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Kumar A, Bahal A, Singh L, Ninawe S, Grover N, Suman N. Utility of multiplex real-time PCR for diagnosing paediatric acute respiratory tract infection in a tertiary care hospital. Med J Armed Forces India 2023; 79:286-291. [PMID: 37193516 PMCID: PMC10182280 DOI: 10.1016/j.mjafi.2021.05.007] [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: 05/17/2020] [Accepted: 05/05/2021] [Indexed: 11/30/2022] Open
Abstract
Background Acute respiratory infections (ARIs) are responsible for considerable morbidity and mortality among children all over the world. Many of the etiologic agents of the infections especially viral go undiagnosed for lack of requisite facility and the cost factors. We have used a commercially available platform for diagnosis of ARIs in children receiving inpatient and outpatient services in a tertiary care centre. Methods The framework of the study was prospective and observational. In this study, clinical samples of children suffering from ARIs were subjected to real-time multiplex PCR targeting both viral and bacterial pathogens. Results Of 94 samples received at our centre (49 male and 45 female), the positivity for respiratory pathogens was detected in 50 (53.19%) samples. Clinical symptoms of patients and age distribution have been elaborated in text. A single pathogen (n = 29/50), two pathogens (15/50) and three pathogens (n = 6/50) were detected by multiplex RT-PCR. Of 77 isolates detected, maximum numbers were of human rhinovirus (HRV) (n = 14) (18.18%) Streptococcus pneumoniae (n = 14) (18.18%) followed by Staphylococcus aureus (n = 10) (12.98%). Conclusion The epidemiology of ARIs considering viral etiologies is poorly understood due to less number of studies especially in Indian subcontinent. The advent of latest advanced molecular methods has made it possible to identify common respiratory pathogens and has contributed to cover the gap in existing knowledge.
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Affiliation(s)
- Anshu Kumar
- Graded Specialist (Microbiology), Command Hospital (Western Command), Chandimandir, India
| | - Ashish Bahal
- Classified Specialist (Path & Micro) Army Hospital (R&R), Delhi Cantt, India
| | - Lavan Singh
- Classified Specialist (Path & Micro) Army Hospital (R&R), Delhi Cantt, India
| | - S.M. Ninawe
- Graded Specialist (Microbiology), Army Hospital (R&R), Delhi Cantt, India
| | - Naveen Grover
- Senior Adviser (Path & Micro), Army Hospital (R&R), Delhi Cantt, India
| | - Neha Suman
- Graded Specialist (ENT), Command Hospital (Western Command), Chandimandir, India
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2
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Aune KT, Davis MF, Smith GS. Extreme Precipitation Events and Infectious Disease Risk: A Scoping Review and Framework for Infectious Respiratory Viruses. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 19:165. [PMID: 35010425 PMCID: PMC8751052 DOI: 10.3390/ijerph19010165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 05/28/2023]
Abstract
Extreme precipitation events (EPE) change the natural and built environments and alter human behavior in ways that facilitate infectious disease transmission. EPEs are expected with high confidence to increase in frequency and are thus of great public health importance. This scoping review seeks to summarize the mechanisms and severity of impacts of EPEs on infectious diseases, to provide a conceptual framework for the influence of EPEs on infectious respiratory diseases, and to define areas of future study currently lacking in this field. The effects of EPEs are well-studied with respect to enteric, vector-borne, and allergic illness where they are shown to moderately increase risk of illness, but not well-understood in relation to infectious respiratory illness. We propose a framework for a similar influence of EPEs on infectious respiratory viruses through several plausible pathways: decreased UV radiation, increased ambient relative humidity, and changes to human behavior (increased time indoors and use of heating and cooling systems). However, limited work has evaluated meteorologic risk factors for infectious respiratory diseases. Future research is needed to evaluate the effects of EPEs on infectious respiratory diseases using individual-level case surveillance, fine spatial scales, and lag periods suited to the incubation periods of the disease under study, as well as a full characterization of susceptible, vulnerable, and sensitive population characteristics.
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Affiliation(s)
- Kyle T. Aune
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
| | - Meghan F. Davis
- Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA;
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Genee S. Smith
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA;
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Waghmode R, Jadhav S, Nema V. The Burden of Respiratory Viruses and Their Prevalence in Different Geographical Regions of India: 1970-2020. Front Microbiol 2021; 12:723850. [PMID: 34531842 PMCID: PMC8438434 DOI: 10.3389/fmicb.2021.723850] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
As per the 2019 report of the National Health Portal of India, 41,996,260 cases and 3,740 deaths from respiratory infections were recorded across India in 2018. India contributes to 18% of the global population, with severe acute respiratory infection (SARI) as one of the prominent causes of mortality in children >5 years of age. Measures in terms of the diagnosis and surveillance of respiratory infections are taken up globally to discover their circulating types, detect outbreaks, and estimate the disease burden. Similarly, the purpose of this review was to determine the prevalence of respiratory infections in various regions of India through published reports. Understanding the pattern and prevalence of various viral entities responsible for infections and outbreaks can help in designing better strategies to combat the problem. The associated pathogens comprise respiratory syncytial virus (RSV), rhinovirus, influenza virus, parainfluenza virus, adenovirus, etc. Identification of these respiratory viruses was not given high priority until now, but the pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has sensitized our system to be alert about the burden of existing infections and to have proper checks for emerging ones. Most of the studies reported to date have worked on the influenza virus as a priority. However, the data describing the prevalence of other respiratory viruses with their seasonal pattern have significant epidemiological value. A comprehensive literature search was done to gather data from all geographical regions of India comprising all states of India from 1970 to 2020. The same has been compared with the global scenario and is being presented here.
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Affiliation(s)
- Rushabh Waghmode
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India
| | - Sushama Jadhav
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India
| | - Vijay Nema
- Division of Molecular Biology, ICMR-National AIDS Research Institute, Pune, India
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4
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Ghia C, Rambhad G. Disease Burden Due to Respiratory Syncytial Virus in Indian Pediatric Population: A Literature Review. CLINICAL MEDICINE INSIGHTS-PEDIATRICS 2021; 15:11795565211029250. [PMID: 34285625 PMCID: PMC8264742 DOI: 10.1177/11795565211029250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/03/2021] [Indexed: 11/17/2022]
Abstract
Respiratory syncytial virus (RSV) is one of the leading causes of lower respiratory tract infections in young children. Globally, there is huge disease burden, high treatment cost, and health impact beyond acute episodes due to RSV which necessitate development and implementation of preventive strategies for the control of RSV infection. The disease burden due to RSV in pediatric population across India is still not clearly understood so this literature review was therefore conducted to gather data on disease burden due to RSV in Indian pediatric population. Systematic literature search was performed using PubMed and Google search with different medical subject headings from 2007 to 2020. Studies performed in Indian pediatric population were selected for review. Literature review revealed that in India, epidemiology of RSV infection is well documented in young children (0-5 years) as compared to children from other age groups. The rates of RSV detection in various studies conducted in younger children (0-5 years) vary from 2.1% to 62.4% in India which is higher as compared to children from other age groups. In India, RSV mainly peaks around rainy to early winter season, that is, during months of June through October while smaller peak was noted during December, January, and February. In 2020, higher RSV-associated disease burden was reported among children (<5 years) in low-income and lower-middle-income countries. Considering significant disease burden due to RSV in young Indian children, availability of RSV vaccine would be crucial to prevent RSV infections in children and its spread in the community.
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Affiliation(s)
- Canna Ghia
- Medical and Scientific Affairs, Pfizer Limited, Mumbai, India
| | - Gautam Rambhad
- Medical and Scientific Affairs, Pfizer Limited, Mumbai, India
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5
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Sarkar S, Ratho RK, Singh M, Singh MP, Singh A, Sharma M. Comparative analysis of epidemiology, clinical features and cytokine response of Respiratory Syncytial and Human Metapneumovirus infected children with acute lower respiratory infections. Jpn J Infect Dis 2021; 75:56-62. [PMID: 34193665 DOI: 10.7883/yoken.jjid.2021.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Both Human Respiratory Syncytial virus (RSV) and Human Metapneumovirus (hMPV) cause immune-mediated under-five acute respiratory infections (ARI), but differences in their disease pathogenesis, if any, are not well-known. This study was undertaken to analyze the epidemio-clinico-immunological features of RSV and hMPV infections. Naso-pharyngeal aspirates from children (aged two months to five years) with ARI presenting to our tertiary care center between December 2013 to March 2016 were subjected to real-time polymerase chain reaction for detection of RSV and hMPV. Positive samples were analyzed for co-infections and levels of cytokines. Of 349 naso-pharyngeal aspirates, RSV was detected in 40.68% (142/349), hMPV in 6.59% (23/349) and both in 1.4% (5/349). Co-infections were common, rhinovirus being the commonest co-offender. The demographical and clinical parameters of RSV- and hMPV-infected children were comparable. MMP-9/TIMP-1 ratio was significantly higher in RSV-mediated ARI and IFN-γ in hMPV-mediated ARI. Both RSV and hMPV are common among north Indian children with ARI and coinfections are not uncommon. Their clinical features being non-discriminatory, molecular diagnosis should be utilized to ascertain their individual epidemiology. The differences in their immune-pathogenesis (MMP-9/TIMP-1 ratio in RSV and IFN-γ in hMPV) could serve as useful tools for developing newer drugs.
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Affiliation(s)
- Subhabrata Sarkar
- Department of Virology, Postgraduate Institute of Medical Education and Research, India
| | - Radha Kanta Ratho
- Department of Virology, Postgraduate Institute of Medical Education and Research, India
| | - Meenu Singh
- Department of Pediatric Pulmonology, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, India
| | - Mini Pritam Singh
- Department of Virology, Postgraduate Institute of Medical Education and Research, India
| | - Amarjeet Singh
- School and Public Health, Postgraduate Institute of Medical Education and Research, India
| | - Megha Sharma
- Department of Virology, Postgraduate Institute of Medical Education and Research, India
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Zhou J, Qin L, Meng X, Liu N. The interactive effects of ambient air pollutants-meteorological factors on confirmed cases of COVID-19 in 120 Chinese cities. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:27056-27066. [PMID: 33501581 PMCID: PMC7837878 DOI: 10.1007/s11356-021-12648-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/20/2021] [Indexed: 05/05/2023]
Abstract
Emerging evidence has confirmed meteorological factors and air pollutants affect novel coronavirus disease 2019 (COVID-19). However, no studies to date have considered the impact of interactions between meteorological factors and air pollutants on COVID-19 transmission. This study explores the association between ambient air pollutants (PM2.5, NO2, SO2, CO, and O3), meteorological factors (average temperature, diurnal temperature range, relative humidity, wind velocity, air pressure, precipitation, and hours of sunshine), and their interaction on confirmed case counts of COVID-19 in 120 Chinese cities. We modeled total confirmed cases of COVID-19 as the dependent variable with meteorological factors, air pollutants, and their interactions as the independent variables. To account for potential migration effects, we included the migration scale index (MSI) from Wuhan to each of the 120 cities included in the model, using data from 15 Jan. to 18 Mar. 2020. As an important confounding factor, MSI was considered in a negative binomial regression analysis. Positive associations were found between the number of confirmed cases of COVID-19 and CO, PM2.5, relative humidity, and O3, with and without MSI-adjustment. Negative associations were also found for SO2 and wind velocity both with and without controlling for population migration. In addition, air pollutants and meteorological factors had interactive effects on COVID-19 after controlling for MSI. In conclusion, air pollutants, meteorological factors, and their interactions all affect COVID-19 cases.
