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Jain A, Mahesh S, Prakash O, Khan DN, Verma AK, Rastogi Y. Effect of COVID-19 pandemic on influenza; observation of a tertiary level virology laboratory. Virusdisease 2024; 35:27-33. [PMID: 38817401 PMCID: PMC11133273 DOI: 10.1007/s13337-024-00860-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/02/2024] [Indexed: 06/01/2024] Open
Abstract
The lockdown enforced amid the COVID-19 pandemic has affected the occurrence and trends of various respiratory virus infections, with a particular focus on influenza. Our study seeks to analyze the repercussions of the COVID-19 pandemic on the positivity of the influenza virus throughout a 4-year span, encompassing both the pre-COVID-19 era (2018 and 2019) and the COVID-19 period (2020 and 2021). Data collected from patients clinically diagnosed with Influenza-like Illness and Severe Acute Respiratory Illness (SARI) from January 2018 to December 2021 for influenza virus detection were acquired and analyzed through multiplex RT-qPCR. The statistical analysis was conducted using SPSS (Statistical Package for Social Sciences) Version 21.0 Software. A total of 4464 samples were tested over 4 years (2018-2021), with 3201 samples from the pre-COVID era and 1263 samples from the COVID era. Influenza A positivity dropped from 17.7 to 9.57% and Influenza B positivity decreased from 3.74 to 2.61%. Subtyping revealed changes in prevalence for both viruses. Seasonal variations showed more pronounced peaks in the pre-COVID-19 era with reduced activity during lockdown. Influenza A saw a resurgence in August 2021. Throughout the COVID-19 pandemic (2020-2021) SARI cases did not decrease. The positivity rate for Influenza A slightly rose to 7.79% from 4.23% in the COVID period (2020-2021). This increase correlates with heightened hospitalization rates during the pandemic, sparking concerns of potential coinfection with coronavirus and Influenza A. The notable drop in influenza cases in 2020-2021 is likely due to stringent precautions, lockdowns, drug repurposing, and prioritized testing, indicating no reduction in influenza transmission. Increased influenza positivity in SARI patients during COVID-19 highlights a heightened risk of coinfection. Emphasizing solely on COVID-19 may lead to underreporting of other respiratory pathogens, including influenza viruses.
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Affiliation(s)
- Amita Jain
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Shreya Mahesh
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Om Prakash
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Danish N. Khan
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Anil Kumar Verma
- Department of Microbiology, King George’s Medical University, Lucknow, India
| | - Yashasvi Rastogi
- Department of Microbiology, King George’s Medical University, Lucknow, India
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Singh N, Batra K, Chaudhary D, Punia M, Kumar A, Maan NS, Maan S. Prevalence of porcine viral respiratory diseases in India. Anim Biotechnol 2023; 34:1642-1654. [PMID: 35112631 DOI: 10.1080/10495398.2022.2032117] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The pig industry is growing rapidly in India and contributes a major share of growth in the livestock sector. Over the last few years, there is a gradual increase in the adoption of pigs for production by economically weaker sections of the country. However, this production is affected by many respiratory diseases which are responsible for significant economic loss. The occurrence and impact of these diseases are still under-documented. The four important pathogens including porcine circovirus type 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSV), swine influenza A viruses (SIV) and classical swine fever virus (CSFV) are documented here. These diseases are highly devastating in nature and frequent outbreaks have been reported from different parts of the country. The rapid and specific diagnosis, effective prevention and control measures are required for the eradication of these diseases which is urgently required for the growth of the pig industry. This review highlights the prevalence, epidemiology, diagnostics and information gaps on important respiratory viral pathogens of pigs reported from different parts of India. This review also emphasizes the importance of these viral diseases and the urgent need to develop vaccines and effective measures for the eradication of these diseases.
