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Park K, Sung H, Kim MN. Evaluation of the cobas Liat detection test for SARS-CoV-2 and influenza viruses following the emergence of the SARS-CoV-2 Omicron variant. Diagn Microbiol Infect Dis 2023; 105:115891. [PMID: 36738537 PMCID: PMC9810546 DOI: 10.1016/j.diagmicrobio.2023.115891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/24/2022] [Accepted: 01/01/2023] [Indexed: 01/05/2023]
Abstract
OBJECTIVES This study assessed the clinical performance of the cobas Liat SARS‑CoV‑2 & Influenza A/B assay (LiatCOVID/flu) for the detection of both severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses during the SARS-CoV-2 Omicron outbreak. METHODS Residual nasopharyngeal swab samples (NPS) previously tested with cobas SARS-CoV-2 & Influenza A/B for SARS-CoV-2 and with the Allplex Respiratory Panel 1 for influenza viruses were collected. All samples were submitted to the LiatCOVID/flu assay. RESULTS A total of 1147 samples were collected comprising 167 SARS-CoV-2-positive, 556 SARS-CoV-2-negative, 224 influenza-positive, and 200 influenza-negative cases. The positive percent agreement (PPA)/negative percent agreement (NPA) of LiatCOVID/flu for SARS-CoV-2 and influenza viruses compared to the previously tested methods were 100% of 100% and 99.6% of 100%, respectively. CONCLUSIONS The LiatCOVID/flu assay shows an acceptable performance in the detection of SARS-CoV-2 and influenza viruses using NPS samples.
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Affiliation(s)
- Kuenyoul Park
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea; Department of Laboratory Medicine, Sanggye Paik Hospital, Inje University College of Medicine, Seoul, Republic of Korea
| | - Heungsup Sung
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea.
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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2
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Dai Y, Zhong J, Lan Y. Virus-virus interactions of febrile respiratory syndrome among patients in China based on surveillance data from February 2011 to December 2020. J Med Virol 2022; 94:4369-4377. [PMID: 35514049 DOI: 10.1002/jmv.27833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/17/2022] [Accepted: 05/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND The burden of acute respiratory infections is still considerable, and virus-virus interactions may affect their epidemics, but previous evidence is inconclusive. OBJECTIVE To quantitatively investigate the interactions among respiratory viruses at both the population and individual levels. METHODS Cases tested for influenza virus (IV), respiratory syncytial virus (RSV), human parainfluenza virus (PIV), human Adenovirus (AdV), human coronavirus (CoV), human bocavirus (BoV) and rhinoviruses (RV) were collected from the pathogen surveillance for febrile respiratory syndrome (FRS) in China from February 2011 to December 2020. We used spearman's rank correlation coefficients and binary logistic regression models to analyze the interactions between any two of the viruses at the population and individual levels, respectively. RESULTS Among 120,237 cases, 4.5% were co-infected with two or more viruses. Correlation coefficients showed 7 virus pairs were positively correlated, namely: IV and RSV, PIV and AdV, PIV and CoV, PIV and BoV, PIV and RV, AdV and BoV, CoV and RV. Regression models showed except for the negative interaction between IV and RV (OR=0.70, 95%CI: 0.61-0.81), all other virus pairs had positive interactions. CONCLUSION Most of the respiratory viruses interact positively, while IV and RV interact negatively. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yucen Dai
- Department of Epidemiology and Health Statistics, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Jiao Zhong
- Department of Occupational and Environmental Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041.,Department of Osteoporosis, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China, 610041
| | - Yajia Lan
- Department of Occupational and Environmental Medicine, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China, 610041
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3
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Pinky L, Dobrovolny HM. Epidemiological Consequences of Viral Interference: A Mathematical Modeling Study of Two Interacting Viruses. Front Microbiol 2022; 13:830423. [PMID: 35369460 PMCID: PMC8966706 DOI: 10.3389/fmicb.2022.830423] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/14/2022] [Indexed: 12/21/2022] Open
Abstract
Some viruses have the ability to block or suppress growth of other viruses when simultaneously present in the same host. This type of viral interference or viral block has been suggested as a potential interaction between some respiratory viruses including SARS-CoV-2 and other co-circulating respiratory viruses. We explore how one virus' ability to block infection with another within a single host affects spread of the viruses within a susceptible population using a compartmental epidemiological model. We find that population-level effect of viral block is a decrease in the number of people infected with the suppressed virus. This effect is most pronounced when the viruses have similar epidemiological parameters. We use the model to simulate co-circulating epidemics of SARS-CoV-2 and influenza, respiratory syncytial virus (RSV), and rhinovirus, finding that co-circulation of SARS-CoV-2 and RSV causes the most suppression of SARS-CoV-2. Paradoxically, co-circulation of SARS-CoV-2 and influenza or rhinovirus results in almost no change in the SARS-CoV-2 epidemic, but causes a shift in the timing of the influenza and rhinovirus epidemics.
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Affiliation(s)
- Lubna Pinky
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Hana M. Dobrovolny
- Department of Physics & Astronomy, Texas Christian University, Fort Worth, TX, United States
- *Correspondence: Hana M. Dobrovolny
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Rai R, Tamang JP. In vitro and genetic screening of probiotic properties of lactic acid bacteria isolated from naturally fermented cow-milk and yak-milk products of Sikkim, India. World J Microbiol Biotechnol 2022; 38:25. [PMID: 34989904 DOI: 10.1007/s11274-021-03215-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022]
Abstract
A total of 272 isolates of lactic acid bacteria (LAB) were isolated from 22 samples of naturally fermented milk products of Sikkim in India viz. dahi, soft-variety chhurpi, hard-variety chhurpi, mohi and philu, out of which, 68 LAB isolates were randomly grouped on the basis of phenotypic characteristics, and were identified by 16S rRNA gene sequence analysis. Leuconostoc mesenteroides was the most dominant genus, followed by Leuc. mesenteroides subsp. jonggajibkimchii, Lactococcus lactis subsp. cremoris, Lc. lactis, Lc. lactis subsp. hordniae, Lc. lactis subsp. tructae, Enterococcus faecalis, E. italicus and E. pseudoavium. LAB strains were tested for probiotics attributes by in vitro and genetic screening, based on marker genes. LAB strains showed tolerance to pH 3.0, bile salt, resistance to lysozyme and β-galactosidase activity. Enterococcus faecalis YS4-11 and YS4-14 and Lactococcus lactis subsp. cremoris SC3 showed more than 85% of hydrophobicity. Genes clp L and tdc encoding for low pH tolerance, agu A and Ir1516 encoding for bile tolerance, LBA1446 gene encoding for BSH activity, map A, apf, mub 1 and msa encoding for mucosal binding property were detected. Gene mesY for bacteriocin production was detected only in Leuconostoc spp. Based on the in vitro and genetic screening of probiotic attributes, Leuc. mesenteroides; Leuc. mesenteroides subsp. jonggajibkimchii and Lc. lactis subsp. cremoris were tentatively selected for possible probiotic candidates.
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Affiliation(s)
- Ranjita Rai
- Department of Microbiology, School of Life Sciences, DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Sikkim University, Gangtok, 737102, Sikkim, India
| | - Jyoti Prakash Tamang
- Department of Microbiology, School of Life Sciences, DAICENTER (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Sikkim University, Gangtok, 737102, Sikkim, India.