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Affiliation(s)
- Jianli Zhou
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Linyuan Qin
- Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University, Guilin, 541001, People's Republic of China
| | - Xiaojing Meng
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China.
| | - Nan Liu
- Department of Occupational Health and Occupational Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, People's Republic of China.
- Pinghu Hospital, Health Science Center, Shenzhen University, Shenzhen, 518116, People's Republic of China.
- Institute of Public Health, School of Nursing, Henan University, Kaifeng, 475004, People's Republic of China.
- College of Public Health, Zhengzhou University, Zhengzhou, 540001, People's Republic of China.
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7
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Lindner-Cendrowska K, Bröde P. Impact of biometeorological conditions and air pollution on influenza-like illnesses incidence in Warsaw. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2021; 65:929-944. [PMID: 33454853 PMCID: PMC8149351 DOI: 10.1007/s00484-021-02076-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 05/13/2023]
Abstract
In order to assess the influence of atmospheric conditions and particulate matter (PM) on the seasonally varying incidence of influenza-like illnesses (ILI) in the capital of Poland-Warsaw, we analysed time series of ILI reported for the about 1.75 million residents in total and for different age groups in 288 approximately weekly periods, covering 6 years 2013-2018. Using Poisson regression, we predicted ILI by the Universal Thermal Climate Index (UTCI) as biometeorological indicator, and by PM2.5 and PM10, respectively, as air quality measures accounting for lagged effects spanning up to 3 weeks. Excess ILI incidence after adjusting for seasonal and annual trends was calculated by fitting generalized additive models. ILI morbidity increased with rising PM concentrations, for both PM2.5 and PM10, and with cooler atmospheric conditions as indicated by decreasing UTCI. While the PM effect focused on the actual reporting period, the atmospheric influence exhibited a more evenly distributed lagged effect pattern over the considered 3-week period. Though ILI incidence adjusted for population size significantly declined with age, age did not significantly modify the effect sizes of both PM and UTCI. These findings contribute to better understanding environmental conditionings of influenza seasonality in a temperate climate. This will be beneficial to forecasting future dynamics of ILI and to planning clinical and public health resources under climate change scenarios.
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Affiliation(s)
- Katarzyna Lindner-Cendrowska
- Institute of Geography and Spatial Organization, Polish Academy of Sciences, Twarda 51/55, 00-818 Warsaw, Poland
| | - Peter Bröde
- Leibniz Research Centre for Working Environment and Human Factors at TU Dortmund (IfADo), Dortmund, Germany
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8
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Tan KWJ, Yung CF, Maiwald M, Saffari SE, Thoon KC, Chong CY. Respiratory viral infections in hospitalised paediatric patients in the tropics. J Paediatr Child Health 2021; 57:559-565. [PMID: 33185937 DOI: 10.1111/jpc.15267] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/05/2020] [Accepted: 10/14/2020] [Indexed: 12/18/2022]
Abstract
AIM Respiratory viruses are a huge disease burden globally. An understanding of the seasonal trends and the ability to predict peak periods of respiratory virus disease incidence is useful for clinical care. METHODS This is a retrospective analysis of paediatric hospitalizations of laboratory-confirmed viral respiratory tract infections in KK Women's and Children's Hospital, Singapore, from 1 January 2011 to 31 December 2016. Standard direct immunofluorescence was used to detect respiratory syncytial virus (RSV), influenza A and B viruses, parainfluenza 1, 2 and 3 viruses, metapneumovirus and adenovirus. RESULTS A total of 97 840 specimens were analysed with a positive detection rate of 23.8%. RSV made up the largest proportion (42% of the total positive results), predominating between May to September. Influenza A had two peaks, June to July and December to January. Type 3 was the most common parainfluenza virus and showed annually recurring peaks. In contrast, parainfluenza 1 and 2, metapneumovirus and adenovirus had a biennial pattern. The test of seasonality detected identifiable seasonality for RSV and parainfluenza 3 virus. CONCLUSIONS In conclusion, respiratory viruses have different and overlapping seasonality in tropical Singapore. Respiratory virus testing for patients admitted for acute respiratory infection is useful to target antiviral therapies and appropriate infection control practices.
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Affiliation(s)
| | - Chee Fu Yung
- Department of Infectious Disease, KK Women's and Children's Hospital, Singapore
| | - Matthias Maiwald
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore
| | - Seyed E Saffari
- Health Services and Systems Research, Duke-NUS Medical School, Singapore
| | - Koh Cheng Thoon
- Department of Infectious Disease, KK Women's and Children's Hospital, Singapore
| | - Chia Yin Chong
- Department of Infectious Disease, KK Women's and Children's Hospital, Singapore
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9
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Saadi S, Kallala O, Fodha I, Jerbi A, BenHamida-Rebai M, Ben Hadj Fredj M, Ben Hamouda H, Mathlouthi J, Khlifa M, Boussofara R, Boussetta K, Abroug S, Trabelsi A. Correlation between Children Respiratory Virus Infections and Climate Factors. J PEDIAT INF DIS-GER 2021. [DOI: 10.1055/s-0040-1722569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Objective Respiratory viruses are the most important cause of lower respiratory tract infections (LRTI) in children. Meteorological factors can influence viral outbreaks. The objective of this study was to determine the association between climate variables and respiratory virus detection.
Methods Multicenter prospective 1-year surveillance was conducted among children hospitalized for LRTI in Tunisia. Nasopharyngeal aspirates were tested by direct immunofluorescence assay (DIFA) for the detection of respiratory syncytial virus (RSV); adenovirus (AdV); influenza virus (IFV) A and B; and parainfluenza virus 1, 2, and 3 (PIV1/2/3). Samples were further analyzed by reverse-transcription polymerase chain reaction for the detection of human metapneumovirus (hMPV). Monthly meteorological data were determined by consulting the National Institute of Meteorology and the World Weather Online Meteorological Company websites. Pearson's correlation tests were used to determine the statistical association between the detection of respiratory viruses and climatic characteristics.
Results Among 572 patients, 243 (42.5%) were positive for at least one virus. The most frequently detected viruses by DIFA were RSV (30.0%), followed by IFVA (3.8%), IFVB (3.5%), PIV (0.9%), and AdV (0.9%). HMPV was detected in 13 RSV-negative samples (3.3%). Dual infections were detected in seven cases (1.2%). Monthly global respiratory viruses and RSV detections correlated significantly with temperature, rainfall, cloud cover, wind speed, wind temperature, and duration of sunshine. Monthly IFV detection significantly correlated with rainfall, wind speed, wind temperature, and duration of sunshine. HMPV detection significantly correlated with temperature and wind temperature.
Conclusion Respiratory viral outbreaks are clearly related to meteorological factors in Tunisia.
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Affiliation(s)
- Souhir Saadi
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Ouafa Kallala
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Imene Fodha
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Amira Jerbi
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Meriem BenHamida-Rebai
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
| | - Mouna Ben Hadj Fredj
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Sciences and Techniques, University of Kairouan, Kairouan, Tunisia
| | | | - Jihen Mathlouthi
- Neonatology Ward, Farhat Hached University Hospital, Sousse, Tunisia
| | - Monia Khlifa
- Pediatric Ward, Regional Hospital of Msaken, Sousse, Tunisia
| | | | | | - Saoussen Abroug
- Pediatric Ward, Sahloul University Hospital, Sousse, Tunisia
| | - Abdelhalim Trabelsi
- Research Laboratory for “Epidemiology and Immunogenetics of Viral Infections,” Sahloul University Hospital, University of Sousse, Sousse, Tunisia
- Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
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Salom I, Rodic A, Milicevic O, Zigic D, Djordjevic M, Djordjevic M. Effects of Demographic and Weather Parameters on COVID-19 Basic Reproduction Number. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.617841] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
It is hard to overstate the importance of a timely prediction of the COVID-19 pandemic progression. Yet, this is not possible without a comprehensive understanding of environmental factors that may affect the infection transmissibility. Studies addressing parameters that may influence COVID-19 progression relied on either the total numbers of detected cases and similar proxies (which are highly sensitive to the testing capacity, levels of introduced social distancing measures, etc.), and/or a small number of analyzed factors, including analysis of regions that display a narrow range of these parameters. We here apply a novel approach, exploiting widespread growth regimes in COVID-19 detected case counts. By applying nonlinear dynamics methods to the exponential regime, we extract basic reproductive number R0 (i.e., the measure of COVID-19 inherent biological transmissibility), applying to the completely naïve population in the absence of social distancing, for 118 different countries. We then use bioinformatics methods to systematically collect data on a large number of potentially interesting demographics and weather parameters for these countries (where data was available), and seek their correlations with the rate of COVID-19 spread. While some of the already reported or assumed tendencies (e.g., negative correlation of transmissibility with temperature and humidity, significant correlation with UV, generally positive correlation with pollution levels) are also confirmed by our analysis, we report a number of both novel results and those that help settle existing disputes: the absence of dependence on wind speed and air pressure, negative correlation with precipitation; significant positive correlation with society development level (human development index) irrespective of testing policies, and percent of the urban population, but absence of correlation with population density per se. We find a strong positive correlation of transmissibility on alcohol consumption, and the absence of correlation on refugee numbers, contrary to some widespread beliefs. Significant tendencies with health-related factors are reported, including a detailed analysis of the blood type group showing consistent tendencies on Rh factor, and a strong positive correlation of transmissibility with cholesterol levels. Detailed comparisons of obtained results with previous findings, and limitations of our approach, are also provided.