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Affiliation(s)
- Neha Singh
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Kanisht Batra
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Deepika Chaudhary
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Monika Punia
- Department of Biotechnology, Ch. Devi Lal University, Sirsa, India
| | - Aman Kumar
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Narender Singh Maan
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
| | - Sushila Maan
- College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Science (LUVAS), Hisar, India
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Potdar V, Vijay N, Mukhopadhyay L, Aggarwal N, Bhardwaj SD, Choudhary ML, Gupta N, Kaur H, Narayan J, Kumar P, Singh H, Abdulkader RS, Murhekar M, Mishra M, Thangavel S, Nagamani K, Dhodapkar R, Fomda BA, Varshney U, Majumdar A, Dutta S, Vijayachari P, Turuk J, Majumdar T, Sahoo GC, Pandey K, Bhargava A, Negi SS, Khatri PK, Kalawat U, Biswas D, Khandelwal N, Borkakoty B, Manjushree S, Singh MP, Iravane J, Kaveri K, Shantala GB, Brijwal M, Choudhary A, Dar L, Malhotra B, Jain A. Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis. Front Public Health 2023; 11:1218292. [PMID: 37927860 PMCID: PMC10624221 DOI: 10.3389/fpubh.2023.1218292] [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: 05/06/2023] [Accepted: 09/18/2023] [Indexed: 11/07/2023] Open
Abstract
Background Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2. Methods In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022. Findings Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8 years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement. Interpretation The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.
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Affiliation(s)
| | - Neetu Vijay
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Labanya Mukhopadhyay
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Neeraj Aggarwal
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | | | | | - Nivedita Gupta
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Harmanmeet Kaur
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Jitendra Narayan
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Prabhat Kumar
- Biomedical Informatics (BMI) Division, Indian Council of Medical Research, New Delhi, India
| | - Harpreet Singh
- Biomedical Informatics (BMI) Division, Indian Council of Medical Research, New Delhi, India
| | | | | | - Meena Mishra
- VRDL, All India Institute of Medical Sciences, Nagpur, India
| | | | - K. Nagamani
- VRDL, Gandhi Medical College, Secunderabad, India
| | - Rahul Dhodapkar
- VRDL, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India
| | | | | | - Agniva Majumdar
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - P. Vijayachari
- ICMR-Regional Medical Research Centre, Port Blair, India
| | | | | | | | - Krishna Pandey
- ICMR-Rajendra Memorial Research Institute of Medical Sciences, Patna, India
| | | | | | | | - Usha Kalawat
- VRDL, Sri Venkateswara Institute of Medical Sciences, Tirupati, India
| | - Debasis Biswas
- VRDL, All India Institute of Medical Sciences, Bhopal, India
| | | | | | | | - Mini P. Singh
- VRDL, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | | | - K. Kaveri
- VRDL, King Institute of Preventive Medicine and Research, Chennai, India
| | - G. B. Shantala
- VRDL, Bangalore Medical College and Research Institute, Bangalore, India
| | - Megha Brijwal
- VRDL, All India Institute of Medical Sciences, New Delhi, India
| | | | - Lalit Dar
- VRDL, All India Institute of Medical Sciences, New Delhi, India
| | | | - Amita Jain
- VRDL, King George’s Medical University, Lucknow, India
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Bhattacharjee U, Chakrabarti AK, Kanungo S, Dutta S. Evolutionary dynamics of influenza A/H1N1 virus circulating in India from 2011 to 2021. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105424. [PMID: 36913995 DOI: 10.1016/j.meegid.2023.105424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/18/2023] [Accepted: 03/09/2023] [Indexed: 03/13/2023]
Abstract
Influenza A viruses (IAV) are fast-evolving pathogens with a very high mutation rate (2.0 × 10-6 to 2.0 × 10-4) compared to the influenza B (IBV) and influenza C (ICV) viruses. Generally, the tropical regions are considered as the reservoir for the IAV's genetic and antigenic evolutionary modification to be reintroduced into the temperate region. Therefore, in connection to the above facts, the present study emphasized on the evolutionary dynamic of the pandemic-2009 H1N1 (pdmH1N1) influenza virus in India. A total of Ninety-two whole genome sequences of pdmH1N1 viruses circulating in India during the 2009 post-pandemic era were analysed. The temporal signal of the study, indicating strict molecular clock evolutionary process and the overall substitution rate is 2.21 × 10-3/site/year. We are using the nonparametric Bayesian Skygrid coalescent model to estimates the effective past population dynamic or size over time. The study exhibits a strong relation between the genetic distances and collection dates of the Indian pdmH1N1 strain. The skygrid plot represents the highest exponential growth of IAV in rainy and winter seasons. All the genes of Indian pdmH1N1 were under purifying selective pressure. The Bayesian time-imprinted phylogenetic tree represents the following clade distributions in the country within the last 10 years; I) clade 6, 6C, and 7 were co-circulating between the 2011 to 2012 flu season; II) the clade 6B was introduced into circulation in the late seasons of 2012; III) lastly, the clade 6B remain existing in the circulation and segregated into subclade 6B.1 with five different subgroup (6B.1A, 6B.1A.1, 6B.1A.5a, 6B.1A.5a.2, 6B.1A.7). The recent circulating strain of Indian H1N1 strain represent the insertion of basic-amino acid arginine (R) in the cleavage site (325/K-R) of HA protein and amino acid mutation (314/I-M) on the lateral head surface domain of NA protein. Moreover, the study indicates the sporadic presence of the oseltamivir-resistant (275/H-Y) H1N1 variant in circulation. The present study suggests the purifying selective pressure and stochastic ecological factors for the existence and adaptation of a certain clade 6B in the host populations and additional information on the emergence of mutated strains in the circulation.