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Yakovlev AS, Belyaletdinova IK, Mazankova LN, Samitova ER, Osmanov IM, Gavelya NV, Volok VP, Kolpakova ES, Shishova AA, Dracheva NA, Kozlovskaya LI, Karganova GG, Ishmukhametov AA. SARS-CoV-2 infection in children in Moscow in 2020: clinical features and impact on circulation of other respiratory viruses: SARS-CoV-2 infection in children in Moscow in 2020. Int J Infect Dis 2022; 116:331-338. [PMID: 34986407 PMCID: PMC8720385 DOI: 10.1016/j.ijid.2021.12.358] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Objectives This study aimed to estimate the impact of the COVID-19 pandemic on the circulation of non-SARS-CoV-2 respiratory viruses and the clinical characteristics of COVID-19 in hospitalized children. Methods A total of 226 and 864 children admitted to the Children's City Clinical Hospital with acute respiratory infection in September to November of 2018 and 2020 in Moscow were tested for respiratory viruses using multiplex polymerase chain reaction (PCR) and Mycoplasma pneumoniae/Chlamydia pneumoniae using enzyme-linked immunosorbent assay. Results The detection rate of non-SARS-CoV-2 viruses in 2020 was lower than in 2018, 16.9% versus 37.6%. An increase in the median age of children with respiratory viruses was observed during the pandemic (3 years vs 1 year). There was no significant difference in the frequency of intensive care unit (ICU) admission in children with SARS-CoV-2 and other respiratory virus infections (2.7% vs 2.9%). SARS-CoV-2 and human rhinoviruses, human metapneumoviruses, and human adenoviruses showed significantly lower than expected co-detection rates during co-circulation. An increase in body mass index (BMI) or bacterial coinfection leads to an increased risk of ICU admission and a longer duration of COVID-19 in children. Conclusions The COVID-19 pandemic led to significant changes in the epidemiological characteristics of non-SARS-CoV-2 respiratory viruses during the autumn peak of the 2020 pandemic, compared with the same period in 2018.
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Affiliation(s)
- Alexander S Yakovlev
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
| | - Ilmira K Belyaletdinova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia.
| | - Lyudmila N Mazankova
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russian Federation, Moscow, 125993, Russia; Z.A. Bashlyaeva Children's Municipal Clinical Hospital, Moscow, 125373, Russia.
| | - Elmira R Samitova
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russian Federation, Moscow, 125993, Russia; Z.A. Bashlyaeva Children's Municipal Clinical Hospital, Moscow, 125373, Russia.
| | - Ismail M Osmanov
- Z.A. Bashlyaeva Children's Municipal Clinical Hospital, Moscow, 125373, Russia.
| | - Nataly V Gavelya
- Z.A. Bashlyaeva Children's Municipal Clinical Hospital, Moscow, 125373, Russia
| | - Viktor P Volok
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia; Department of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Ekaterina S Kolpakova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia.
| | - Anna A Shishova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia.
| | - Natalia A Dracheva
- Russian Medical Academy of Continuous Professional Education of the Ministry of Healthcare of the Russian Federation, Moscow, 125993, Russia
| | - Liubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia.
| | - Galina G Karganova
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia; Department of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia.
| | - Aydar A Ishmukhametov
- Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of Russian Academy of Sciences, Moscow 108819, Russia; Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia.
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Lee YM, Kim T, Park KH, Choi SH, Kwak YG, Choo EJ, Chung JW, Lee MS. Dual respiratory virus detection in adult patients with acute respiratory illness. BMC Infect Dis 2021; 21:997. [PMID: 34556046 PMCID: PMC8460188 DOI: 10.1186/s12879-021-06699-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 09/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nonrandom multiple respiratory virus (RV) detection provides evidence for viral interference among respiratory viruses. However, little is known as to whether it occurs randomly. METHODS The prevalence of dual RV detection (DRVD) in patients with acute respiratory illnesses (ARIs) at 4 academic medical centers was investigated; data about the prevalence of 8 RVs were collected from the Korean national RV surveillance dataset. Linear regression analysis was performed to assess the correlation between observed and estimated prevalence of each type of DRVD. RESULTS In total, 108 patients with ARIs showing DRVD were included in this study between 2011 and 2017. In several types of regression analysis, a strong correlation was observed between the observed and estimated prevalence of each type of DRVD. Excluding three DRVD types (influenza/picornavirus, influenza/human metapneumovirus, and adenovirus/respiratory syncytial virus), the slope of the regression line was higher than that of the line of random occurrence (1.231 > 1.000) and the 95% confidence interval of the regression line was located above the line of random occurrence. CONCLUSIONS Contrary to the results of previous epidemiologic studies, most types of DRVD occur more frequently than expected from the prevalence rates of individual RV, except for three underrepresented pairs above.
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Affiliation(s)
- Yu-Mi Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Tark Kim
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Ki-Ho Park
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
| | - Seong-Ho Choi
- Division of Infectious Diseases, Department of Internal Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102 Heukseok-ro, Dongjak-gu, Seoul, 06973, Republic of Korea.
| | - Yee Gyung Kwak
- Division of Infectious Diseases, Department of Internal Medicine, Inje University Ilsan Paik Hospital, Goyang, Republic of Korea
| | - Eun Ju Choo
- Division of Infectious Diseases, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Jin-Won Chung
- Division of Infectious Diseases, Department of Internal Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, 102 Heukseok-ro, Dongjak-gu, Seoul, 06973, Republic of Korea
| | - Mi Suk Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul, Republic of Korea
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Waterlow NR, Flasche S, Minter A, Eggo RM. Competition between RSV and influenza: Limits of modelling inference from surveillance data. Epidemics 2021; 35:100460. [PMID: 33838587 PMCID: PMC8193815 DOI: 10.1016/j.epidem.2021.100460] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2021] [Accepted: 03/24/2021] [Indexed: 10/28/2022] Open
Abstract
Respiratory Syncytial Virus (RSV) and Influenza cause a large burden of disease. Evidence of their interaction via temporary cross-protection implies that prevention of one could inadvertently lead to an increase in the burden of the other. However, evidence for the public health impact of such interaction is sparse and largely derives from ecological analyses of peak shifts in surveillance data. To test the robustness of estimates of interaction parameters between RSV and Influenza from surveillance data we conducted a simulation and back-inference study. We developed a two-pathogen interaction model, parameterised to simulate RSV and Influenza epidemiology in the UK. Using the infection model in combination with a surveillance-like stochastic observation process we generated a range of possible RSV and Influenza trajectories and then used Markov Chain Monte Carlo (MCMC) methods to back-infer parameters including those describing competition. We find that in most scenarios both the strength and duration of RSV and Influenza interaction could be estimated from the simulated surveillance data reasonably well. However, the robustness of inference declined towards the extremes of the plausible parameter ranges, with misleading results. It was for instance not possible to tell the difference between low/moderate interaction and no interaction. In conclusion, our results illustrate that in a plausible parameter range, the strength of RSV and Influenza interaction can be estimated from a single season of high-quality surveillance data but also highlights the importance to test parameter identifiability a priori in such situations.
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Affiliation(s)
- Naomi R Waterlow
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, UK.
| | - Stefan Flasche
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, UK
| | - Amanda Minter
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, UK
| | - Rosalind M Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, UK
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Probiotic properties of lactic acid bacteria isolated from traditionally prepared dry starters of the Eastern Himalayas. World J Microbiol Biotechnol 2021; 37:7. [PMID: 33392833 DOI: 10.1007/s11274-020-02975-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022]
Abstract
The Himalayan people prepare dry and oval to round-shaped starter cultures to ferment cereals into mild-alcoholic beverages, which contain lactic acid bacteria (LAB) as one of the essential microbiota. There is no report on probiotic characters of LAB isolated from dry starters. Hence, we screened the probiotic and some functional properties of 37 LAB strains isolated from dry starters of the Eastern Himalayas viz. marcha, phab, paa, pee and phut. About 38% of the LAB strains showed high survival rate (> 50%) at pH 3 and 0.3% bile salts. Enterococcus durans BPB21 and SMB7 showed the highest hydrophobicity percentage of 98%. E. durans DMB4 and SMB7 showed maximum cholesterol assimilation activity. About 65% of the LAB strains showed the ability to produce β galactosidase. Majority of the strains showed phytase activity, whereas none of the strain showed amylase activity. About 86% of LAB strains showed an optimum tolerance of 10% ethanol concentration. Genetic screening of some probiotic and functional marker genes have also been analysed. The occurrence of clp L gene, agu A gene (survival of gastrointestinal tract conditions), apf, mub1 and map A gene (adhesion genes) was higher compared to other genes. The occurrence of bsh gene (bile salt tolerance) was detected in Pediococcus pentosaceus SMB13-1 and Enterococcus faecium BPB11. Gene ped B for pediocin with amplicon size of 375 bp was detected in E. durans DMB13 and Pediococcus acidilactici AKB3. Detection of nutritional marker gene rib A and fol P in some strains showed the potential ability to synthesize riboflavin and folic acid. LAB with probiotic and functional properties may be explored for food industry in future.