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11
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Saha P, Biswas M, Gupta R, Majumdar A, Mitra S, Banerjee A, Mukherjee A, Dutta S, Chawla-Sarkar M. Molecular characterization of Influenza A pandemic H1N1 viruses circulating in eastern India during 2017-19: Antigenic diversity in comparison to the vaccine strains. INFECTION GENETICS AND EVOLUTION 2020; 81:104270. [PMID: 32142936 DOI: 10.1016/j.meegid.2020.104270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/08/2020] [Accepted: 03/02/2020] [Indexed: 11/27/2022]
Abstract
In the endemic settings of India, high CFR (3.6-7.02%) was observed in the consecutive 2009, 2015 and 2017 A/H1N1pdm09 outbreaks, though in eastern India CFR varied between 0 and 5.5% during same period. Recurrent outbreaks of pandemic Influenza A/H1N1pdm09, fragmented nationwide incidence data, lack of national policy for Influenza vaccination in India underscores the necessity for generating regional level data. Thus, during 2017-19, 4106 referred samples from patients hospitalized with severe acute respiratory illness (SARI) in eastern India were tested for A/H1N1pdm09 infection. Among which 16.5% (n = 677/4106) were found A/H1N1pdm09 positive. Individuals <20 years and middle-aged persons (40-60 years) were most susceptible to A/H1N1pdm09 infection. The vaccine strain (A/human/California/07/2009) which was globally used before 2017, clustered in a different lineage away from the representative eastern Indian strains in the phylogenetic dendrogram. The vaccine strain (A/human/Michigan/45/2015) used in India during the study period and the WHO recommended strain (A/human/Brisbane/02/2018) for 2019-20 flu season for the northern hemisphere, clustered with the circulating isolates in the same lineage-6b. Dissimilarities in the amino acids encompassing the antigenic epitopes were seen to be highest with the vaccine strain- A/human/California/07/2009. The significant amino acid variations in the circulating strains with the current WHO recommended vaccine strain, implies the exigency of continuous pandemic A/H1N1pdm09 surveillance studies in this epidemiological setting. The absence of any Oseltamivir resistant mutation (H275Y) in the neuraminidase gene of the current isolates suggests continuing use of Tamiflu® as an antiviral therapy in suspected subjects in this region.
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Affiliation(s)
- Priyanka Saha
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Madhumonti Biswas
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Rudrak Gupta
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Agniva Majumdar
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Anindita Banerjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Shanta Dutta
- Regional Virus Research and Diagnostic Lab, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India.
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12
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Ahmed AT, Ghanem AS. A statistical study for impacts of environmental conditions on the rapid spread of new corona virus. INTERNATIONAL JOURNAL OF ENVIRONMENTAL SCIENCE AND TECHNOLOGY : IJEST 2020; 17:4343-4352. [PMID: 32837523 PMCID: PMC7391236 DOI: 10.1007/s13762-020-02858-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/27/2020] [Accepted: 07/16/2020] [Indexed: 05/10/2023]
Abstract
The new coronavirus, COVID-19, spread quickly and causes the death for thousands of people, and a major freeze for the economy and people activities worldwide. This study made statistical analysis for the influences of the environmental conditions such as temperature, humidity, precipitation, wind, and air pollution, which may aid in spreading this virus very fast. The study also investigated statistically the impact of people customs such as smoking, drinking wine, and eating pig meat on the number of deaths among infected people. The study depicted reasons for spreading it in some places much more than others over the world. A statistical software SPSS was adopted to find a correlation among the different variables affecting the virus spread. The results exhibited a significant relationship between the suggested conditions and the virus spread. The study introduced two regression equations for expecting infected people and deaths based on the examined conditions for any region.
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Affiliation(s)
- A. T. Ahmed
- Environmental and Civil Engineering, Faculty of Engineering, Aswan University, Aswan, Egypt
- Civil Engineering, Faculty of Engineering, Islamic University, Medina, Saudi Arabia
| | - A. S. Ghanem
- Tropical Medicine Department, Dairout Hospital, Assuit, Egypt
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Epidemiology of respiratory syncytial virus infections in Chennai, south India. CLINICAL EPIDEMIOLOGY AND GLOBAL HEALTH 2019. [DOI: 10.1016/j.cegh.2018.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Farrar DS, Awasthi S, Fadel SA, Kumar R, Sinha A, Fu SH, Wahl B, Morris SK, Jha P. Seasonal variation and etiologic inferences of childhood pneumonia and diarrhea mortality in India. eLife 2019; 8:e46202. [PMID: 31453804 PMCID: PMC6759316 DOI: 10.7554/elife.46202] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/21/2019] [Indexed: 12/16/2022] Open
Abstract
Control of pneumonia and diarrhea mortality in India requires understanding of their etiologies. We combined time series analysis of seasonality, climate region, and clinical syndromes from 243,000 verbal autopsies in the nationally representative Million Death Study. Pneumonia mortality at 1 month-14 years was greatest in January (Rate ratio (RR) 1.66, 99% CI 1.51-1.82; versus the April minimum). Higher RRs at 1-11 months suggested respiratory syncytial virus (RSV) etiology. India's humid subtropical region experienced a unique summer pneumonia mortality. Diarrhea mortality peaked in July (RR 1.66, 1.48-1.85) and January (RR 1.37, 1.23-1.48), while deaths with fever and bloody diarrhea (indicating enteroinvasive bacterial etiology) showed little seasonality. Combining mortality at ages 1-59 months with prevalence surveys, we estimate 40,600 pneumonia deaths from Streptococcus pneumoniae, 20,700 from RSV, 12,600 from influenza, and 7200 from Haemophilus influenzae type b and 24,700 diarrheal deaths from rotavirus occurred in 2015. Careful mortality studies can elucidate etiologies and inform vaccine introduction.
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Affiliation(s)
- Daniel S Farrar
- Centre for Global Health ResearchSt. Michael’s Hospital and Dalla Lana School of Public Health, University of TorontoOntarioCanada
| | - Shally Awasthi
- Department of PediatricsKing George's Medical UniversityLucknowIndia
| | - Shaza A Fadel
- Centre for Global Health ResearchSt. Michael’s Hospital and Dalla Lana School of Public Health, University of TorontoOntarioCanada
| | - Rajesh Kumar
- Department of Community Medicine, School of Public HealthPost Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Anju Sinha
- Division of Reproductive Biology, Maternal and Child HealthIndian Council of Medical ResearchNew DelhiIndia
| | - Sze Hang Fu
- Centre for Global Health ResearchSt. Michael’s Hospital and Dalla Lana School of Public Health, University of TorontoOntarioCanada
| | - Brian Wahl
- International Vaccine Access CenterJohns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Shaun K Morris
- Centre for Global Child Health, Division of Infectious DiseasesHospital for Sick Children and Dalla Lana School of Public Health, University of TorontoTorontoCanada
| | - Prabhat Jha
- Centre for Global Health ResearchSt. Michael’s Hospital and Dalla Lana School of Public Health, University of TorontoOntarioCanada
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Broor S, Parveen S, Maheshwari M. Respiratory syncytial virus infections in India: Epidemiology and need for vaccine. Indian J Med Microbiol 2019; 36:458-464. [PMID: 30880691 DOI: 10.4103/ijmm.ijmm_19_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Respiratory syncytial virus (RSV) has been identified as a leading cause of lower respiratory tract infections in young children and elderly. It is an enveloped negative-sense RNA virus belonging to Genus Orthopneumovirus. The clinical features of RSV infection range from mild upper-respiratory-tract illnesses or otitis media to severe lower-respiratory-tract illnesses. Current estimates show that about 33.1 million episodes of RSV-acute lower respiratory infection (ALRI) occurred in young children in 2015, of these majority that is, about 30 million RSV-ALRI episodes occurred in low-middle-income countries. In India, the rates of RSV detection in various hospital- and community-based studies mostly done in children vary from 5% to 54% and from 8% to 15%, respectively. Globally, RSV epidemics start in the South moving to the North. In India, RSV mainly peaks in winter in North India and some correlation with low temperature has been observed. Different genotypes of Group A (GA2, GA5, NA1 and ON1) and Group B (GB2, SAB4 and BA) have been described from India. The burden of RSV globally has kept it a high priority for vaccine development. After nearly 50 years of attempts, there is still no licensed vaccine and challenges to obtain a safe and effective vaccine is still facing the scientific community. The data in this review have been extracted from PubMed using the keywords RSV and Epidemiology and India. The data have been synthesised by the authors.
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Affiliation(s)
- Shobha Broor
- Department of Microbiology, Faculty of Medicine and Health Sciences, SGT University, Gurugram, Haryana, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Megha Maheshwari
- Department of Microbiology, Dr. Baba Saheb Ambedkar Medical College and Hospital, New Delhi, India
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Hossain MZ, Bambrick H, Wraith D, Tong S, Khan AF, Hore SK, Hu W. Sociodemographic, climatic variability and lower respiratory tract infections: a systematic literature review. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2019; 63:209-219. [PMID: 30680618 DOI: 10.1007/s00484-018-01654-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/15/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Pneumonia is the leading cause of mortality and morbidity in developing countries, particularly for children and elderly. The main objective of this review paper is to review the epidemiological evidence about the effects of sociodemographic and climatic variability on pneumonia and other lower respiratory tract infections. A detailed literature search was conducted in PubMed and Scopus following PRISMA guidelines. The articles, which considered the effect of only climatic or both climatic and sociodemographic factors on pneumonia and other lower respiratory tract infections, included in this review. A total thirty-four relevant articles were reviewed. Of 34 studies, only 14 articles (41%) examined the joint effects of sociodemographic and climate factors on pneumonia and other lower respiratory infections while most of them (59%) assessed climate factors separately. Among these fourteen, only three articles (8.8%) considered detailed sociodemographic factors. All of the reviewed articles suggested different degrees of positive or negative relationship of temperature with pneumonia or other lower respiratory tract infections. Fifteen (44%) articles suggested an association with relative humidity and 13 (38%) with rainfall. Only 3 articles (8.8%) found a relationship with wind speed. Three articles (8.8%) considered other risk factors such as particulate matter 2.5 (PM2.5) and particulate matter 10 (PM10). One study among the reviewed articles used spatial analysis methods but this study did not examine the joint effects. Among the reviewed articles, 18 (53%) articles used different time series models, one article (3%) used spatiotemporal time series model, 8 (23%) studies used other models and rest 7 (21%) studies used simple descriptive analysis. A total of 18 studies (53%) were conducted in Asia, most of them in China. There were 6 studies (17%) in Europe and 8 studies (23%) in America (South, North and Central). In Africa and Oceania, only one study was found for each region. The joint effect of climate and sociodemographic factors on pneumonia and other lower respiratory tract infections remain to be determined and further research is highly recommended for future prevention of this important and common disease.