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Affiliation(s)
- Uttaran Bhattacharjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, P-33, C.I.T, Road, Beliaghata, Kolkata 10, India
| | - Alok Kumar Chakrabarti
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, P-33, C.I.T, Road, Beliaghata, Kolkata 10, India.
| | - Suman Kanungo
- Division of Epidemiology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, P-33, C.I.T, Road, Beliaghata, Kolkata 10, India
| | - Shanta Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, P-33, C.I.T, Road, Beliaghata, Kolkata 10, India
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Mutation in Hemagglutinin Antigenic Sites in Influenza A pH1N1 Viruses from 2015–2019 in the United States Mountain West, Europe, and the Northern Hemisphere. Genes (Basel) 2022; 13:genes13050909. [PMID: 35627294 PMCID: PMC9141826 DOI: 10.3390/genes13050909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we characterize antigenic drift events observed in the hemagglutinin (HA) sequence of the pandemic H1N1 lineage from 2015–2019. We observed the substitutions S200P, K147N, and P154S, together with other mutations in structural, functional, and/or epitope regions in 2015–2019 HA protein sequences from the Mountain West region of the United States, the larger United States, Europe, and other Northern Hemisphere countries. We reconstructed multiple phylogenetic trees to track the relationships and spread of these mutations and tested for evidence of selection pressure on HA. We found that the prevalence of amino acid substitutions at positions 147, 154, 159, 200, and 233 significantly changed throughout the studied geographical regions between 2015 and 2019. We also found evidence of coevolution among a subset of these amino acid substitutions. The results from this study could be relevant for future epidemiological tracking and vaccine prediction efforts. Similar analyses in the future could identify additional sequence changes that could affect the pathogenicity and/or infectivity of this virus in its human host.
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Zhang Z, Ma P, Ahmed R, Wang J, Akin D, Soto F, Liu BF, Li P, Demirci U. Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2103646. [PMID: 34623709 DOI: 10.1002/adma.202103646] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/25/2021] [Indexed: 04/14/2023]
Abstract
The ever-growing global threats to human life caused by the human acute respiratory virus (RV) infections have cost billions of lives, created a significant economic burden, and shaped society for centuries. The timely response to emerging RVs could save human lives and reduce the medical care burden. The development of RV detection technologies is essential for potentially preventing RV pandemic and epidemics. However, commonly used detection technologies lack sensitivity, specificity, and speed, thus often failing to provide the rapid turnaround times. To address this problem, new technologies are devised to address the performance inadequacies of the traditional methods. These emerging technologies offer improvements in convenience, speed, flexibility, and portability of point-of-care test (POCT). Herein, recent developments in POCT are comprehensively reviewed for eight typical acute respiratory viruses. This review discusses the challenges and opportunities of various recognition and detection strategies and discusses these according to their detection principles, including nucleic acid amplification, optical POCT, electrochemistry, lateral flow assays, microfluidics, enzyme-linked immunosorbent assays, and microarrays. The importance of limits of detection, throughput, portability, and specificity when testing clinical samples in resource-limited settings is emphasized. Finally, the evaluation of commercial POCT kits for both essential RV diagnosis and clinical-oriented practices is included.
