.3%) with the FTD® Respiratory Pathogens 33 multiplex test. Excellent or satisfactory agreement was obtained for all viruses (k > 0.6) except Parainfluenzavirus 4 (k = 0.24) and influenza B (k = 0.51). Conclusion: Although the multiplex FTD kits were more expensive than the singleplex assay, the FTD kits yielded rapid results in a shorter timeframe, increasing efficiency of diagnosis.
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Affiliation(s)
- Sebastien Kenmoe
- Department of Virology, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Clarisse Tcharnenwa
- Department of Virology, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon; Department of Microbiology, Faculty of Sciences, University of Yaoundé I, P.O. Box 337, Yaoundé, Cameroon
| | - Gwladys C Monamele
- Department of Virology, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon; Department of Microbiology and Parasitology, University of Buea, Buea, Cameroon
| | | | - Mohamadou Njankouo Ripa
- Department of Virology, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon
| | - Brett Whitaker
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Karen A Alroy
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - S Arunmozhi Balajee
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Richard Njouom
- Department of Virology, Centre Pasteur of Cameroon, 451 Rue 2005, P.O. Box 1274, Yaoundé, Cameroon.
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Tine RC, Ndiaye LA, Niang MN, Kiori DE, Dia N, Gaye O, Broutin H. Upper respiratory infections in a rural area with reduced malaria transmission in Senegal: a pathogens community study. BMC Infect Dis 2018; 18:459. [PMID: 30200897 PMCID: PMC6131886 DOI: 10.1186/s12879-018-3362-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 08/24/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Acute Respiratory Infections (ARI) are common causes of febrile illnesses in many settings in Senegal. These infections are usually managed presumptively due to lack of appropriate diagnostic tools. This situation, can lead to poor management of febrile illness or antibiotic misuse. In addition, there are limited data on the spectrum of pathogens commonly responsible for these ARI. This study was conducted to explore the pathogens community among patients with acute respiratory infection in a rural area in Senegal. METHODS A cross sectional study was conducted from August to December 2015. Children and adult patients attending Keur Socé health post for signs suggestive of acute respiratory infection were enrolled after providing inform consent. Eligible participants were recruited using a consecutive sampling method. Paired nose and throat swabs were collected for pathogen detection. Samples were processed using a multiplex PCR designed to identify 21 pathogens including both virus and bacteria. RESULTS Two hundred and fifty patients participated in the study. Samples positivity rate was evaluated at 95.2% (238/250). Streptococcus pneumoniae was the predominant pathogen (74%) and was present in all months and all age-groups, followed by Staphylococcus aureus (28,8%) and rhinovirus (28,4%). Respiratory syncytial virus (RSV) was detected only among children under 5 years old in August and September while coronavirus was present in all age groups, during the months of October and December. CONCLUSION This pilot study revealed a diversity of pathogens over the time and across all age groups, highlighting the need for further exploration. A pathogen community approach including both virus and bacteria at a larger scale becomes crucial for a better understanding of transmission dynamics at population level in order to help shape ARI control strategies.
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Affiliation(s)
- Roger C Tine
- Service de Parasitologie, Faculté de Médecine, Université Cheikh Anta Diop de Dakar (UCAD), BP5005, Dakar-Fann, Senegal.
| | - Léon A Ndiaye
- Service de Parasitologie, Faculté de Médecine, Université Cheikh Anta Diop de Dakar (UCAD), BP5005, Dakar-Fann, Senegal
| | - Mbayame N Niang
- Laboratoire des Virus respiratoires, Institut Pasteur de Dakar, Dakar, Senegal
| | - Davy E Kiori
- Laboratoire des Virus respiratoires, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ndongo Dia
- Laboratoire des Virus respiratoires, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oumar Gaye
- Service de Parasitologie, Faculté de Médecine, Université Cheikh Anta Diop de Dakar (UCAD), BP5005, Dakar-Fann, Senegal
| | - Hélène Broutin
- Service de Parasitologie, Faculté de Médecine, Université Cheikh Anta Diop de Dakar (UCAD), BP5005, Dakar-Fann, Senegal.,MIVEGEC, UMR CNRS -IRD -University of Montpellier - 911, Avenue Agropolis BP 64501, Cédex 5 34394, Montpellier, France
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Wrotek A, Czajkowska M, Zawłocka E, Jackowska T. Influenza: Underestimated in Children Below 2 Years of Age. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1108:81-91. [PMID: 29995212 DOI: 10.1007/5584_2018_240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Children under 2 years of age may receive antiviral therapy when influenza is suspected. Signs of influenza are frequently unclear and testing is indicated. The aim of the study was to assess the usefulness of clinical signs and the rapid influenza diagnostic test (RIDT) in diagnosing influenza and in choosing the appropriate treatment. In the 2015-2016 influenza season, 89 children under 2 years of age (56.7% of 157 children diagnosed with influenza) were hospitalized. There were 74 RIDT and 70 reverse transcription polymerase chain reactions (RT-PCR) performed for the purpose of diagnosis, either test per child. Eighty-three percent of children (74/89) presented with fever, 55.1% (49/89) with cough, and 39.3% (35/89) with both cough and fever. The RIDT was positive in 31.1% (23/74) of cases. The highest percentage of positive RIDT was within the first 24 h of disease, decreasing dramatically thereafter (70% vs. 13-17%, respectively). The RIDT shortened the time to diagnosis by 43.8 h/patient (an average €149 gain in treatment costs). The mean delay for RT-PCR-based diagnosis was 33.5 h/patient (an average €114 loss in treatment costs). We conclude that clinical signs have a low diagnostic sensitivity in children under 2 years of age. Likewise, RIDT is of low sensitivity, being diagnostically useful only in the first 24 h. The PCR is recommended for the diagnosis, but that requires a constant access to the method.