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Affiliation(s)
- Mohammad Zahid Hossain
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Hilary Bambrick
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Darren Wraith
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Shilu Tong
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
- Shanghai Children's Medical Centre, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Public Health, Institute of Environment and Population Health, Anhui Medical University, Hefei, China
| | - Al Fazal Khan
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, 1212, Bangladesh
| | - Samar Kumar Hore
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, 1212, Bangladesh
| | - Wenbiao Hu
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.
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Ram Purakayastha D, Vishnubhatla S, Rai SK, Broor S, Krishnan A. Estimation of Burden of Influenza among under-Five Children in India: A Meta-Analysis. J Trop Pediatr 2018; 64:441-453. [PMID: 29112737 DOI: 10.1093/tropej/fmx087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND We estimated the burden of influenza-related acute respiratory tract infection (ARI) among under-fives in India through meta-analysis. METHODOLOGY We estimated pooled incidence and proportional positivity of laboratory-diagnosed influenza among under-fives using data from observational studies published from 1 January 1961 to 31 December 2016. Death due to influenza was estimated using a multiplier model. RESULTS Influenza-associated ARI incidence was estimated as 132 per 1000 child-years (115-149). The patients positive for influenza among ARI in outpatients and inpatients were estimated to be 11.2% (8.8-13.6) and 7.1% (5.5-8.8), respectively. We estimated total influenza cases during 2016 as 16 009 207 (13 942 916-18 082 769) in India. Influenza accounted for 10 913 476 (9 504 666-12 362 310) outpatient visits and 109 431 (83 882-134 980) hospitalizations. A total of 27 825 (21 382-34 408) influenza-associated under-five deaths were estimated in India in 2016. CONCLUSION Influenza imposes a substantial burden among under-fives in India. Public health approach for its prevention and control needs to be explored.
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Affiliation(s)
- Debjani Ram Purakayastha
- Centre for Community Medicine, All India Institute of Medical Sciences, AIIMS Campus, Ansari Nagar East, New Delhi, India
| | - Sreenivas Vishnubhatla
- Department of Biostatistics, All India Institute of Medical Sciences, AIIMS Campus, Ansari Nagar East, New Delhi, India
| | - Sanjay Kumar Rai
- Centre for Community Medicine, All India Institute of Medical Sciences, AIIMS Campus, Ansari Nagar East, New Delhi, India
| | - Sobha Broor
- Department of Microbiology, Faculty of Medicine and health Sciences, SGT University, Chandu-Budhera, Gurugram-Badli Road, Gurgaon, Haryana, India
| | - Anand Krishnan
- Centre for Community Medicine, All India Institute of Medical Sciences, AIIMS Campus, Ansari Nagar East, New Delhi, India
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Althouse BM, Flasche S, Minh LN, Thiem VD, Hashizume M, Ariyoshi K, Anh DD, Rodgers GL, Klugman KP, Hu H, Yoshida LM. Seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in Nha Trang, Vietnam. Int J Infect Dis 2018; 75:18-25. [PMID: 30118916 PMCID: PMC7110808 DOI: 10.1016/j.ijid.2018.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 01/21/2023] Open
Abstract
Hospitalizations for respiratory viruses are seasonal in Vietnam Respiratory syncytial virus peaks in the late summer months, and inuenza A in April to June No clear seasonality is seen for human rhinovirus Human parainuenza 3 and human rhinovirus are positively associated with dew point This work can inform the timing of inuenza and RSV vaccination and the judicious use of antibiotics in Vietnam
Background Acute respiratory infections (ARIs) are the most common causes of death in children under 5 years of age. While the etiology of most pneumonia and ARI episodes is undiagnosed, a broad range of ARI-causing viruses circulate widely in South East Asia. However, the patterns and drivers of the seasonal transmission dynamics are largely unknown. Here we identify the seasonal patterns of multiple circulating viruses associated with hospitalizations for ARIs in Nha Trang, Vietnam. Methods Hospital based enhanced surveillance of childhood ARI is ongoing at Khanh Hoa General Hospital in Nha Trang. RT-PCR was performed to detect 13 respiratory viruses in nasopharyngeal samples from enrolled patients. Seasonal patterns of childhood ARI hospital admissions of various viruses were assessed, as well as their association with rainfall, temperature, and dew point. Results Respiratory syncytial virus peaks in the late summer months, and influenza A in April to June. We find significant associations between detection of human parainfluenza 3 and human rhinovirus with the month's mean dew point. Using a cross-wavelet transform we find a significant out-of-phase relationship between human parainfluenza 3 and temperature and dew point. Conclusions Our results are important for understanding the temporal risk associated with circulating pathogens in Southern Central Vietnam. Specifically, our results can inform timing of routing seasonal influenza vaccination and for when observed respiratory illness is likely viral, leading to judicious use of antibiotics in the region.
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Affiliation(s)
- Benjamin M Althouse
- Institute for Disease Modeling, Bellevue, WA, USA; University of Washington, Seattle, WA, USA; New Mexico State University, Las Cruces, NM, USA.
| | - Stefan Flasche
- London School of Hygiene and Tropical Medicine, London, UK, USA
| | - Le Nhat Minh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Vu Dinh Thiem
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Koya Ariyoshi
- Institute of Tropical Medicine, Nagasaki University, Japan
| | - Dang Duc Anh
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | | | - Hao Hu
- Institute for Disease Modeling, Bellevue, WA, USA
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Advanced Pathology Techniques for Detecting Emerging Infectious Disease Pathogens. ADVANCED TECHNIQUES IN DIAGNOSTIC MICROBIOLOGY 2018. [PMCID: PMC7120861 DOI: 10.1007/978-3-319-95111-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/29/2022]
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20
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Smith GS, Messier KP, Crooks JL, Wade TJ, Lin CJ, Hilborn ED. Extreme precipitation and emergency room visits for influenza in Massachusetts: a case-crossover analysis. Environ Health 2017; 16:108. [PMID: 29041975 PMCID: PMC5645981 DOI: 10.1186/s12940-017-0312-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/26/2017] [Indexed: 05/28/2023]
Abstract
BACKGROUND Influenza peaks during the wintertime in temperate regions and during the annual rainy season in tropical regions - however reasons for the observed differences in disease ecology are poorly understood. We hypothesize that episodes of extreme precipitation also result in increased influenza in the Northeastern United States, but this association is not readily apparent, as no defined 'rainy season' occurs. Our objective was to evaluate the association between extreme precipitation (≥ 99th percentile) events and risk of emergency room (ER) visit for influenza in Massachusetts during 2002-2008. METHODS A case-crossover analysis of extreme precipitation events and influenza ER visits was conducted using hospital administrative data including patient town of residence, date of visit, age, sex, and associated diagnostic codes. Daily precipitation estimates were generated for each town based upon data from the National Oceanic and Atmospheric Administration. Odds ratio (OR) and 95% confidence intervals (CI) for associations between extreme precipitation and ER visits for influenza were estimated using conditional logistic regression. RESULTS Extreme precipitation events were associated with an OR = 1.23 (95%CI: 1.16, 1.30) for ER visits for influenza at lag days 0-6. There was significant effect modification by race, with the strongest association observed among Blacks (OR = 1.48 (1.30, 1.68)). CONCLUSIONS We observed a positive association between extreme precipitation events and ER visits for influenza, particularly among Blacks. Our results suggest that influenza is associated with extreme precipitation in a temperate area; this association could be a result of disease ecology, behavioral changes such as indoor crowding, or both. Extreme precipitation events are expected to increase in the Northeastern United States as climate change progresses. Additional research exploring the basis of this association can inform potential interventions for extreme weather events and influenza transmission.
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Affiliation(s)
- Genee S. Smith
- Oak Ridge Institute for Science and Education, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Kyle P. Messier
- University of North Carolina, Gillings School of Global Public Health, Chapel Hill, NC USA
| | - James L. Crooks
- National Jewish Health, Division of Biostatistics and Bioinformatics, Denver, CO USA
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO USA
| | - Timothy J. Wade
- United States Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Environmental Public Health Division, MD 58A, Research Triangle Park, Chapel Hill, NC 27711 USA
| | - Cynthia J. Lin
- Oak Ridge Institute for Science and Education, Oak Ridge National Laboratory, Oak Ridge, TN USA
- University of North Carolina, Gillings School of Global Public Health, Chapel Hill, NC USA
| | - Elizabeth D. Hilborn
- United States Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Environmental Public Health Division, MD 58A, Research Triangle Park, Chapel Hill, NC 27711 USA
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Otto CC, Kaplan SE, Stiles J, Mikhlina A, Lee C, Babady NE, Tang YW. Rapid Molecular Detection and Differentiation of Influenza Viruses A and B. J Vis Exp 2017. [PMID: 28190065 DOI: 10.3791/54312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Influenza is a contagious respiratory illness caused by influenza viruses A and B in humans and causes a significant amount of morbidity and mortality every year. The Influenza A and B assay was the first CLIA-waived molecular rapid flu test available. The Influenza A and B test works by employing isothermal amplification with influenza-specific primers followed by target detection with molecular beacon probes. Here, the performance of the Influenza A and B assay on frozen, archived nasopharyngeal swab (NPS) specimens stored in viral transport medium (VTM) were compared to a respiratory panel assay. The performance of the Influenza A and B assay was evaluated by comparing the results to the respiratory panel reference method. The sensitivity for total influenza virus A was 67.5% (95% CI (CI), 56.6-78.5) and the specificity was 86.9% (CI, 71.0-100). For influenza virus B testing, the sensitivity and specificity were 90.2% (CI, 68.5-100) and 98.8% (CI, 68.5-100), respectively. This system has the advantage of a significantly shorter test time than any other currently available molecular assay and the simple, pipette-free procedure runs on a fully integrated, closed, small-footprint system. Overall, the Influenza A and B assay evaluated in this study has the potential to serve as a point-of-care rapid influenza diagnostic test.