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Affiliation(s)
- Zhaowei Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, National Reference Laboratory for Agricultural Testing (Biotoxin), Key Laboratory of Biology and Genetic Improvement of Oil Crops, Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Peng Ma
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Rajib Ahmed
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Jie Wang
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Demir Akin
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Fernando Soto
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Peiwu Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, National Reference Laboratory for Agricultural Testing (Biotoxin), Key Laboratory of Biology and Genetic Improvement of Oil Crops, Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Utkan Demirci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
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Silent Infection of B and CD8 + T Lymphocytes by Influenza A Virus in Children with Tonsillar Hypertrophy. J Virol 2020; 94:JVI.01969-19. [PMID: 32075928 DOI: 10.1128/jvi.01969-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/12/2020] [Indexed: 12/11/2022] Open
Abstract
Influenza A viruses (IAVs) cause more than 2 million annual episodes of seasonal acute respiratory infections (ARI) and approximately 500,000 deaths worldwide. Depending on virus strain and host immune status, acute infections by IAV may reach sites other than the respiratory tract. In the present study, IAV RNA and antigens were searched for in tissues of palatine tonsils and adenoids removed from patients without ARI symptoms. A real-time reverse transcriptase PCR (RT-PCR) screening revealed that 8 tissue samples from 7 patients out of 103 were positive for IAV. Positive samples were subjected to next-generation sequencing (NGS) and 3 of 8 tissues yielded complete IAV pH1N1 genomes, whereas in 5 samples, the PB1 gene was not fully assembled. Phylogenetic analysis placed tonsil-derived IAV in clusters clearly segregated from contemporaneous Brazilian viruses. Flow cytometry of dispersed tissue fragments and serial immunohistochemistry of paraffin-embedded sections of naturally infected biopsies indicated that CD20+ B lymphocytes, CD8+ T lymphocytes, and CD11c+ cells are susceptible to IAV infection. We sought to investigate whether these lymphoid tissues could be sites of viral replication and sources of viable virus particles. MDCK cells were inoculated with tissue lysates, enabling recovery of one IAV isolate confirmed by immunofluorescence, reverse transcriptase quantitative PCR (RT-qPCR), and NGS. The data indicate that lymphoid tissues not only harbor expression of IAV proteins but also contain infectious virus. Asymptomatic long-term infection raises the possibility of IAV shedding from tonsils, which may have an impact on host-to-host transmission.IMPORTANCE Influenza A virus (IAV) infections are important threats to human health worldwide. Although extensively studied, some aspects of virus pathogenesis and tissue tropism remain unclear. Here, by different strategies, we describe the asymptomatic infection of human lymphoid organs by IAV in children. Our results indicate that IAV was not only detected and isolated from human tonsils but displayed unique genetic features in comparison with those of contemporaneous IAVs circulating in Brazil and detected in swabs and nasal washes. Inside the tissue microenvironment, immune cells were shown to be carrying IAV antigens, especially B and T CD8+ lymphocytes. Taken together, these results suggest that human lymphoid tissues can be sites of silent IAV infections with possible impact on virus shedding to the population.
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Prasad R, Mohanakumari VV, Sasi RV, Nair R, Jones S, Pillai MR. Complete Genome Analysis of Influenza A(H1N1) Viruses Isolated in Kerala, India. Microbiol Resour Announc 2020; 9:e00062-20. [PMID: 32193233 PMCID: PMC7082452 DOI: 10.1128/mra.00062-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/27/2020] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete sequence of four influenza A(H1N1) virus samples isolated from cases that occurred during the 2017 epidemic season in Kerala in South India. Sequence analysis showed mutations that differentiate this strain from the reference strain A/California/07/2009 virus.