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Vanderburg S, Wijayaratne G, Danthanarayana N, Jayamaha J, Piyasiri B, Halloluwa C, Sheng T, Amarasena S, Kurukulasooriya R, Nicholson BP, Peiris JSM, Gray GC, Gunasena S, Nagahawatte A, Bodinayake CK, Woods CW, Devasiri V, Tillekeratne LG. Outbreak of severe acute respiratory infection in Southern Province, Sri Lanka in 2018: a cross-sectional study. BMJ Open 2020; 10:e040612. [PMID: 33158834 PMCID: PMC7651749 DOI: 10.1136/bmjopen-2020-040612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVES To determine aetiology of illness among children and adults presenting during outbreak of severe respiratory illness in Southern Province, Sri Lanka, in 2018. DESIGN Prospective, cross-sectional study. SETTING 1600-bed, public, tertiary care hospital in Southern Province, Sri Lanka. PARTICIPANTS 410 consecutive patients, including 371 children and 39 adults, who were admitted with suspected viral pneumonia (passive surveillance) or who met case definition for acute respiratory illness (active surveillance) in May to June 2018. RESULTS We found that cocirculation of influenza A (22.6% of cases), respiratory syncytial virus (27.8%) and adenovirus (AdV) (30.7%; type B3) was responsible for the outbreak. Mortality was noted in 4.5% of paediatric cases identified during active surveillance. Virus type and viral coinfection were not significantly associated with mortality. CONCLUSIONS This is the first report of intense cocirculation of multiple respiratory viruses as a cause of an outbreak of severe acute respiratory illness in Sri Lanka, and the first time that AdV has been documented as a cause of a respiratory outbreak in the country. Our results emphasise the need for continued vigilance in surveying for known and emerging respiratory viruses in the tropics.
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Affiliation(s)
- Sky Vanderburg
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Medicine, University of California San Francisco School of Medicine, San Francisco, California, USA
| | | | | | - Jude Jayamaha
- Medical Research Institute Sri Lanka, Colombo, Sri Lanka
| | | | | | - Tianchen Sheng
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
| | | | | | | | | | - Gregory C Gray
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
| | | | - Ajith Nagahawatte
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Duke Global Health Institute, Durham, North Carolina, USA
| | - Champica K Bodinayake
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Duke Global Health Institute, Durham, North Carolina, USA
| | - Christopher W Woods
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Duke Global Health Institute, Durham, North Carolina, USA
| | | | - L Gayani Tillekeratne
- Medicine, Duke University School of Medicine, Durham, North Carolina, USA
- Faculty of Medicine, University of Ruhuna, Galle, Sri Lanka
- Duke Global Health Institute, Durham, North Carolina, USA
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Dynamics and predisposition of respiratory viral co-infections in children and adults. Clin Microbiol Infect 2020; 27:631.e1-631.e6. [PMID: 32540470 DOI: 10.1016/j.cmi.2020.05.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/26/2020] [Accepted: 05/30/2020] [Indexed: 01/06/2023]
Abstract
OBJECTIVES The epidemiology of respiratory co-infection pairings is poorly understood. Here we assess the dynamics of respiratory viral co-infections in children and adults and determine predisposition for or against specific viral pairings. METHODS Over five respiratory seasons from 30 November 2013 through 6 June 2018, the mono-infection and co-infection prevalence of 13 viral pathogens was tabulated at The Cleveland Clinic. Employing a model to proportionally distribute viral pairs using individual virus co-infection rate with prevalence patterns of concurrent co-circulating viruses, we compared predicted occurrence with observed occurrence of 132 viral pairing permutations using binomial analysis. RESULTS Of 30 535 respiratory samples, 9843 (32.2%) were positive for at least one virus and 1018 (10.8%) of these were co-infected. Co-infected samples predominantly originated from children. Co-infection rate in paediatric population was 35.0% (2068/5906), compared with only 5.8% (270/4591) in adults. Adenovirus C (ADVC) had the highest co-infection rate (426/623, 68.3%) while influenza virus B had the lowest (55/546, 10.0%). ADVC-rhinovirus (HRV), respiratory syncytial virus A (RSVA)-HRV and RSVB-HRV pairings occurred at significantly higher frequencies than predicted by the proportional distribution model (p < 0.05). Additionally, several viral pairings had fewer co-infections than predicted by our model: notably metapneumovirus (hMPV)-parainfluenza virus 3, hMPV-RSVA and RSVA-RSVB. CONCLUSIONS This is one of the largest studies on respiratory viral co-infections in children and adults. Co-infections are substantially more common in children, especially under 5 years of age, and the most frequent pairings occurred at a higher frequency than would be expected by random. Specific pairings occur at altered rates compared with those predicted by proportional distribution, suggesting either direct or indirect interactions result between specific viral pathogens.
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ASTHMA EXACERBATIONS IN REUNION ISLAND: ENVIRONMENTAL FACTORS. Respir Med Res 2020; 81:100779. [DOI: 10.1016/j.resmer.2020.100779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 11/17/2022]
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12
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Mair C, Nickbakhsh S, Reeve R, McMenamin J, Reynolds A, Gunson RN, Murcia PR, Matthews L. Estimation of temporal covariances in pathogen dynamics using Bayesian multivariate autoregressive models. PLoS Comput Biol 2019; 15:e1007492. [PMID: 31834896 PMCID: PMC6934324 DOI: 10.1371/journal.pcbi.1007492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 12/27/2019] [Accepted: 10/16/2019] [Indexed: 11/22/2022] Open
Abstract
It is well recognised that animal and plant pathogens form complex ecological communities of interacting organisms within their hosts, and there is growing interest in the health implications of such pathogen interactions. Although community ecology approaches have been used to identify pathogen interactions at the within-host scale, methodologies enabling robust identification of interactions from population-scale data such as that available from health authorities are lacking. To address this gap, we developed a statistical framework that jointly identifies interactions between multiple viruses from contemporaneous non-stationary infection time series. Our conceptual approach is derived from a Bayesian multivariate disease mapping framework. Importantly, our approach captures within- and between-year dependencies in infection risk while controlling for confounding factors such as seasonality, demographics and infection frequencies, allowing genuine pathogen interactions to be distinguished from simple correlations. We validated our framework using a broad range of synthetic data. We then applied it to diagnostic data available for five respiratory viruses co-circulating in a major urban population between 2005 and 2013: adenovirus, human coronavirus, human metapneumovirus, influenza B virus and respiratory syncytial virus. We found positive and negative covariances indicative of epidemiological interactions among specific virus pairs. This statistical framework enables a community ecology perspective to be applied to infectious disease epidemiology with important utility for public health planning and preparedness. Disease-causing microorganisms, including viruses, bacteria, protozoa and fungi, form complex communities within animals and plants. These microorganisms can coexist harmoniously or even beneficially, or they may competitively interact for host resources. Well-studied examples include interactions between viruses and bacteria in the respiratory tract. Whilst ecological studies have revealed that some pathogens do interact within their hosts, identifying interactions from available population scale data from health authorities is challenging. This is exacerbated by a lack of large-scale data describing the infection patterns of multiple pathogens within single populations over long time frames. Furthermore, methods for evaluating whether infection frequencies of different pathogens fluctuate together or not over time cannot readily account for alternative explanations. For example, human pathogens may have related seasonal patterns depending on the age groups they infect and the weather conditions they survive in, and not because they are interacting. We developed a robust statistical framework to identify pathogen-pathogen interactions from population scale diagnostic data. This framework serves as a crucial step in identifying such important interactions and will guide new studies to elucidate their underpinning mechanisms. This will have important consequences for public health preparedness and the design of effective disease control interventions.