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Affiliation(s)
- Caitlin C Otto
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Samuel E Kaplan
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Jeffrey Stiles
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Albina Mikhlina
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Cindy Lee
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - N Esther Babady
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center
| | - Yi-Wei Tang
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center;
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Kamigaki T, Chaw L, Tan AG, Tamaki R, Alday PP, Javier JB, Olveda RM, Oshitani H, Tallo VL. Seasonality of Influenza and Respiratory Syncytial Viruses and the Effect of Climate Factors in Subtropical-Tropical Asia Using Influenza-Like Illness Surveillance Data, 2010 -2012. PLoS One 2016; 11:e0167712. [PMID: 28002419 PMCID: PMC5176282 DOI: 10.1371/journal.pone.0167712] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/18/2016] [Indexed: 12/04/2022] Open
Abstract
INTRODUCTION The seasonality of influenza and respiratory syncytial virus (RSV) is well known, and many analyses have been conducted in temperate countries; however, this is still not well understood in tropical countries. Previous studies suggest that climate factors are involved in the seasonality of these viruses. However, the extent of the effect of each climate variable is yet to be defined. MATERIALS AND METHODS We investigated the pattern of seasonality and the effect of climate variables on influenza and RSV at three sites of different latitudes: the Eastern Visayas region and Baguio City in the Philippines, and Okinawa Prefecture in Japan. Wavelet analysis and the dynamic linear regression model were applied. Climate variables used in the analysis included mean temperature, relative and specific humidity, precipitation, and number of rainy days. The Akaike Information Criterion estimated in each model was used to test the improvement of fit in comparison with the baseline model. RESULTS At all three study sites, annual seasonal peaks were observed in influenza A and RSV; peaks were unclear for influenza B. Ranges of climate variables at the two Philippine sites were narrower and mean variables were significantly different among the three sites. Whereas all climate variables except the number of rainy days improved model fit to the local trend model, their contributions were modest. Mean temperature and specific humidity were positively associated with influenza and RSV at the Philippine sites and negatively associated with influenza A in Okinawa. Precipitation also improved model fit for influenza and RSV at both Philippine sites, except for the influenza A model in the Eastern Visayas. CONCLUSIONS Annual seasonal peaks were observed for influenza A and RSV but were less clear for influenza B at all three study sites. Including additional data from subsequent more years would help to ascertain these findings. Annual amplitude and variation in climate variables are more important than their absolute values for determining their effect on the seasonality of influenza and RSV.
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Affiliation(s)
- Taro Kamigaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Liling Chaw
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Alvin G. Tan
- Department of Epidemiology and Biostatistics, Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
| | - Raita Tamaki
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Portia P. Alday
- Department of Epidemiology and Biostatistics, Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
| | - Jenaline B. Javier
- Department of Epidemiology and Biostatistics, Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
| | - Remigio M. Olveda
- Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Veronica L. Tallo
- Department of Epidemiology and Biostatistics, Research Institute for Tropical Medicine, Department of Health, Manila, Philippines
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Sundell N, Andersson LM, Brittain-Long R, Lindh M, Westin J. A four year seasonal survey of the relationship between outdoor climate and epidemiology of viral respiratory tract infections in a temperate climate. J Clin Virol 2016; 84:59-63. [PMID: 27723525 PMCID: PMC7106483 DOI: 10.1016/j.jcv.2016.10.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 09/20/2016] [Accepted: 10/04/2016] [Indexed: 01/02/2023]
Abstract
BACKGROUND The relation between weather conditions, viral transmission and seasonal activity of respiratory viruses is not fully understood. OBJECTIVES To investigate the impact of outdoor weather in a temperate climate setting on the seasonal epidemiology of viruses causing respiratory tract infections, particularly influenza A (IFA). STUDY DESIGN In total, 20,062 clinical nasopharyngeal swab samples referred for detection of respiratory pathogens using a multiplex PCR panel, between October 2010 and July 2013, were included. Results of PCR detection were compared with local meteorological data for the same period. RESULTS Low temperature and vapor pressure (VP) were associated with weekly incidence of IFA, respiratory syncytial virus, metapneumovirus, bocavirus and adenovirus but no association with relative humidity was found. The incidence of human rhinovirus and enterovirus was independent of temperature. During seasonal IFA outbreaks, the weekly drop of average temperature (compared with the week before) was strongly associated with the IFA incidence recorded the following week. CONCLUSION A sudden drop in outdoor temperature might activate the annual influenza epidemic in a temperate climate by facilitating aerosol spread in dry air. These conditions also seem to affect the incidence of other respiratory pathogens but not human rhino- or enterovirus, suggesting that routes of infection other than aerosol may be relevant for these agents.
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Affiliation(s)
- Nicklas Sundell
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Sweden.
| | - Lars-Magnus Andersson
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Sweden
| | - Robin Brittain-Long
- Department of Infectious Diseases, Aberdeen Royal Infirmary, Aberdeen, Scotland, UK
| | - Magnus Lindh
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Sweden
| | - Johan Westin
- Department of Infectious Diseases/Clinical Virology, University of Gothenburg, Sweden
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Roy S, Dahake R, Patil D, Tawde S, Mukherjee S, Athlekar S, Chowdhary A, Deshmukh R. Characterization of influenza virus among influenza like illness cases in Mumbai, India. Virusdisease 2015; 25:372-5. [PMID: 25674606 DOI: 10.1007/s13337-013-0190-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 12/26/2013] [Indexed: 12/01/2022] Open
Abstract
The present study was carried out to monitor influenza viruses by identifying the virus and studying the seasonal variation during 2007-2009 in Mumbai. A total of 193 clinical respiratory samples (nasal and throat swab) were collected from patients having influenza like illness in Mumbai region. One-step real-time reverse-transcriptase PCR (rRTPCR) was used to detect Influenza type A (H1 and H3) and Influenza type B virus. Isolation of the virus was carried out using in vitro system which was further confirmed and typed by hemagglutination assay and hemagglutination inhibition assay. Out of 193 samples 24 (12.4 3%) samples tested positive for influenza virus, of which 13 (6.73 %) were influenza type A virus and 10 (5.18 %) were influenza type B virus, while 1 sample (0.51 %) was positive for both. By culture methods, 3 (1.55 %) viral isolates were obtained. All the three isolates were found to be Influenza type B/Malaysia (Victoria lineage) by Hemagglutination Inhibition Assay. The data generated from the present study reveals that both Influenza type A and B are prevalent in Mumbai with considerable activity. The peak activity was observed during monsoon season.
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Affiliation(s)
- Soumen Roy
- Department of Virology, Haffkine Institute, Aacharya donde Marg, Parel, Mumbai, India
| | - Ritwik Dahake
- Department of Virology, Haffkine Institute, Aacharya donde Marg, Parel, Mumbai, India
| | - Deepak Patil
- Department of Virology, Haffkine Institute, Aacharya donde Marg, Parel, Mumbai, India
| | - Shweta Tawde
- Department of Virology, Haffkine Institute, Aacharya donde Marg, Parel, Mumbai, India
| | - Sandeepan Mukherjee
- Department of Virology, Haffkine Institute, Aacharya donde Marg, Parel, Mumbai, India
| | - Shrikant Athlekar
- Department of Virology, Haffkine Institute, Aacharya donde Marg, Parel, Mumbai, India
| | - Abhay Chowdhary
- Department of Virology, Haffkine Institute, Aacharya donde Marg, Parel, Mumbai, India
| | - Ranjana Deshmukh
- Department of Virology, Haffkine Institute, Aacharya donde Marg, Parel, Mumbai, India
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Abstract
The environmental drivers of influenza outbreaks are largely unknown. Despite more than 50 years of research, there are conflicting lines of evidence on the role of the environment in influenza A virus (IAV) survival, stability, and transmissibility. With the increasing and looming threat of pandemic influenza, it is important to understand these factors for early intervention and long-term control strategies. The factors that dictate the severity and spread of influenza would include the virus, natural and acquired hosts, virus-host interactions, environmental persistence, virus stability and transmissibility, and anthropogenic interventions. Virus persistence in different environments is subject to minor variations in temperature, humidity, pH, salinity, air pollution, and solar radiations. Seasonality of influenza is largely dictated by temperature and humidity, with cool-dry conditions enhancing IAV survival and transmissibility in temperate climates in high latitudes, whereas humid-rainy conditions favor outbreaks in low latitudes, as seen in tropical and subtropical zones. In mid-latitudes, semiannual outbreaks result from alternating cool-dry and humid-rainy conditions. The mechanism of virus survival in the cool-dry or humid-rainy conditions is largely determined by the presence of salts and proteins in the respiratory droplets. Social determinants of heath, including health equity, vaccine acceptance, and age-related illness, may play a role in influenza occurrence and spread.
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Affiliation(s)
- Harini Sooryanarain
- Department of Biomedical Sciences and Pathobiology, Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061;
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Evaluation of Alere i Influenza A&B for rapid detection of influenza viruses A and B. J Clin Microbiol 2014; 52:3339-44. [PMID: 24989611 DOI: 10.1128/jcm.01132-14] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rapid and accurate diagnosis of influenza is important for infection control, as well as for patient management. Alere i Influenza A&B is an isothermal nucleic acid amplification-based integrated system for detection and differentiation of influenza virus A and influenza virus B. The performance of the Alere i Influenza A&B was screened using frozen nasopharyngeal-swab specimens collected in viral transport medium (VTM) that were originally tested fresh with the FilmArray Respiratory Panel (RP) assay during the 2012-2013 influenza outbreak. In total, 360 VTM specimens were selected for Alere i Influenza A&B testing: 40 influenza virus A H1N1-2009 (influenza virus A-1), 40 influenza virus A H3N2 (influenza virus A-3), 37 influenza virus A "equivocal" or "no subtype detected" (influenza virus A-u), 41 influenza virus B, and 202 influenza virus-negative specimens, as initially determined by the FilmArray RP assay. The Alere assay showed sensitivities of 87.2%, 92.5%, 25.0%, and 97.4% for influenza virus A-1, influenza virus A-3, influenza virus A-u, and influenza virus B, respectively, after discordant resolution by Prodesse ProFLU+ PCR. The specificities were 100% for both influenza virus A and influenza virus B. In general, the Alere i Influenza A&B provided good sensitivity, although the assay did show poorer sensitivity with samples determined to have low influenza virus A titers by Prodesse ProFlu+ PCR (a mean real-time PCR threshold cycle [CT] value of 31.9 ± 2.0), which included the majority of the samples called influenza virus A "equivocal" or "no subtype detected" by a single BioFire FilmArray RP test. The integrated, rapid, and simple characteristics of the Alere i Influenza A&B assay make it a potential candidate for point-of-care testing, with a test turnaround time of less than 15 min.