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Affiliation(s)
- Raji Prasad
- Pathogen Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | | | - Remya Vasanthi Sasi
- Pathogen Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Radhakrishnan Nair
- Laboratory Medicine and Molecular Diagnostic, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Sara Jones
- Pathogen Biology Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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Potdar V, Vijay N, Gupta N, Arunkumar G, Borkakoty B, Malhotra B, Rabha D, Hinge D, Kaur H, Chadha M. Molecular characterization of influenza A(H1N1)pdm09 viruses circulating at various geographical locations in India, 2017. Indian J Med Res 2020; 149:783-789. [PMID: 31496532 PMCID: PMC6755778 DOI: 10.4103/ijmr.ijmr_925_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background & objectives Influenza virological surveillance is an essential tool for the early detection of novel genetic variants of epidemiologic and clinical significance. This study was aimed to genetically characterize A(H1N1)pdm09 virus circulating in 2017 and to compare it with the global data. Methods The regional/State Viral Research and Diagnostic Laboratories (VRDLs) provided influenza diagnosis for referred clinical samples and shared influenza A(H1N1)pdm09 positives with the Indian Council of Medical Research-National Institute of Virology (ICMR-NIV), Pune, India, for hemagglutinin (HA) gene phylogenetic analysis. Sites at Manipal, Jaipur and Dibrugarh performed the sequencing and shared the sequence data for analysis. The antiviral susceptibility of influenza viruses was assessed for known molecular marker H275Y at the ICMR-NIV, Pune. Results All the eight VRDLs had well-established influenza diagnostic facilities and showed increased activity of influenza A(H1N1)pdm09 during 2017. Phylogenetic analysis showed that the viruses from the different regions of the country were similar to A/Michigan/45/2015 strain which was the 2017-2018 recommended vaccine strain and were clustered with the globally circulating clade 6B.1 with signature mutations S84N, S162N and I216T. The clade 6B.1 showed further subgrouping with additional mutations S74R, S164T and I295V; however, there was no significant association between the presence of these mutations and severity of disease due to influenza. All the study viruses were sensitive to oseltamivir. Interpretation & conclusions During the study period, all the study sites reported globally circulating A/Michigan/45/2015 vaccine strain of influenza A(H1N1)pdm09 viruses and remained sensitive to oseltamivir. Further genetic and antigenic characterization of influenza viruses is recommended to address public health concerns.
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Affiliation(s)
- Varsha Potdar
- Influenza Group, ICMR-National Institute of Virology, Pune, India
| | - Neetu Vijay
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi, India
| | - Nivedita Gupta
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research, Headquarters, New Delhi, India
| | - G Arunkumar
- Manipal Institute of Virology, Manipal Academy of Higher Education (Deemed to be University), Manipal, India
| | | | - Bharti Malhotra
- Department of Microbiology, Sawai Man Singh Medical College, Jaipur, India
| | - Debajit Rabha
- Department of Microbiology, Guwahati Medical College, Guwahati, India
| | - Dilip Hinge
- Influenza Group, ICMR-National Institute of Virology, Pune, India
| | - Harmanmeet Kaur
- Department of Health Research, Ministry of Health & Family Welfare, Government of India, New Delhi, India
| | - Mandeep Chadha
- Influenza Group, ICMR-National Institute of Virology, Pune, India
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Sharma V, Sharma M, Dhull D, Kaushik S, Kaushik S. Phylogenetic analysis of the hemagglutinin gene of influenza A(H1N1)pdm09 and A(H3N2) virus isolates from Haryana, India. Virusdisease 2019; 30:336-343. [DOI: 10.1007/s13337-019-00532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/03/2019] [Indexed: 10/26/2022] Open
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Alam A, Taye N, Patel S, Thube M, Mullick J, Shah VK, Pant R, Roychowdhury T, Banerjee N, Chatterjee S, Bhattacharya R, Roy R, Mukhopadhyay A, Mogare D, Chattopadhyay S. SMAR1 favors immunosurveillance of cancer cells by modulating calnexin and MHC I expression. Neoplasia 2019; 21:945-962. [PMID: 31422285 PMCID: PMC6706529 DOI: 10.1016/j.neo.2019.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/17/2019] [Indexed: 01/17/2023] Open
Abstract
Down-regulation or loss of MHC class I expression is a major mechanism used by cancer cells to evade immunosurveillance and increase their oncogenic potential. MHC I mediated antigen presentation is a complex regulatory process, controlled by antigen processing machinery (APM) dictating immune response. Transcriptional regulation of the APM that can modulate gene expression profile and their correlation to MHC I mediated antigen presentation in cancer cells remain enigmatic. Here, we reveal that Scaffold/Matrix-Associated Region 1- binding protein (SMAR1), positively regulates MHC I surface expression by down-regulating calnexin, an important component of antigen processing machinery (APM) in cancer cells. SMAR1, a bonafide MAR binding protein acts as a transcriptional repressor of several oncogenes. It is down-regulated in higher grades of cancers either through proteasomal degradation or through loss of heterozygosity (LOH) at the Chr.16q24.3 locus where the human homolog of SMAR1 (BANP) has been mapped. It binds to a short MAR region of the calnexin promoter forming a repressor complex in association with GATA2 and HDAC1. A reverse correlation between SMAR1 and calnexin was thus observed in SMAR1-LOH cells and also in tissues from breast cancer patients. To further extrapolate our findings, influenza A (H1N1) virus infection assay was performed. Upon viral infection, the levels of SMAR1 significantly increased resulting in reduced calnexin expression and increased MHC I presentation. Taken together, our observations establish that increased expression of SMAR1 in cancers can positively regulate MHC I surface expression thereby leading to higher chances of tumor regression and elimination of cancer cells.