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Affiliation(s)
- Colette Mair
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Mathematics and Statistics, College of Science and Engineering, University of Glasgow, Glasgow, United Kingdom
- * E-mail:
| | - Sema Nickbakhsh
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jim McMenamin
- Health Protection Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Arlene Reynolds
- Health Protection Scotland, NHS National Services Scotland, Glasgow, United Kingdom
| | - Rory N. Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow and Clyde, Glasgow, United Kingdom
| | - Pablo R. Murcia
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Louise Matthews
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Price OH, Sullivan SG, Sutterby C, Druce J, Carville KS. Using routine testing data to understand circulation patterns of influenza A, respiratory syncytial virus and other respiratory viruses in Victoria, Australia. Epidemiol Infect 2019; 147:e221. [PMID: 31364539 PMCID: PMC6625191 DOI: 10.1017/s0950268819001055] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/18/2019] [Accepted: 03/27/2019] [Indexed: 12/29/2022] Open
Abstract
Several studies have reported evidence of interference between respiratory viruses: respiratory viruses rarely reach their epidemic peak concurrently and there appears to be a negative association between infection with one respiratory virus and co-infection with another. We used results spanning 16 years (2002-2017) of a routine diagnostic multiplex panel that tests for nine respiratory viruses to further investigate these interactions in Victoria, Australia. Time series analyses were used to plot the proportion positive for each virus. The seasonality of all viruses included was compared with respiratory syncytial virus (RSV) and influenza A virus using cross-correlations. Logistic regression was used to explore the likelihood of co-infection with one virus given infection with another. Seasonal peaks were observed each year for influenza A and RSV and less frequently for influenza B, coronavirus and parainfluenza virus. RSV circulated an average of 6 weeks before influenza A. Co-infection with another respiratory virus was less common with picornavirus, RSV or influenza A infection. Our findings provide further evidence of a temporal relationship in the circulation of respiratory viruses. A greater understanding of the interaction between respiratory viruses may enable better prediction of the timing and magnitude of respiratory virus epidemics.
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Affiliation(s)
- O. H. Price
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
| | - S. G. Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - C. Sutterby
- School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - J. Druce
- Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
| | - K. S. Carville
- Victorian Infectious Diseases Reference Laboratory, at the Peter Doherty Institute for Infection and Immunity, Victoria 3000, Australia
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Pisareva MM, Eder VA, Buzitskaya ZV, Musaeva TD, Afanaseva VS, Go AA, Obraztsova EA, Sukhovetskaya VF, Komissarov AB. [Etiological structure of influenza and other ARVI in St. Petersburg during epidemic seasons 2012-2016.]. Vopr Virusol 2018; 63:233-239. [PMID: 30550100 DOI: 10.18821/0507-4088-2018-63-5-233-239] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/06/2018] [Indexed: 11/17/2022]
Abstract
The etiological structure of influenza and other acute respiratory viral infections including their rate of incidence in St. Petersburg and Leningrad region during 4 epidemic seasons has been studied. Seasonality of some respiratory viruses was shown and peaks of circulation of RSV, adenovirus, parainfluenza viruses, rhinovirus, bocavirus, metapneumovirus and coronavirus were marked. The interference of influenza A viruses and RSV, RSV and rhinoviruses was highlighted. A high incidence of adenovirus infection in organized communities and RSV infection in children was revealed.
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Affiliation(s)
- M M Pisareva
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
| | - V A Eder
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
| | - Zh V Buzitskaya
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
| | - T D Musaeva
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
| | - V S Afanaseva
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
| | - A A Go
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
| | - E A Obraztsova
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
| | - V F Sukhovetskaya
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
| | - A B Komissarov
- Federal State Research Institute of Influenza, St. Petersburg, 197376, Russian Federation
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15
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Furuya-Kanamori L, Yakob L. Heterogeneous and Dynamic Prevalence of Asymptomatic Influenza Virus Infections. Emerg Infect Dis 2018; 24:951. [PMID: 29664719 PMCID: PMC5938779 DOI: 10.3201/eid2405.180075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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16
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Attenuation of Influenza A Virus Disease Severity by Viral Coinfection in a Mouse Model. J Virol 2018; 92:JVI.00881-18. [PMID: 30232180 DOI: 10.1128/jvi.00881-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
Influenza viruses and rhinoviruses are responsible for a large number of acute respiratory viral infections in human populations and are detected as copathogens within hosts. Clinical and epidemiological studies suggest that coinfection by rhinovirus and influenza virus may reduce disease severity and that they may also interfere with each other's spread within a host population. To determine how coinfection by these two unrelated respiratory viruses affects pathogenesis, we established a mouse model using a minor serogroup rhinovirus (rhinovirus strain 1B [RV1B]) and mouse-adapted influenza A virus (A/Puerto Rico/8/1934 [PR8]). Infection of mice with RV1B 2 days before PR8 reduced the severity of infection by a low or medium, but not high, dose of PR8. Disease attenuation was associated with an early inflammatory response in the lungs and enhanced clearance of PR8. However, coinfection by RV1B did not reduce PR8 viral loads early in infection or inhibit replication of PR8 within respiratory epithelia or in vitro Inflammation in coinfected mice remained focal compared to diffuse inflammation and damage in the lungs of mice infected by PR8. The timing of RV1B coinfection was a critical determinant of protection, suggesting that sufficient time is needed to induce this response. Finally, disease attenuation was not unique to RV1B: dose-dependent coinfection by a murine coronavirus (mouse hepatitis virus strain 1 [MHV-1]) also reduced the severity of PR8 infection. Unlike RV1B, coinfection with MHV-1 reduced early PR8 replication, which was associated with upregulation of beta interferon (IFN-β) expression. This model is critical for understanding the mechanisms responsible for influenza disease attenuation during coinfection by unrelated respiratory viruses.IMPORTANCE Viral infections in the respiratory tract can cause severe disease and are responsible for a majority of pediatric hospitalizations. Molecular diagnostics have revealed that approximately 20% of these patients are infected by more than one unrelated viral pathogen. To understand how viral coinfection affects disease severity, we inoculated mice with a mild viral pathogen (rhinovirus or murine coronavirus), followed 2 days later by a virulent viral pathogen (influenza A virus). This model demonstrated that rhinovirus can reduce the severity of influenza A virus, which corresponded with an early but controlled inflammatory response in the lungs and early clearance of influenza A virus. We further determined the dose and timing parameters that were important for effective disease attenuation and showed that influenza disease is also reduced by coinfection with a murine coronavirus. These findings demonstrate that coinfecting viruses can alter immune responses and pathogenesis in the respiratory tract.
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Epidemiology of viral respiratory infections in Australian working-age adults (20–64 years): 2010–2013. Epidemiol Infect 2018; 146:619-626. [DOI: 10.1017/s0950268818000286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractAcute respiratory infections cause significant morbidity and mortality accounting for 5.8 million deaths worldwide. In Australia, influenza-like illness (ILI), defined as cough, fever and fatigue is a common presentation in general practice and results in reduced productivity and lost working days. Little is known about the epidemiology of ILI in working-age adults. Using data from the ASPREN influenza surveillance network in Australia (2010–2013) we found that working-age adults made up 45.2% of all ILI notifications with 55% of samples positive for at least one respiratory virus. Viruses most commonly detected in our study included influenza A (20.6%), rhinovirus (18.6%), influenza B (6.2%), human meta-pneumovirus (3.4%), respiratory syncytial virus (3.1%), para-influenza virus (2.6%) and adenovirus (1.3%). We also demonstrated that influenza A is the predominant virus that increases ILI (by 1.2% per month for every positive influenza A case) in working-age adults during autumn–winter months while other viruses are active throughout the year. Understanding the epidemiology of viral respiratory infections through a year will help clinicians make informed decisions about testing, antibiotic and antiviral prescribing and when the beginning of the ‘flu season’ can be more confidently predicted.
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Opatowski L, Baguelin M, Eggo RM. Influenza interaction with cocirculating pathogens and its impact on surveillance, pathogenesis, and epidemic profile: A key role for mathematical modelling. PLoS Pathog 2018; 14:e1006770. [PMID: 29447284 PMCID: PMC5814058 DOI: 10.1371/journal.ppat.1006770] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Evidence is mounting that influenza virus interacts with other pathogens colonising or infecting the human respiratory tract. Taking into account interactions with other pathogens may be critical to determining the real influenza burden and the full impact of public health policies targeting influenza. This is particularly true for mathematical modelling studies, which have become critical in public health decision-making. Yet models usually focus on influenza virus acquisition and infection alone, thereby making broad oversimplifications of pathogen ecology. Herein, we report evidence of influenza virus interactions with bacteria and viruses and systematically review the modelling studies that have incorporated interactions. Despite the many studies examining possible associations between influenza and Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Neisseria meningitidis, respiratory syncytial virus (RSV), human rhinoviruses, human parainfluenza viruses, etc., very few mathematical models have integrated other pathogens alongside influenza. The notable exception is the pneumococcus-influenza interaction, for which several recent modelling studies demonstrate the power of dynamic modelling as an approach to test biological hypotheses on interaction mechanisms and estimate the strength of those interactions. We explore how different interference mechanisms may lead to unexpected incidence trends and possible misinterpretation, and we illustrate the impact of interactions on public health surveillance using simple transmission models. We demonstrate that the development of multipathogen models is essential to assessing the true public health burden of influenza and that it is needed to help improve planning and evaluation of control measures. Finally, we identify the public health, surveillance, modelling, and biological challenges and propose avenues of research for the coming years.