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Affiliation(s)
- A Wrotek
- Department of Pediatrics, Center of Postgraduate Medical Education, Warsaw, Poland
- Department of Pediatrics, Bielanski Hospital, Warsaw, Poland
| | - M Czajkowska
- Department of Pediatrics, Center of Postgraduate Medical Education, Warsaw, Poland
- Department of Pediatrics, Bielanski Hospital, Warsaw, Poland
| | - E Zawłocka
- Department of Pediatrics, Center of Postgraduate Medical Education, Warsaw, Poland
- Department of Pediatrics, Bielanski Hospital, Warsaw, Poland
| | - T Jackowska
- Department of Pediatrics, Center of Postgraduate Medical Education, Warsaw, Poland.
- Department of Pediatrics, Bielanski Hospital, Warsaw, Poland.
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Kadjo HA, Adjogoua E, Dia N, Adagba M, Abdoulaye O, Daniel S, Kouakou B, Ngolo DC, Coulibaly D, Ndahwouh TN, Dosso M. DETECTION OF NON-INFLUENZA VIRUSES IN ACUTE RESPIRATORY INFECTIONS IN CHILDREN UNDER FIVE-YEAR-OLD IN COTE D'IVOIRE (JANUARY - DECEMBER 2013). Afr J Infect Dis 2018; 12:78-88. [PMID: 30109291 PMCID: PMC6085743 DOI: 10.21010/ajid.v12i2.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Influenza sentinel surveillance in Cote d'Ivoire showed that 70% of Acute Respiratory Infections (ARI) cases remained without etiology. This work aims to describe the epidemiological, clinical, and virological pattern of ARI that tested negative for influenza virus, in children under five years old. MATERIALS AND METHODS one thousand and fifty nine samples of patients presenting influenza Like Illness (ILI) or Severe Acute Respiratory Infections (SARI) symptoms were tested for other respiratory viruses using multiplex RT-PCR assays targeting 10 respiratory viruses. RESULTS The following pathogens were detected as follows, hRV 31,92% (98/307), hRSV 24.4% (75/329), PIV 20.5% (63/307), HCoV 229E 12,05% (37/307), hMPV 6.2% (19/307), HCoVOC43 1.0% (3/307) and EnV 1.0% (3/307). Among the 1,059 specimens analyzed, 917 (86.6%) were ILI samples and 142 (23.4%) were SARI samples. The proportion of children infected with at least one virus was 29.8% (273/917) in ILI cases and 23.9% (34/142) in SARI cases. The most prevalent viruses, responsible for ILI cases were hRV with 35.89% (98/273) and hRSV in SARI cases with 41.2% (14/34) of cases. Among the 1,059 patients, only 22 (2.1%) children presented risk factors related to the severity of influenza virus infection. CONCLUSION This study showed that respiratory viruses play an important role in the etiology of ARI in children. For a better understanding of the epidemiology of ARI and improved case management, it would be interesting in this context to expand the surveillance of influenza to other respiratory viruses.