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Jain B, Singh AK, Dangi T, Agarwal A, Verma AK, Dwivedi M, Singh KP, Jain A. High prevalence of human metapneumovirus subtype B in cases presenting as severe acute respiratory illness: an experience at tertiary care hospital. CLINICAL RESPIRATORY JOURNAL 2014; 8:225-33. [DOI: 10.1111/crj.12064] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 09/25/2013] [Accepted: 10/13/2013] [Indexed: 01/09/2023]
Affiliation(s)
- Bhawana Jain
- Department of Microbiology; King George Medical University; Lucknow India
| | - Ajay Kr Singh
- Department of Microbiology; King George Medical University; Lucknow India
| | - Tanushree Dangi
- Department of Microbiology; King George Medical University; Lucknow India
| | - Anjali Agarwal
- Department of Microbiology; King George Medical University; Lucknow India
| | - Anil Kumar Verma
- Department of Microbiology; King George Medical University; Lucknow India
| | - Mukesh Dwivedi
- Department of Microbiology; King George Medical University; Lucknow India
| | - Kaleshwar P. Singh
- Department of Microbiology; King George Medical University; Lucknow India
| | - Amita Jain
- Department of Microbiology; King George Medical University; Lucknow India
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Roy Mukherjee T, Chanda S, Mullick S, De P, Dey‐Sarkar M, Chawla‐Sarkar M. Spectrum of respiratory viruses circulating in eastern India: prospective surveillance among patients with influenza-like illness during 2010-2011. J Med Virol 2013; 85:1459-65. [PMID: 23765782 PMCID: PMC7166942 DOI: 10.1002/jmv.23607] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2013] [Indexed: 11/07/2022]
Abstract
In developing countries, viruses causing respiratory disease are a major concern of public health. During January 2010-December 2011, 2,737 patients with acute respiratory infection from the outpatient departments as well as patients admitted to hospitals were screened for different respiratory viruses. Nasal and or throat swabs were collected and transported to the laboratory where initial screening of influenza A and influenza B viruses was performed. The samples were tested further for influenza C virus, parainfluenza viruses 1-4, human rhinovirus, metapneumovirus and respiratory syncytial virus by conventional RT- PCR. The study revealed that the majority of the patients were under 5 years of age; both due to their higher susceptibility to respiratory infections and presentation to hospitals. Out of 2,737 patients enrolled in this study, 59% were found positive for one or more respiratory viruses. Influenza B infection was detected in 12% of patients followed by influenza A (11.7%), respiratory syncytial virus (7.1%), parainfluenza virus-2 (6%), metapneumovirus (3%), parainfluenza virus-3 (1%), parainfluenza virus-4 (0.6%), parainfluenza virus-1 (0.3%), influenza C (0.2%) and human rhinovirus (0.2%). Distinct seasonal infection was observed only for influenza A and influenza B viruses.
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Affiliation(s)
| | - Shampa Chanda
- National Institute of Cholera and Enteric DiseasesBeliaghata, KolkataIndia
| | - Satarupa Mullick
- National Institute of Cholera and Enteric DiseasesBeliaghata, KolkataIndia
| | - Papiya De
- National Institute of Cholera and Enteric DiseasesBeliaghata, KolkataIndia
| | - Malay Dey‐Sarkar
- National Institute of Cholera and Enteric DiseasesBeliaghata, KolkataIndia
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Tang JW, Loh TP. Correlations between climate factors and incidence-a contributor to RSV seasonality. Rev Med Virol 2013; 24:15-34. [DOI: 10.1002/rmv.1771] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Julian W. Tang
- Alberta Provincial Laboratory for Public Health; University of Alberta Hospital; Edmonton Canada
- Department of Medical Microbiology and Immunology; University of Alberta; Edmonton Canada
| | - Tze Ping Loh
- Department of Laboratory Medicine; National University Hospital; Singapore
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Karadag-Oncel E, Ciblak MA, Ozsurekci Y, Badur S, Ceyhan M. Viral etiology of influenza-like illnesses during the influenza season between December 2011 and April 2012. J Med Virol 2013; 86:865-71. [PMID: 24105787 PMCID: PMC7159362 DOI: 10.1002/jmv.23747] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2013] [Indexed: 01/26/2023]
Abstract
The aim of this study was to determine the frequency of respiratory viruses responsible for respiratory tract infections in Turkish children during the 2011–2012 influenza season. Nasal swabs were obtained from patients with symptoms suggestive of an influenza‐like illness between December 2011 and April 2012. Samples were analyzed with multiplex real‐time polymerase chain reaction (RT‐PCR) to help identify the causative viral pathogen. A total of 200 patients were enrolled in the study. A respiratory virus was detected successfully in 102 (51%) children; influenza A (H3N2) in 39.2%, influenza B in 23.5%, RSV in 15.6%, rhinovirus in 13.7%, bocavirus in 2.9%, coronavirus in 2.9%, and metapneumovirus in 0.9% of patients. Only one patient was co‐infected with bocavirus and influenza A virus. A statistically significant difference in the mean age of presentation was observed between the various viral pathogens (P < 0.001). Patients with RSV were significantly younger whereas children infected with the influenza viruses were significantly older. Comparison of symptoms revealed that fever and headache occurred more frequently with the influenza viruses than the other viruses combined (P < 0.001, <0.05). Durations of symptoms such as fever, cough, nasal congestion, and rhinorrhea were also significantly longer in the influenza group (P < 0.001, <0.005, <0.001, <0.005, respectively). Demographic analyses revealed that the school/daycare attendance was the only parameter associated with a significantly increased risk for influenza infection. With an overall viral pathogen detection rate of 51%, findings of the present study suggest other respiratory pathogens, whether viral or bacterial, may also lead to hospital visits due to influenza‐like illnesses in children. J. Med. Virol. 86:865–871, 2014. © 2013 Wiley Periodicals, Inc.
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Affiliation(s)
- Eda Karadag-Oncel
- Department of Pediatrics, Pediatric Infectious Disease Unit, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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Roy Mukherjee T, Mukherjee A, Mullick S, Chawla-Sarkar M. Full genome analysis and characterization of influenza C virus identified in Eastern India. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 16:419-25. [PMID: 23523822 DOI: 10.1016/j.meegid.2013.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 02/18/2013] [Accepted: 02/22/2013] [Indexed: 11/22/2022]
Abstract
In tropical countries of Asia, like India, approximately 0.5 million children of <5 years of age die annually due to acute respiratory illness (ARI). Of common respiratory pathogens, influenza viruses (A & B) are associated with annual worldwide epidemics; while the information on influenza C virus is inadequate. During January 2011 through December 2012, 2737 nasal and/or throat swabs were collected from patients reporting at outpatient department of hospitals in eastern India with ARI. Nucleotide sequencing was carried out using gene specific primers followed by pair-wise sequence alignments, multiple alignments, construction of phylogenetic tree and analysis of deduced amino acid sequences. Study reveals that, out of 2737 samples, 1616 (59.04%) were positive for one or more respiratory viruses; of which 23.72% were positive for influenza A and B viruses. From influenza A & B negative samples, influenza C virus was screened and detected with a frequency of 0.18%. Phylogenetic analysis showed that the HE, matrix, NS, PB1 and PB2 gene of the studied strain (C/Eastern-India/1202/2011) possessed a close relatedness to C/Yamagata/26/81 like strains. The P3 gene shows proximity with C/Mississipi/80 like strains whereas NP gene revealed similarity with C/Miyagi/1/93 like strains. The outcome of the whole genome analysis of the strain C/Eastern-India/1202/2011 provided useful information regarding genetic diversity of influenza C strains in India.
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Mukherjee TR, Agrawal AS, Chakrabarti S, Chawla-Sarkar M. Full genomic analysis of an influenza A (H1N2) virus identified during 2009 pandemic in Eastern India: evidence of reassortment event between co-circulating A(H1N1)pdm09 and A/Brisbane/10/2007-like H3N2 strains. Virol J 2012; 9:233. [PMID: 23057530 PMCID: PMC3576275 DOI: 10.1186/1743-422x-9-233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 09/27/2012] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND During the pandemic [Influenza A(H1N1)pdm09] period in 2009-2010, an influenza A (Inf-A) virus with H1N2 subtype (designated as A/Eastern India/N-1289/2009) was detected from a 25 years old male from Mizoram (North-eastern India). OBJECTIVE To characterize full genome of the H1N2 influenza virus. METHODS For initial detection of Influenza viruses, amplification of matrix protein (M) gene of Inf-A and B viruses was carried out by real time RT-PCR. Influenza A positive viruses are then further subtyped with HA and NA gene specific primers. Sequencing and the phylogenetic analysis was performed for the H1N2 strain to understand its origin. RESULTS The outcome of this full genome study revealed a unique reassortment event where the N-1289 virus acquired it's HA gene from a 2009 pandemic H1N1 virus with swine origin and the other genes from H3N2-like viruses of human origin. CONCLUSIONS This study provides information on possibility of occurrence of reassortment events during influenza season when infectivity is high and two different subtypes of Inf-A viruses co-circulate in same geographical location.
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Affiliation(s)
| | - Anurodh S Agrawal
- National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Sekhar Chakrabarti
- National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - Mamta Chawla-Sarkar
- National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
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Roy S, Patil D, Dahake R, Mukherjee S, Athlekar SV, Deshmukh RA, Chowdhary A. Prevalence of influenza virus among the paediatric population in Mumbai during 2007-2009. Indian J Med Microbiol 2012; 30:155-8. [PMID: 22664429 DOI: 10.4103/0255-0857.96670] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE Influenza has a major impact on public heath, annually affecting 15-20% of the global population. Information on the activity of influenza virus in Mumbai is limited. The present study was carried out to determine the prevalence of influenza viruses causing acute respiratory infections in children by molecular methods. OBJECTIVE To study the prevalence of influenza viruses among the paediatric population in Mumbai by real-time reverse-transcriptase polymerase chain reaction (rRT-PCR). MATERIALS AND METHODS From July 2007 to July 2009, 100 respiratory samples (nasal and throat swabs) were collected from paediatric patients with acute respiratory symptoms. attending out patients department, and admitted to the paediatric wards of B. J. Wadia Hospital for Children, Mumbai. The samples were collected and processed as per World Health Organization (WHO) guidelines. Viral RNA was extracted and one-step rRT-PCR was performed to detect influenza type A (H1 and H3) and influenza type B virus. RESULTS Out of 100 samples processed by rRT-PCR, a total of 11 samples (11%) were positive for influenza virus. The typing for influenza A subtypes showed 1% (1) positivity for H1 and 5% (5) positivity for H3 subtypes and 5% (5) samples tested positive for influenza type B virus. CONCLUSION It was observed that both influenza type A and B viruses were prevalent in Mumbai during the study period. Such surveillance data are important in the early detection of any antigenic variants that may be helpful in global influenza vaccine preparation and for any pandemic preparedness activity.