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Affiliation(s)
- Lulla Opatowski
- Université de Versailles Saint Quentin, Institut Pasteur, Inserm, Paris, France
| | - Marc Baguelin
- London School of Hygiene & Tropical Medicine, London, United Kingdom
- Public Health England, London, United Kingdom
| | - Rosalind M. Eggo
- London School of Hygiene & Tropical Medicine, London, United Kingdom
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Nguyen VH, Dubot-Pérès A, Russell FM, Dance DAB, Vilivong K, Phommachan S, Syladeth C, Lai J, Lim R, Morpeth M, Mayxay M, Newton PN, Richet H, De Lamballerie X. Acute respiratory infections in hospitalized children in Vientiane, Lao PDR - the importance of Respiratory Syncytial Virus. Sci Rep 2017; 7:9318. [PMID: 28839157 PMCID: PMC5571090 DOI: 10.1038/s41598-017-09006-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/14/2017] [Indexed: 01/12/2023] Open
Abstract
The Human respiratory syncytial virus (RSV) is one of the most important viral pathogens, causing epidemics of acute respiratory infection (ARI), especially bronchiolitis and pneumonia, in children worldwide. To investigate the RSV burden in Laos, we conducted a one-year study in children <5 years old admitted to Mahosot Hospital, Vientiane Capital, to describe clinical and epidemiological characteristics and predictive factors for severity of RSV-associated ARI. Pooled nasal and throat swabs were tested using multiplex real-time PCR for 33 respiratory pathogens (FTD® kit). A total of 383 patients were included, 277 (72.3%) of whom presented with pneumonia. 377 (98.4%) patients were positive for at least one microorganism, of which RSV was the most common virus (41.0%), with a peak observed between June and September, corresponding to the rainy season. Most RSV inpatients had pneumonia (84.1%), of whom 35% had severe pneumonia. Children <3-months old were a high-risk group for severe pneumonia, independently of RSV infection. Our study suggests that RSV infection is frequent in Laos and commonly associated with pneumonia in hospitalized young children. Further investigations are required to provide a better overall view of the Lao nationwide epidemiology and public health burden of RSV infection over time.
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Affiliation(s)
- Van Hoan Nguyen
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille university - IRD190 - Inserm 1207 - EHESP), Marseille, France
- Institut hospitalo-universitaire Méditerranée infection, APHM Public Hospitals of Marseille, Marseille, France
- Department of Infectious Diseases, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
| | - Audrey Dubot-Pérès
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille university - IRD190 - Inserm 1207 - EHESP), Marseille, France.
- Institut hospitalo-universitaire Méditerranée infection, APHM Public Hospitals of Marseille, Marseille, France.
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Vientiane, Lao PDR.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, United Kingdom.
| | - Fiona M Russell
- Dept. of Paediatrics, The University of Melbourne, Melbourne, Australia
- Pneumococcal Research Group, Murdoch Childrens Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Keoudomphone Vilivong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Vientiane, Lao PDR
| | - Souphatsone Phommachan
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Vientiane, Lao PDR
| | - Chanthaphone Syladeth
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Vientiane, Lao PDR
| | - Jana Lai
- Pneumococcal Research Group, Murdoch Childrens Research Institute, The Royal Children's Hospital, Melbourne, Australia
- National Centre for Epidemiology & Population Health, Australian National University, Canberra, Australia
| | - Ruth Lim
- Pneumococcal Research Group, Murdoch Childrens Research Institute, The Royal Children's Hospital, Melbourne, Australia
| | - Melinda Morpeth
- Dept. of Paediatrics, The University of Melbourne, Melbourne, Australia
- The Royal Children's Hospital, Melbourne, Australia
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Vientiane, Lao PDR
- Faculty of Postgraduate Studies, University of Health Sciences, Vientiane, Lao PDR, Vientiane, Laos
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Vientiane, Lao PDR
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Old Road Campus, University of Oxford, Oxford, United Kingdom
| | - Hervé Richet
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille university - IRD190 - Inserm 1207 - EHESP), Marseille, France
| | - Xavier De Lamballerie
- UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille university - IRD190 - Inserm 1207 - EHESP), Marseille, France
- Institut hospitalo-universitaire Méditerranée infection, APHM Public Hospitals of Marseille, Marseille, France
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Boikos C, Papenburg J, Martineau C, Joseph L, Scheifele D, Chilvers M, Lands LC, De Serres G, Quach C. Viral interference and the live-attenuated intranasal influenza vaccine: Results from a pediatric cohort with cystic fibrosis. Hum Vaccin Immunother 2017; 13:1-7. [PMID: 28273006 PMCID: PMC5489283 DOI: 10.1080/21645515.2017.1287641] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/03/2017] [Accepted: 01/24/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The objective of this study was to explore the effects of viral co-detection in individuals recently vaccinated with the live-attenuated intranasal influenza virus vaccine (LAIV) on the detection of influenza RNA. METHODS Before the 2013-2014 influenza season, nasal swabs were obtained from 59 pediatric participants with cystic fibrosis (CF) and 17 of their healthy siblings immediately before vaccination and 4 times during the week of follow-up. Real-time RT-PCR assays were used to detect influenza RNA. Co-detection of a non-influenza respiratory virus (NIRV) at the time of vaccination was determined by a multiplex RT-PCR assay. Differences in the proportions and rates of influenza detection and their 95% credible intervals (CrI) were estimated. RESULTS Influenza RNA was detected in 16% fewer participants (95% CrI: -7, 39%) throughout follow-up in the NIRV-positive group compared with the NIRV-negative group (59% vs. 75%). This was also observed in participants with CF alone (66% vs. 74%; RD = 8% 95% CrI: -16, 33%) as well as in healthy participants only (75% vs. 30%; RD = 45%, 95% CrI: -2, 81%). Influenza was detected in NIRV-negative subjects for 0.49 d more compared with NIRV-positive subjects (95% CrI: -0.37, 1.26). CONCLUSION The observed proportion of subjects in whom influenza RNA was detected and the duration of detection differed slightly between NIRV- positive and -negative subjects. However, wide credible intervals for the difference preclude definitive conclusions. If true, this observed association may be related to a recent viral respiratory infection, a phenomenon known as viral interference.
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Affiliation(s)
- Constantina Boikos
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, QC, Canada
| | - Jesse Papenburg
- Department of Pediatrics, Division of Infectious Diseases, The Montreal Children's Hospital, McGill University, Montreal, QC, Canada
| | - Christine Martineau
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, QC, Canada
| | - Lawrence Joseph
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, QC, Canada
| | - David Scheifele
- Vaccine Evaluation Center, Child & Family Research Institute, University of British Columbia, BC, Canada
| | - Mark Chilvers
- Director, Cystic Fibrosis Clinic, University of British Columbia, BC, Canada
| | - Larry C. Lands
- Department of Pediatrics, Division of Respiratory Medicine, The Montreal Children's Hospital, McGill University, Montreal, QC, Canada
| | - Gaston De Serres
- Direction des risques biologiques et de la santé au travail, Institut national de santé publique du Québec, QC, Canada
| | - Caroline Quach
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, QC, Canada
- Department of Pediatrics, Division of Infectious Diseases, The Montreal Children's Hospital, McGill University, Montreal, QC, Canada
- Direction des risques biologiques et de la santé au travail, Institut national de santé publique du Québec, QC, Canada
- McGill University Health Centre, Vaccine Study Centre, Research Institute of the MUHC, Montreal, QC, Canada
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Fernandes-Matano L, Monroy-Muñoz IE, Angeles-Martínez J, Sarquiz-Martinez B, Palomec-Nava ID, Pardavé-Alejandre HD, Santos Coy-Arechavaleta A, Santacruz-Tinoco CE, González-Ibarra J, González-Bonilla CR, Muñoz-Medina JE. Prevalence of non-influenza respiratory viruses in acute respiratory infection cases in Mexico. PLoS One 2017; 12:e0176298. [PMID: 28467515 PMCID: PMC5415110 DOI: 10.1371/journal.pone.0176298] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/07/2017] [Indexed: 01/10/2023] Open
Abstract
Background Acute respiratory infections are the leading cause of morbidity and mortality worldwide. Although a viral aetiological agent is estimated to be involved in up to 80% of cases, the majority of these agents have never been specifically identified. Since 2009, diagnostic and surveillance efforts for influenza virus have been applied worldwide. However, insufficient epidemiological information is available for the many other respiratory viruses that can cause Acute respiratory infections. Methods This study evaluated the presence of 14 non-influenza respiratory viruses in 872 pharyngeal exudate samples using RT-qPCR. All samples met the operational definition of a probable case of an influenza-like illness or severe acute respiratory infection and had a previous negative result for influenza by RT-qPCR. Results The presence of at least one non-influenza virus was observed in 312 samples (35.8%). The most frequent viruses were rhinovirus (RV; 33.0%), human respiratory syncytial virus (HRSV; 30.8%) and human metapneumovirus (HMPV; 10.6%). A total of 56 cases of co-infection (17.9%) caused by 2, 3, or 4 viruses were identified. Approximately 62.5% of all positive cases were in children under 9 years of age. Conclusion In this study, we identified 13 non-influenza respiratory viruses that could occur in any season of the year. This study provides evidence for the prevalence and seasonality of a wide range of respiratory viruses that circulate in Mexico and constitute a risk for the population. Additionally, our data suggest that including these tests more widely in the diagnostic algorithm for influenza may reduce the use of unnecessary antibiotics, reduce the hospitalisation time, and enrich national epidemiological data with respect to the infections caused by these viruses.