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Affiliation(s)
- Herve A. Kadjo
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | | | - Marius Adagba
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | - Saraka Daniel
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | - Bertin Kouakou
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | - David C. Ngolo
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | - Talla Nzussouo Ndahwouh
- Noguchi Memorial Institute for Medical Research (NMIMR) University of Ghana, Legon, Accra, Ghana
| | - Mireille Dosso
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
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Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis. Methods Mol Biol 2018; 1838:125-140. [PMID: 30128994 PMCID: PMC7121196 DOI: 10.1007/978-1-4939-8682-8_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A large number of viruses can individually and concurrently cause various respiratory illnesses. Metagenomic sequencing using next-generation sequencing (NGS) technology is capable of identifying a variety of pathogens. Here, we describe a method using a large panel of oligo probes to enrich sequence targets of 34 respiratory DNA and RNA viruses that reduces non-viral reads in NGS data and achieves high performance of sequencing-based pathogen identification. The approach can be applied to total nucleic acids purified from respiratory swabs stored in viral transport medium. Illumina TruSeq RNA Access Library procedure is used in targeted sequencing of respiratory viruses. The samples are subjected to RNA fragmentation, random reverse transcription, random PCR amplification, and ligation with barcoded library adaptors. The libraries are pooled and subjected to two rounds of enrichments by using a large panel of oligos designed to capture whole genomes of 34 respiratory viruses. The enriched libraries are amplified and sequenced using Illumina MiSeq sequencing system and reagents. This method can achieve viral detection sensitivity comparable with molecular assay and obtain partial to complete genome sequences for each virus to allow accurate genotyping and variant analysis.
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Swamy MA, Malhotra B, Janardhan Reddy PV, Tiwari J. Profile of Respiratory Pathogens Causing Acute Respiratory Infections in Hospitalised Children at Rajasthan a 4 Year’s Study. Indian J Med Microbiol 2018; 36:163-171. [DOI: 10.4103/ijmm.ijmm_18_84] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Rodrigues CMC, Groves H. Community-Acquired Pneumonia in Children: the Challenges of Microbiological Diagnosis. J Clin Microbiol 2018; 56:e01318-17. [PMID: 29237789 PMCID: PMC5824044 DOI: 10.1128/jcm.01318-17] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Community-acquired pneumonia (CAP) is the leading cause of mortality in children under 5 years of age globally. To improve the management of CAP, we must distinguish CAP from other common pediatric conditions and develop better diagnostic methods to detect the causative organism, so as to best direct appropriate resources in both industrialized and developing countries. Here, we review the diagnostic modalities available for identifying viruses and bacteria in the upper and lower respiratory tract of children, with a discussion of their utility and limitations in diagnosing CAP in children.
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Affiliation(s)
- C M C Rodrigues
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Paediatric Infectious Diseases and Immunology, Great North Children's Hospital, Newcastle Upon Tyne, United Kingdom
| | - H Groves
- Centre for Experimental Medicine, Queens University, Belfast, United Kingdom
- Department of Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, United Kingdom
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Márquez-Escobar VA. Current developments and prospects on human metapneumovirus vaccines. Expert Rev Vaccines 2017; 16:419-431. [PMID: 28116910 DOI: 10.1080/14760584.2017.1283223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Human metapneumovirus (hMPV) has become one of the major pathogens causing acute respiratory infections (ARI) mainly affecting young children, immunocompromised patients, and the elderly. Currently there are no licensed vaccines against this virus. Areas covered: Since the discovery of hMPV in 2001, many groups have focused on developing vaccines against this pathogen. This review presents the outcomes and perspectives derived from preclinical studies performed in cell cultures and animals as well as the only candidate that has reached evaluation in a clinical trial. Limitations of the current vaccine candidates are discussed and perspectives for the development of plant-based vaccines are analyzed. Expert commentary: Several hMPV vaccine candidates are under development with the potential to progress into clinical trials. In parallel, the molecular farming field offers new opportunities to generate innovative vaccines that will offer several advantages in the fight against hMPV.
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Affiliation(s)
- Verónica Araceli Márquez-Escobar
- a Facultad de Ciencias Químicas , Universidad Autónoma de San Luis Potosí , Av. Dr. Manuel Nava 6, San Luis Potosí 78210 , SLP , Mexico
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A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses. Int J Mol Sci 2016; 17:ijms17111880. [PMID: 27886052 PMCID: PMC5133880 DOI: 10.3390/ijms17111880] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/30/2016] [Accepted: 11/01/2016] [Indexed: 01/17/2023] Open
Abstract
Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 102 copies for HCoV-OC43, and 3 × 101 copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 μL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples.
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Abstract
Infections represent an ongoing challenge for immunocompromised patients. Children are particularly vulnerable because of several age-related issues that relate in part to immune prematurity. This review addresses the challenges in managing infections among immunocompromised children and highlights several general principles that guide management. Statement of novelty: This work provides important guidance to clinicians who are involved in the management of pediatric patients with an ever-expanding spectrum of immunocompromising disorders.
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