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Affiliation(s)
- S Roy
- Department of Virology, Haffkine Institute, Mumbai 400 012, India
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Zhu N, Li P, Yu J, Li Y, Zhao J, Xia H, Tang S, Zhang Z, Kou Z, Yin S, Fan Z, Li T. Molecular characterization of influenza B viruses isolated in east-central China in 2009-2010. Virus Genes 2012; 46:28-38. [PMID: 23011776 DOI: 10.1007/s11262-012-0826-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 09/13/2012] [Indexed: 11/24/2022]
Abstract
The current circulating influenza B viruses can be divided into two major phylogenetic lineages: the Victoria and Yamagata lineages. We conducted a survey of influenza B viruses in Hubei and Zhejiang provinces during 2009-2010. Out of 341 throat swabs, 18 influenza B viruses were isolated. Five isolates were selected for genetic and phylogenetic analysis. The molecular analyses revealed that all the isolates had similar antigenic characteristics to B/Brisbane/60/2008. However, in the three viruses isolated from Zhejiang, a single asparagine to aspartic acid substitution in position 197 was observed, thereby eliminating the glycosylation at that site and possibly causing an antigenic change. None of the viruses had amino acid mutations at positions 116, 149, 152, 198, 222, 250, 291, and 402 of the neuraminidase (NA) gene, predicting that the viruses would still be sensitive to NA inhibitors. Phylogenetic analyses revealed that all five isolates were closely related to B/Brisbane/60/2008-the 2010 vaccine strain-and contained Victoria-like hemagglutinin and Yamagata-like NA genes, suggesting that reassortment may had occurred. In addition, similar phylogenetic patterns among the acidic polymerase, nucleoprotein and matrix protein genes, as well as between the basic polymerase 1 and basic polymerase 2 genes, were observed, suggesting possible functional interactions among these proteins. All the results highlighted the importance of molecular monitoring of influenza B viruses for reassortment and antigenic drift.
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Affiliation(s)
- Na Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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Sawian CE, Lourembam SD, Banerjee A, Baruah S. Polymorphisms and expression of TLR4 and 9 in malaria in two ethnic groups of Assam, northeast India. Innate Immun 2012; 19:174-83. [DOI: 10.1177/1753425912455675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Infectious diseases have been postulated to play an important role in exerting pressure and in selection of TLR polymorphisms. Single nucelotide polymorphisms (SNPs) of TLR4 have been reported to show unique distributions in populations from Africa, Asia and Europe, and malaria is suggested to influence these patterns. In this context, we examined association of TLR polymorphisms with the risk of malaria in two ethnic groups—the Austro-Asiatics and Tibeto-Burmans—from malaria endemic districts of Assam to understand the influence of malaria in selection of TLRs in these genetically-distinct populations. TLR9 (T-1237C) mutation was positively associated with complicated ( P = 0.001) and frequent ( P = 0.035) malaria in Austro-Asiatics (relative risk = 0.595 95% CI: 0.479–0.836), but not in Tibeto-Burmans. Nonetheless, these alleles were not in Hardy-Weinberg Equilibrium in Tibeto-Burmans ( P < 0.001). In contrast, the TLR9 1486T/C genotype was favourable where it was negatively associated with complicated malaria (Fishers exact P = 0.014). Sequencing data revealed that the two populations differed in nucleotide diversity of the TLR9 promoter region. Enhanced expression of TLR4 ( P = 0.05), but not of TLR9, was associated with complicated malaria. Austro-Asiatics appeared to have accumulated favourable genotypes of TLR9, perhaps because of their longer exposure to malaria.
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Affiliation(s)
- Clara E Sawian
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | - Sonia D Lourembam
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | - Arunabha Banerjee
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | - Shashi Baruah
- Department of Molecular Biology and Biotechnology, Tezpur University, India
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Pica N, Bouvier NM. Environmental factors affecting the transmission of respiratory viruses. Curr Opin Virol 2012; 2:90-5. [PMID: 22440971 PMCID: PMC3311988 DOI: 10.1016/j.coviro.2011.12.003] [Citation(s) in RCA: 167] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 11/04/2022]
Abstract
Many viruses are capable of infecting the human respiratory tract to cause disease. These viruses display various transmission patterns among humans; however, they all share the ability to transmit from person to person, and their human transmissibility is influenced by the environment in which pathogen and host meet. This review aims to summarize recent and significant observations regarding the impact of environmental factors such as weather and climate, humidity, temperature, and airflow on the transmission of human respiratory viruses. Where possible, knowledge gaps that require further scientific study will be identified.
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Affiliation(s)
- Natalie Pica
- Department of Microbiology, Mount Sinai School of Medicine, New York, NY, USA
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Gupta S, Shamsundar R, Shet A, Chawan R, Srinivasa H. Prevalence of respiratory syncytial virus infection among hospitalized children presenting with acute lower respiratory tract infections. Indian J Pediatr 2011; 78:1495-7. [PMID: 21660398 DOI: 10.1007/s12098-011-0491-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2010] [Accepted: 05/16/2011] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To evaluate the prevalence of RSV among hospitalized young children presenting with ALRI in Bangalore, India. METHODS Respiratory syncytial virus (RSV) antigen detection was performed by direct fluorescent antibody (DFA) staining on 77 nasopharyngeal wash samples collected from hospitalized children below 2 years of age with a diagnosis of acute lower respiratory tract infection (ALRI). RESULTS Out of 77 samples tested for RSV with DFA, 17 (22.1%) were found RSV-positive with a mean age of 8.24 ± 7.21 months (M:F = 1.8:1). Three children had congenital cardiac disease and one child had a history of prematurity. One child had re-infection within one month of primary infection. RSV-infected children were more likely to have a diagnosis of bronchiolitis than RSV-negative children (p < 0.001). CONCLUSIONS RSV infection is a significant cause of morbidity among children presenting with ALRI in southern India. In resource-limited settings, DFA can be used as an important tool for rapid detection of RSV and can potentially eliminate prolonged hospitalization and unnecessary use of antibiotics.
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Affiliation(s)
- Soham Gupta
- Department of Microbiology, St. John's Medical College and Hospital, Bangalore, 560034 Karnataka, India
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Brittain-Long R, Andersson LM, Olofsson S, Lindh M, Westin J. Seasonal variations of 15 respiratory agents illustrated by the application of a multiplex polymerase chain reaction assay. ACTA ACUST UNITED AC 2011; 44:9-17. [PMID: 21867470 DOI: 10.3109/00365548.2011.598876] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Nucleic acid amplification tests are increasingly being used to diagnose viral and bacterial respiratory tract infections. The high sensitivity of these tests affects our understanding of the epidemiology of respiratory tract infections. We have assessed the detection rate of a multiplex real-time polymerase chain reaction (PCR) test, with emphasis on epidemiology and seasonal distribution of the most common respiratory tract infections. METHODS Seven thousand eight hundred and fifty-three nasopharyngeal samples from 7220 patients (age range 0-98 y, median 22 y) obtained during 36 consecutive months (November 2006-October 2009), were analyzed with a multiplex PCR panel including influenza A (IfA) and B (IfB) virus, parainfluenza virus (PIV) 1-3, respiratory syncytial virus (RSV), human rhinovirus (HRV), human coronavirus (CoV) OC43, NL63, and 229E, human metapneumovirus (HMPV), adenovirus (AdV), enterovirus (EV), and 2 bacteria--Mycoplasma pneumoniae and Chlamydophila pneumoniae. RESULTS Of the total samples, 44.5% (n = 3496) were positive for at least 1 agent, with HRV being the most common (n = 1482, 38.0%), followed by RSV (n = 526, 13.5%) and IfA (n = 403, 10.3%). The diagnostic yield was significantly higher during the winter and early spring compared to the summer (n = 2439 of 4458 samples, 54.7% and n = 1057 of 3395 samples, 31.1%, respectively; p < 0.001). CONCLUSIONS The diagnostic yield was highly dependent on the month of sampling and the age of the patient. However, the overall detection rate per month was above 30%, apart for August and September. Our findings support the use of similar tests in routine clinical care all year round. HRV was the most common finding in the respiratory tract, independent of season.
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Affiliation(s)
- Robin Brittain-Long
- Department of Infectious Diseases, Sahlgrenska University Hospital, Gothenburg, Sweden.
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Broor S, Gupta S, Mohapatra S, Kaushik S, Mir MA, Jain P, Dar L, Lal RB. Emergence of 2009A/H1N1 cases in a tertiary care hospital in New Delhi, India. Influenza Other Respir Viruses 2011; 5:e552-7. [PMID: 21816007 PMCID: PMC5780673 DOI: 10.1111/j.1750-2659.2011.00274.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Please cite this paper as: Broor et al. (2011) Emergence of 2009A/H1N1 cases in a tertiary care hospital in New Delhi, India. Influenza and Other Respiratory Viruses 5(6), e552–e557. Objective To determine virologic and epidemiologic characteristics of pandemic (H1N1) 2009 at All India Institute of Medical Sciences (AIIMS) a tertiary care hospital in New Delhi, India. Methods Nasal and throat swabs from patients with febrile acute respiratory illness (FARI) from August to December 2009 (n = 1401) were tested for 2009A/H1N1 and seasonal influenza A viruses by real‐time RT‐PCR. Results Of 1401 samples tested, 475 (33·9%) were positive for influenza A, of these majority (412; 87%) were 2009A/H1N1, whereas the remaining 63 (13%) were seasonal influenza A (49 were A/H3 and 14 were A/H1). While co‐circulation of 2009A/H1N1 and A/H3 was observed in August–September, subsequent months had exclusive pandemic influenza activity (October–December 2009). Pandemic 2009A/H1N1 emergence did not follow typical seasonal influenza seasonality in New Delhi, which normally peaks in July–August, but instead showed bimodal peaks in weeks 39 and 48 in 2009. The percent of specimens testing positive for 2009A/H1N1 influenza virus was found to be highest in >5‐ to 18‐year age group (41·2%; OR = 2·3; CI = 1·6–3·2; P = 0·00). Conclusions Taken together, our data provide high prevalence of pandemic 2009A/H1N1 in urban New Delhi with bimodal peaks in weeks 39 and 48 and highest risk group being the children of school‐going age (aged >5–18).
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Affiliation(s)
- Shobha Broor
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India.