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Affiliation(s)
| | - Irma Eloísa Monroy-Muñoz
- Laboratorio de Genómica, Departamento de Genética y Genómica Humana, Instituto Nacional de Perinatología “Isidro Espinosa de los Reyes”. Ciudad de México, México
| | - Javier Angeles-Martínez
- Laboratorio de Genómica, Departamento de Biología Molecular, Instituto Nacional de Cardiología “Ignacio Chávez”. Ciudad de México, México
| | - Brenda Sarquiz-Martinez
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Iliana Donají Palomec-Nava
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Hector Daniel Pardavé-Alejandre
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Andrea Santos Coy-Arechavaleta
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Clara Esperanza Santacruz-Tinoco
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Joaquín González-Ibarra
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - Cesar Raúl González-Bonilla
- División de Laboratorios de Vigilancia e Investigación Epidemiológica, Instituto Mexicano del Seguro Social. Ciudad de México, México
| | - José Esteban Muñoz-Medina
- Laboratorio Central de Epidemiología, Centro Médico Nacional La Raza, Instituto Mexicano del Seguro Social. Ciudad de México, México
- * E-mail:
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Brottet E, Jaffar-Bandjee MC, Li-Pat-Yuen G, Filleul L. Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012. PLoS One 2016; 11:e0163377. [PMID: 27654509 PMCID: PMC5031398 DOI: 10.1371/journal.pone.0163377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 09/06/2016] [Indexed: 11/23/2022] Open
Abstract
In Réunion Island, despite an influenza surveillance established since 1996 by the sentinel general practitioner’s network, little is known about the etiology of Influenza like-illness (ILI) that differs from influenza viruses in a tropical area. We set up a retrospective study using nasal swabs collected by sentinel GPs from ILI patients in 2011 and 2012. A total of 250 swabs were randomly selected and analyzed by multiplex reverse transcriptase polymerase chain reaction (RT-PCR) including research of 18 viruses and 4 bacteria. We detected respiratory viruses in 169/222 (76.1%) samples, mostly rhinovirus (23.4%), influenza A virus (21.2%), influenza B virus (12.6%), coronavirus (4.9%) and Human metapneumovirus (3.6%). Nine swabs (5.3% of positive swabs) revealed co-infections with two viruses identified, among which six concerned co-infections with influenza viruses. We observed important seasonal differences, with circulation of Human Metapneumoviruses, RSV A and B and coronavirus only during summer; whereas parainfluenza viruses were identified only during winter. In conclusion, this study highlights a substantial circulation of multiple respiratory pathogens in Réunion Island throughout the year. It shows that ILI are not only attributable to influenza and underlines the need for biological surveillance. As the use of multiplex RT-PCR showed its efficacy, it is now used routinely in the surveillance of ILI.
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Affiliation(s)
- Elise Brottet
- Santé publique France, French national public health agency, Regional unit (Cire) Océan Indien, Réunion, France
- * E-mail:
| | | | - Ghislaine Li-Pat-Yuen
- Laboratory of virology, Centre Hospitalier Universitaire, Saint-Denis, Réunion, France
| | - Laurent Filleul
- Santé publique France, French national public health agency, Regional unit (Cire) Océan Indien, Réunion, France
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Sullivan SG, Tchetgen Tchetgen EJ, Cowling BJ. Theoretical Basis of the Test-Negative Study Design for Assessment of Influenza Vaccine Effectiveness. Am J Epidemiol 2016; 184:345-53. [PMID: 27587721 DOI: 10.1093/aje/kww064] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 01/14/2016] [Indexed: 12/31/2022] Open
Abstract
Influenza viruses undergo frequent antigenic changes. As a result, the viruses circulating change within and between seasons, and the composition of the influenza vaccine is updated annually. Thus, estimation of the vaccine's effectiveness is not constant across seasons. In order to provide annual estimates of the influenza vaccine's effectiveness, health departments have increasingly adopted the "test-negative design," using enhanced data from routine surveillance systems. In this design, patients presenting to participating general practitioners with influenza-like illness are swabbed for laboratory testing; those testing positive for influenza virus are defined as cases, and those testing negative form the comparison group. Data on patients' vaccination histories and confounder profiles are also collected. Vaccine effectiveness is estimated from the odds ratio comparing the odds of testing positive for influenza among vaccinated patients and unvaccinated patients, adjusting for confounders. The test-negative design is purported to reduce bias associated with confounding by health-care-seeking behavior and misclassification of cases. In this paper, we use directed acyclic graphs to characterize potential biases in studies of influenza vaccine effectiveness using the test-negative design. We show how studies using this design can avoid or minimize bias and where bias may be introduced with particular study design variations.
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Abstract
Human rhinovirus (HRV) and coronavirus (HCoV) infections are associated with both upper respiratory tract illness (“the common cold”) and lower respiratory tract illness (pneumonia). New species of HRVs and HCoVs have been diagnosed in the past decade. More sensitive diagnostic tests such as reverse transcription-polymerase chain reaction have expanded our understanding of the role these viruses play in both immunocompetent and immunosuppressed hosts. Recent identification of severe acute respiratory syndrome and Middle East respiratory syndrome viruses causing serious respiratory illnesses has led to renewed efforts for vaccine development. The role these viruses play in patients with chronic lung disease such as asthma makes the search for antiviral agents of increased importance.
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Affiliation(s)
- Stephen B Greenberg
- Department of Medicine, Ben Taub Hospital, Baylor College of Medicine, Houston, Texas
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van Asten L, Bijkerk P, Fanoy E, van Ginkel A, Suijkerbuijk A, van der Hoek W, Meijer A, Vennema H. Early occurrence of influenza A epidemics coincided with changes in occurrence of other respiratory virus infections. Influenza Other Respir Viruses 2016; 10:14-26. [PMID: 26369646 PMCID: PMC4687500 DOI: 10.1111/irv.12348] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Viral interaction in which outbreaks of influenza and other common respiratory viruses might affect each other has been postulated by several short studies. Regarding longer time periods, influenza epidemics occasionally occur very early in the season, as during the 2009 pandemic. Whether early occurrence of influenza epidemics impacts outbreaks of other common seasonal viruses is not clear. OBJECTIVES We investigated whether early occurrence of influenza outbreaks coincides with shifts in the occurrence of other common viruses, including both respiratory and non-respiratory viruses. METHODS We investigated time trends of and the correlation between positive laboratory diagnoses of eight common viruses in the Netherlands over a 10-year time period (2003-2012): influenza viruses types A and B, respiratory syncytial virus (RSV), rhinovirus, coronavirus, norovirus, enterovirus, and rotavirus. We compared trends in viruses between early and late influenza seasons. RESULTS Between 2003 and 2012, influenza B, RSV, and coronavirus showed shifts in their occurrence when influenza A epidemics occurred earlier than usual (before week 1). Although shifts were not always consistently of the same type, when influenza type A hit early, RSV outbreaks tended to be delayed, coronavirus outbreaks tended to be intensified, and influenza virus type B tended not to occur at all. Occurrence of rhinovirus, norovirus, rotavirus, and enterovirus did not change. CONCLUSION When influenza A epidemics occured early, timing of the epidemics of several respiratory winter viruses usually occurring close in time to influenza A was affected, while trends in rhinoviruses (occurring in autumn) and trends in enteral viruses were not.