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Olofsson S, Brittain-Long R, Andersson LM, Westin J, Lindh M. PCR for detection of respiratory viruses: seasonal variations of virus infections. Expert Rev Anti Infect Ther 2011; 9:615-26. [PMID: 21819328 PMCID: PMC7103711 DOI: 10.1586/eri.11.75] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Real-time PCR and related methods have revolutionized the laboratory diagnosis of viral respiratory infections because of their high detection sensitivity, rapidness and potential for simultaneous detection of 15 or more respiratory agents. Results from studies with this diagnostic modality have significantly expanded our knowledge about the seasonality of viral respiratory diseases, pinpointed the difficulties to make a reliable etiologic diagnosis without the aid of an unbiased multiplex molecular assay for respiratory viruses, and revealed previously unknown details as to possible infections with multiple agents as aggravating factors. The scope of this article is to review and discuss this new knowledge and its implications for diagnostic strategies and other measures essential for the clinical management of respiratory viral infections and for epidemiological surveillance of seasonal respiratory infections.
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Affiliation(s)
- Sigvard Olofsson
- Department of Clinical Virology, University of Gothenburg, Guldhedsgatan 10B, S-413 46 Gothenburg, Sweden.
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Roy T, Agrawal AS, Mukherjee A, Mishra AC, Chadha MS, Kaur H, Chawla-Sarkar M. Surveillance and molecular characterization of human influenza B viruses during 2006-2010 revealed co-circulation of Yamagata-like and Victoria-like strains in eastern India. INFECTION GENETICS AND EVOLUTION 2011; 11:1595-601. [PMID: 21708292 DOI: 10.1016/j.meegid.2011.05.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 05/25/2011] [Accepted: 05/26/2011] [Indexed: 11/27/2022]
Abstract
Acute respiratory illness (ARI) is one of the major health problems in tropical countries of Asia, like India where approximately 0.5 million children in the age group of < 5 years die annually. Previously we have reported the genetic characterization of influenza A (Inf-A) strains circulating in Kolkata, eastern India. This study was initiated to characterize the genetic diversity of the circulating influenza B (Inf-B) viruses. Of 3035 nasal/throat swabs, 494 (16.3%) samples were identified as influenza A/B positive by real time RT-PCR, of which 244 samples were confirmed having Inf-B infection. Comparison of nucleotide (nt) and amino acid (aa) sequences of HA and NA gene of Inf-B viruses revealed co-circulation of B/Yamagata and B/Victoria lineages. Of the 32 randomly selected Inf-B strains from Kolkata, seventeen strains possessed reassorted NA gene. There was a single Histidine to Asparagine substitution in the 131st position which is a part of 120 loop on HA1 region along with a deletion at position 178 in the Kolkata strains belonging to the Yamagata lineage. Amino acid substitution was observed at position 198 on NA gene in the strains B/Kol/542/2006, B/Kol/1373/2008, B/Kol/1880/2008, B/Kol/2044/2008 and in all the representative strains isolated during 2009 with respect to the circulating vaccine strains. This substitution is responsible for reduced sensitivity of neuraminidase inhibitors. The results highlight the importance of monitoring Inf-B viruses for development of antiviral resistance among circulating strains.
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Affiliation(s)
- Tapasi Roy
- National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, West Bengal, India
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Abstract
In clinical practice, a rapid and accurate identification of pathogens causing viral respiratory tract infections can be problematic because of nonspecific clinical presentations, lack of rapid and sensitive tests, and the emergence of new and mutating viral pathogens. Nucleic acid-targeted molecular techniques are increasingly being used to provide high sensitivity and specificity, short test turnaround time, and automatic and high-throughput processing. In-house and commercially available molecular methods have been developed to qualitatively and quantitatively detect and identify a single or a panel of clinically encountered respiratory tract viruses in a single reaction. Molecular techniques are being gradually introduced in routine laboratory diagnosis of viral respiratory tract infections. However, their performance characteristics and limitations must be clearly understood by both laboratory personnel and clinicians to ensure proper utilization and interpretation.
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Affiliation(s)
- Shu Zhang
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
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Agrawal AS, Roy T, Ghosh S, Chawla-Sarkar M. Genetic variability of attachment (G) and Fusion (F) protein genes of human metapneumovirus strains circulating during 2006-2009 in Kolkata, Eastern India. Virol J 2011; 8:67. [PMID: 21314961 PMCID: PMC3045894 DOI: 10.1186/1743-422x-8-67] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Accepted: 02/12/2011] [Indexed: 11/12/2022] Open
Abstract
Background Human metapneumovirus (hMPV) is associated with the acute respiratory tract infection (ARTI) in all the age groups. However, there is limited information on prevalence and genetic diversity of human metapneumovirus (hMPV) strains circulating in India. Objective To study prevalence and genomic diversity of hMPV strains among ARTI patients reporting in outpatient departments of hospitals in Kolkata, Eastern India. Methods Nasal and/or throat swabs from 2309 patients during January 2006 to December 2009, were screened for the presence of hMPV by RT-PCR of nucleocapsid (N) gene. The G and F genes of representative hMPV positive samples were sequenced. Results 118 of 2309 (5.11%) clinical samples were positive for hMPV. The majority (≈80%) of the positive cases were detected during July−November all through the study period. Genetic analysis revealed that 77% strains belong to A2 subgroup whereas rest clustered in B1 subgroup. G sequences showed higher diversity at the nucleotide and amino acid level. In contrast, less than 10% variation was observed in F gene of representative strains of all four years. Sequence analysis also revealed changes in the position of stop codon in G protein, which resulted in variable length (217-231 aa) polypeptides. Conclusion The study suggests that approximately 5% of ARTI in the region were caused by hMPV. This is the first report on the genetic variability of G and F gene of hMPV strains from India which clearly shows that the G protein of hMPV is continuously evolving. Though the study partially fulfills lacunae of information, further studies from other regions are necessary for better understanding of prevalence, epidemiology and virus evolution in Indian subcontinent.
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Affiliation(s)
- Anurodh S Agrawal
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road Scheme XM, Beliaghata, Kolkata-700010, India
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Abstract
PURPOSE OF REVIEW Data on influenza in tropical countries remain scarce compared with that in temperate countries. However, the emergence of avian influenza virus (H5N1) and the 2009 pandemic represented a major stimulus for advances in knowledge about influenza in many of these countries. This review summarizes recent data on viral and epidemiologic aspects of the condition in tropical countries. RECENT FINDINGS Avian influenza and the influenza pandemic of 2009 have contributed to pioneer production of data on influenza in the tropical settings. Preliminary data on epidemiology, genetic diversity, and antiviral resistance of influenza viruses (seasonal and pandemic) in tropical countries have been published recently. SUMMARY The seasonality of influenza is very diverse in tropical countries. Recent studies on the subject confirm the year-round activity of these viruses in many countries and the regular occurrence of epidemic outbreaks in others. The use of molecular diagnostic methods has led to prevalence rates comparable to those seen in temperate countries. Phylogenetic analysis of hemagglutinin of influenza isolates allows understanding of the evolution and divergence of avian (H5N1) and human influenza viruses (A/H1N1, A/H3N2, and B) in tropical settings. Influenza viruses resistant to oseltamivir and zanamivir have been detected in tropical countries despite the rare use of these drugs in the treatment of influenza in people living in these areas.
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Molecular characterization and comparative analysis of pandemic H1N1/2009 strains with co-circulating seasonal H1N1/2009 strains from eastern India. Arch Virol 2010; 156:207-17. [PMID: 20981560 DOI: 10.1007/s00705-010-0842-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 10/15/2010] [Indexed: 10/18/2022]
Abstract
During the peak outbreak (July-September 2009), a total 1886 patients were screened in eastern India, of which 139 (7.37%) and 52 (2.76%) were positive for pH1N1 and seasonal H1N1, respectively. Full-length HA1, NA, NS1 and PB1-F2 genes of representative strains were sequenced. Phylogenetic analysis of deduced amino acid sequences of pH1N1 strains revealed HA1 and NS1 to be of North American swine lineage, and the NA gene of Eurasian swine lineage. Consistent with previous reports, the PB1-F2 gene of pH1N1 strains was unique due to a mutation resulting in a truncated protein of 11 aa. The HA, NA and NS1 genes of H1N1/2009 strains clustered with H1N1 strains of 2000-2009, whereas a subset of strains contained a pH1N1-like truncated PB1-F2. The truncated PB1-F2 may confer the advantage of lower pathogenicity but higher replication and infectivity to the human H1N1 strains. This is the first report of seasonal H1N1/2009 strains with a pH1N1/2009-like gene segment.
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Agrawal AS, Sarkar M, Ghosh S, Roy T, Chakrabarti S, Lal R, Mishra AC, Chadha MS, Chawla-Sarkar M. Genetic characterization of circulating seasonal Influenza A viruses (2005-2009) revealed introduction of oseltamivir resistant H1N1 strains during 2009 in eastern India. INFECTION GENETICS AND EVOLUTION 2010; 10:1188-98. [PMID: 20678590 DOI: 10.1016/j.meegid.2010.07.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 07/24/2010] [Accepted: 07/26/2010] [Indexed: 11/28/2022]
Abstract
Influenza surveillance was implemented in Kolkata, eastern India in 2005 to identify the circulating subtypes and characterize their genetic diversity. Throat and nasal swabs were collected from outpatients with influenza-like illness (ILI). Of 2844 ILI cases identified at two referral hospitals during October 2005-September 2009, 309 (10.86%) were positive for Influenza A by real time RT-PCR, of which 110 (35.60%) were subtyped as H1N1 and 199 (64.40%) as H3N2. Comparison of the nucleotide (nt) and amino acid (aa) sequences of the HA1 gene for H1N1 and H3N2 strains showed that a subset of strains precede WHO recommended contemporary strains by 1-2 years. The Kolkata H1N1 strains clustered in Clade II, subgroup 2B with A/Brisbane/59/2007 but were distant from the corresponding vaccine strains (New Caledonia/20/99 and A/Solomon Island/3/06). The 2005-06 and 2007 H3N2 strains (15/17) clustered either A/Brisbane/10/2007-like (n=8) or A/Nepal/921/2006 like (n=7) strains, whereas 2008 strains (8/12) and 2009 strains (4/4) were similar to the 2010-11 vaccine strain A/Perth/16/2009. More aa substitutions were found in HA or NA genes of H3N2 than in H1N1 strains. No mutation conferring neuraminidase resistance was observed in any of the strain during 2005-08, however in 2009, drug resistant marker (H275Y) was present in seasonal H1N1, but not in co-circulating H3N2 strains. This is the first report of genetic characterization of circulating Influenza A strains from India. The results also highlight the importance of continuing Influenza surveillance in developing countries of Asia for monitoring unusual strains with pandemic potential and mutations conferring antiviral resistance.
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Affiliation(s)
- Anurodh S Agrawal
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme XM, Beliaghata, Kolkata, West Bengal, India
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