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Affiliation(s)
- Liselotte van Asten
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Paul Bijkerk
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ewout Fanoy
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Annemarijn van Ginkel
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Anita Suijkerbuijk
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Wim van der Hoek
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Adam Meijer
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Harry Vennema
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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Arriaga-Pizano L, Ferat-Osorio E, Rodríguez-Abrego G, Mancilla-Herrera I, Domínguez-Cerezo E, Valero-Pacheco N, Pérez-Toledo M, Lozano-Patiño F, Laredo-Sánchez F, Malagón-Rangel J, Nellen-Hummel H, González-Bonilla C, Arteaga-Troncoso G, Cérbulo-Vázquez A, Pastelin-Palacios R, Klenerman P, Isibasi A, López-Macías C. Differential Immune Profiles in Two Pandemic Influenza A(H1N1)pdm09 Virus Waves at Pandemic Epicenter. Arch Med Res 2015; 46:651-8. [PMID: 26696552 PMCID: PMC4914610 DOI: 10.1016/j.arcmed.2015.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/01/2015] [Indexed: 11/26/2022]
Abstract
Background and Aims Severe influenza A(H1N1)pdm2009 virus infection cases are characterized by sustained immune activation during influenza pandemics. Seasonal flu data suggest that immune mediators could be modified by wave-related changes. Our aim was to determine the behavior of soluble and cell-related mediators in two waves at the epicenter of the 2009 influenza pandemic. Methods Leukocyte surface activation markers were studied in serum from peripheral blood samples, collected from the 1st (April–May, 2009) and 2nd (October 2009–February 2010) pandemic waves. Patients with confirmed influenza A(H1N1)pdm2009 virus infection (H1N1), influenza-like illness (ILI) or healthy donors (H) were analyzed. Results Serum IL-6, IL-4 and IL-10 levels were elevated in H1N1 patients from the 2nd pandemic wave. Additionally, the frequency of helper and cytotoxic T cells was reduced during the 1st wave, whereas CD69 expression in helper T cells was increased in the 2nd wave for both H1N1 and ILI patients. In contrast, CD62L expression in granulocytes from the ILI group was increased in both waves but in monocytes only in the 2nd wave. Triggering Receptor Expressed on Myeloid cells (TREM)-1 expression was elevated only in H1N1 patients at the 1st wave. Conclusions Our results show that during the 2009 influenza pandemic a T cell activation phenotype is observed in a wave-dependent fashion, with an expanded activation in the 2nd wave, compared to the 1st wave. Conversely, granulocyte and monocyte activation is infection-dependent. This evidence collected at the pandemic epicenter in 2009 could help us understand the differences in the underlying cellular mechanisms that drive the wave-related immune profile behaviors that occur against influenza viruses during pandemics.
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Affiliation(s)
- Lourdes Arriaga-Pizano
- Medical Research Unit in Immunochemistry, Specialties Hospital, National Medical Center Siglo XXI, IMSS, Mexico City, Mexico
| | - Eduardo Ferat-Osorio
- Medical Research Unit in Immunochemistry, Specialties Hospital, National Medical Center Siglo XXI, IMSS, Mexico City, Mexico; Gastrointestinal Surgery Service, Specialties Hospital, National Medical Center Siglo XXI, IMSS, Mexico City, Mexico
| | | | - Ismael Mancilla-Herrera
- Infectology and Immunology department, National Institute of Perinatology, SSA, Mexico City, Mexico
| | - Esteban Domínguez-Cerezo
- Medical Research Unit in Immunochemistry, Specialties Hospital, National Medical Center Siglo XXI, IMSS, Mexico City, Mexico; Graduate Program on Immunology, ENCB-IPN, Mexico City, Mexico
| | - Nuriban Valero-Pacheco
- Medical Research Unit in Immunochemistry, Specialties Hospital, National Medical Center Siglo XXI, IMSS, Mexico City, Mexico; Graduate Program on Immunology, ENCB-IPN, Mexico City, Mexico
| | - Marisol Pérez-Toledo
- Medical Research Unit in Immunochemistry, Specialties Hospital, National Medical Center Siglo XXI, IMSS, Mexico City, Mexico; Graduate Program on Immunology, ENCB-IPN, Mexico City, Mexico
| | - Fernando Lozano-Patiño
- Internal Medicine Service, Specialties Hospital of the National Medical Center Siglo XXI, IMSS, Mexico City, Mexico
| | - Fernando Laredo-Sánchez
- Internal Medicine Service, Specialties Hospital of the National Medical Center Siglo XXI, IMSS, Mexico City, Mexico
| | - José Malagón-Rangel
- Internal Medicine Service, Specialties Hospital of the National Medical Center Siglo XXI, IMSS, Mexico City, Mexico
| | - Haiko Nellen-Hummel
- Internal Medicine Service, Specialties Hospital of the National Medical Center Siglo XXI, IMSS, Mexico City, Mexico
| | - César González-Bonilla
- Unit for Epidemiological Surveillance, National Medical Center La Raza, IMSS, Mexico City, Mexico
| | | | | | | | - Paul Klenerman
- Oxford Biomedical Research Centre and Oxford Martin School, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Armando Isibasi
- Medical Research Unit in Immunochemistry, Specialties Hospital, National Medical Center Siglo XXI, IMSS, Mexico City, Mexico
| | - Constantino López-Macías
- Medical Research Unit in Immunochemistry, Specialties Hospital, National Medical Center Siglo XXI, IMSS, Mexico City, Mexico; Visiting Professor of Immunology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Tsang TK, Lau LLH, Cauchemez S, Cowling BJ. Household Transmission of Influenza Virus. Trends Microbiol 2015; 24:123-133. [PMID: 26612500 PMCID: PMC4733423 DOI: 10.1016/j.tim.2015.10.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/05/2015] [Accepted: 10/28/2015] [Indexed: 12/13/2022]
Abstract
Human influenza viruses cause regular epidemics and occasional pandemics with a substantial public health burden. Household transmission studies have provided valuable information on the dynamics of influenza transmission. We reviewed published studies and found that once one household member is infected with influenza, the risk of infection in a household contact can be up to 38%, and the delay between onset in index and secondary cases is around 3 days. Younger age was associated with higher susceptibility. In the future, household transmission studies will provide information on transmission dynamics, including the correlation of virus shedding and symptoms with transmission, and the correlation of new measures of immunity with protection against infection. Historically, household cohort studies have provided valuable information on the incidence of respiratory infections and risk factors for infection. However, these studies require substantial resources and can provide limited information on transmission dynamics. Household transmission studies provide an efficient approach to describing the risk of influenza transmission and factors affecting transmission. In these studies, households with at least one member infected by influenza are eligible and are followed intensively for 1–2 weeks to observe secondary transmission within the household. Transmission studies also provide a model for evaluation of interventions in randomized controlled trials, and have been used to determine the efficacy of antiviral drugs for treatment and prophylaxis, and nonpharmaceutical interventions such as face masks and hand hygiene.
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Affiliation(s)
- Tim K Tsang
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lincoln L H Lau
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Paris, France
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong Special Administrative Region, China.
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Bhattacharyya S, Gesteland PH, Korgenski K, Bjørnstad ON, Adler FR. Cross-immunity between strains explains the dynamical pattern of paramyxoviruses. Proc Natl Acad Sci U S A 2015; 112:13396-400. [PMID: 26460003 PMCID: PMC4629340 DOI: 10.1073/pnas.1516698112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viral respiratory tract diseases pose serious public health problems. Our ability to predict and thus, be able to prepare for outbreaks is strained by the complex factors driving the prevalence and severity of these diseases. The abundance of diseases and transmission dynamics of strains are not only affected by external factors, such as weather, but also driven by interactions among viruses mediated by human behavior and immunity. To untangle the complex out-of-phase annual and biennial pattern of three common paramyxoviruses, Respiratory Syncytial Virus (RSV), Human Parainfluenza Virus (HPIV), and Human Metapneumovirus (hMPV), we adopt a theoretical approach that integrates ecological and immunological mechanisms of disease interactions. By estimating parameters from multiyear time series of laboratory-confirmed cases from the intermountain west region of the United States and using statistical inference, we show that models of immune-mediated interactions better explain the data than those based on ecological competition by convalescence. The strength of cross-protective immunity among viruses is correlated with their genetic distance in the phylogenetic tree of the paramyxovirus family.
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Affiliation(s)
- Samit Bhattacharyya
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; Department of Biology, University of Utah, Salt Lake City, UT 84112;
| | - Per H Gesteland
- Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT 84112; Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112
| | - Kent Korgenski
- Department of Pediatrics, School of Medicine, University of Utah, Salt Lake City, UT 84112; Pediatric Clinical Program, Intermountain Healthcare, Salt Lake City, UT 84111
| | - Ottar N Bjørnstad
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892
| | - Frederick R Adler
- Department of Biology, University of Utah, Salt Lake City, UT 84112; Department of Mathematics, University of Utah, Salt Lake City, UT 84112
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Sherbany H, McCauley J, Meningher T, Hindiyeh M, Dichtiar R, Markovich MP, Mendelson E, Mandelboim M. Return of pandemic H1N1 influenza virus. BMC Infect Dis 2014; 14:710. [PMID: 25551676 PMCID: PMC4375933 DOI: 10.1186/s12879-014-0710-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 12/11/2014] [Indexed: 12/30/2022] Open
Abstract
Background Influenza pandemics are usually caused by the re-assortment of several influenza viruses, results in the emergence of new influenza virus strains that can infect the entire population. These pandemic strains, as well as seasonal influenza viruses, are subjected to extensive antigenic change that has, so far, prevented the generation of a universal vaccine. Methods Samples of patients hospitalized due to infection with the pandemic H1N1 influenza virus (A(H1N1)pdm09) from 2009, when the virus first appeared, until 2013 were analyzed. Results While many patients were hospitalized in 2009 due to infection with the pandemic H1N1 influenza virus, only small percentages of patients were hospitalized later in 2010–2012. Surprisingly, however in 2012–2013, we noticed that the percentages of patients hospitalized due to the pandemic H1N1 influenza infection increased significantly. Moreover, the ages of hospitalized patients differed throughout this entire period (2009–2013) and pregnant women were especially vulnerable to the infection. Conclusions High percentages of patients (especially pregnant women) were hospitalized in 2013 due to the A(H1N1)pdm09 infection, which may have been enabled by an antigenic drift from those which circulated at the onset of the pandemic. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0710-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hilda Sherbany
- Central Virology Laboratory, Ministry of Health, Public Health Services, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel.
| | - John McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Division of Virology, MRC National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK.
| | - Tal Meningher
- Central Virology Laboratory, Ministry of Health, Public Health Services, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel. .,The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
| | - Musa Hindiyeh
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
| | - Rita Dichtiar
- Israel Center for Disease Control, Ministry of Health, Gertner Institute for Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel.
| | - Michal Perry Markovich
- Israel Center for Disease Control, Ministry of Health, Gertner Institute for Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel.
| | - Ella Mendelson
- Central Virology Laboratory, Ministry of Health, Public Health Services, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel. .,Department of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
| | - Michal Mandelboim
- Central Virology Laboratory, Ministry of Health, Public Health Services, Chaim Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel.
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Meningher T, Hindiyeh M, Regev L, Sherbany H, Mendelson E, Mandelboim M. Relationships between A(H1N1)pdm09 influenza infection and infections with other respiratory viruses. Influenza Other Respir Viruses 2014; 8:422-30. [PMID: 24698156 PMCID: PMC4181801 DOI: 10.1111/irv.12249] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2014] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND A(H1N1)pdm09, a new influenza pandemic virus emerged in 2009. The A(H1N1)pdm09 infection had several unique characteristics which included rapid transmissibility and high morbidity in obese individuals, pregnant women and individuals suffering from chronic diseases. OBJECTIVES To study the relationships between A(H1N1)pdm09 influenza infection and infections with other respiratory viruses such as respiratory syncytial virus (RSV), human metapneumo virus (hMPV), adenovirus and seasonal influenza. METHODS Samples (nasopharyngeal swabs or aspirates) collected between 2007 until 2012 from patients of various ages that were hospitalized due to respiratory virus infections were analyzed for the presence of various respiratory viruses, using qRT-PCR. RESULTS In 2009-2010, when the pandemic influenza A(H1N1)pdm09 first appeared, two major infection peaks were noted and individuals of various ages were infected. Following the decline of the A(H1N1)pdm09 virus infection, the percentages of patients infected with adenovirus and hMPV increased, while infection frequency with RSV B and with seasonal influenza virus decreased. Furthermore, RSV infections were delayed and very few percentages of patients were co-infected with more than one virus. Interestingly, the A(H1N1)pdm09 virus lost its dominancy when it reappeared in the winter of 2010-2011, and at this time, only the incidence of RSV infections was affected by the A(H1N1)pdm09 virus. CONCLUSIONS The A(H1N1)pdm09 virus had distinct effects on other respiratory viruses when it first appeared versus later, when it evolved from being a pandemic to a seasonal virus.
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Affiliation(s)
- Tal Meningher
- Central Virology Laboratory, Ministry of Health, Chaim Sheba Medical Center, Ramat-Gan, Israel; The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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Taglioni F, Cartoux M, Dellagi K, Dalban C, Fianu A, Carrat F, Favier F. The influenza A (H1N1) pandemic in Reunion Island: knowledge, perceived risk and precautionary behaviour. BMC Infect Dis 2013; 13:34. [PMID: 23347821 PMCID: PMC3598238 DOI: 10.1186/1471-2334-13-34] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 01/11/2013] [Indexed: 12/26/2022] Open
Abstract
Background The effectiveness of preventive measures depends on prevailing attitudes and mindsets within a population. Perceived risk is central to a shift in mindset and behaviour. The present study aims to investigate the perceived severity, vulnerability and precautionary behaviour adopted in response to the influenza A (H1N1) epidemic that broke out in 2009 on Reunion Island (Indian Ocean). As no H1N1 vaccination was available at the time, non-medical interventions appeared of crucial importance to the control of the epidemic. Methods A cross sectional survey was conducted in Reunion Island between November 2009 and April 2010 within 2 months of the passage of the influenza A (H1N1) epidemic wave. Individual contacts representing 725 households (one contact per household) were interviewed by telephone using validated questionnaires on perceived risks. Mean scores were calculated for perceived severity, vulnerability, efficacy of preventive measures and precautionary behaviour. Univariate analysis was applied to identify preventive measures and attitudes and multivariate analysis was used to study the determinants of precautionary behaviour. Results More than 95% of contacted persons accepted to participate to the survey. Eighty seven percent of respondents believed that prevention was possible. On average, three out of six preventive measures were deemed effective. Spontaneously, 57% of the respondents reported that they took one or more preventive measures. This percentage increased to 87% after the interviewer detailed possible precautions one by one. The main precautions taken were frequent hand washing (59%) and avoidance of crowded places (34%). In multivariate logistic regression analysis the following factors were significantly associated with taking one or more preventive measures: young age, previous vaccination against seasonal influenza, having had seasonal influenza in the last five years, effectiveness of the preventive measures taken and low standards of education. Conclusion Inhabitants of Reunion Island have expressed a preventive approach adapted to the realities of the H1N1 pandemic, a feature that likely reflects some preparedness gained after the large and severe chikungunya epidemic that hit the island in 2006. The degree of severity was well assessed despite the initial alarmist messages disseminated by national and international media. Precautions that were undertaken matched the degree of severity of the epidemic and the recommendations issued by health authorities. Further qualitative studies are needed to help adapting public messages to the social and cultural realities of diverse communities and to prevent misconceptions.
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Affiliation(s)
- François Taglioni
- University of Reunion Island, BP 7151, Saint-Denis cedex 9, Reunion Island, 97715, France.
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