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Affiliation(s)
- Aftab Alam
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Nandaraj Taye
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Sonal Patel
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Milind Thube
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Jayati Mullick
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | - Richa Pant
- National Centre for Cell Science, Pune, Maharashtra, India
| | | | | | | | | | - Rini Roy
- Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | | | - Devraj Mogare
- National Centre for Cell Science, Pune, Maharashtra, India
| | - Samit Chattopadhyay
- National Centre for Cell Science, Pune, Maharashtra, India; Indian Institute of Chemical Biology, Kolkata, India.
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Badar N, Salman M, Aamir UB, Ansari J, Ranjha MA, Khan MA, Ikram A, Nisar N, Mushtaq N, Mirza HA. Evolutionary analysis of influenza A(H1N1)pdm09 during the pandemic and post-pandemic period in Pakistan. J Infect Public Health 2019; 13:407-413. [PMID: 31000492 DOI: 10.1016/j.jiph.2019.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/08/2019] [Accepted: 03/11/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The first case of influenza A(H1N1)pdm09 was detected in Pakistan in June 2009. Since then, it has continued to circulate causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in influenza A(H1N1)pdm09 viruses from 2009 to 2016 and their relevance to the current vaccine viruses. METHODS Respiratory specimens (throat or nasopharyngeal swabs) were collected from patients with influenza-like illness and severe acute respiratory illness. Samples were processed following the protocol of the US Centers for Disease Control and Prevention. Sequencing and phylogenetic analysis of Haemagglutinin and neuraminidase genes were carried out on representative isolates of Pakistan viruses. RESULTS Between January 2009 and February 2016, out of 16,024 samples analysed, 1950 (12%) were positive for influenza A. During the pandemic period (2009-2010), influenza A(H1N1)pdm09 was the dominant strain with 366 out of 808 (45%) total influenza positive cases. In the post-pandemic period (2011-2016), a total of 1078 out of 1911 (56%) cases were positive for influenza A(H1N1)pdm09 with co-circulation of different influenza A subtypes. The Pakistan A(H1N1)pdm09 viruses belonged to two genetic clades: clade 7 in the pandemic period, and clade 7 (2011) and clade 6B (2015) in the post-pandemic period. Sequence analysis of genes coding for surface glycoprotein's of Haemagglutinin and neuraminidase had a high degree of sequence similarity with corresponding genes of regional viruses circulating in South-East Asia. CONCLUSION Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Key substitutions in the receptor binding site and a few changes indicative of virulence were also detected in the post-pandemic strains. Continued monitoring of the viruses is essential for early identification of potential variants of high virulence and their relevance to current vaccine strains.
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Affiliation(s)
- Nazish Badar
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.
| | - Muhammad Salman
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Uzma B Aamir
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Jamil Ansari
- Department of Field Epidemiology & Disease Surveillance Unit, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Muazam A Ranjha
- Department of Field Epidemiology & Disease Surveillance Unit, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Mumtaz A Khan
- Department of Field Epidemiology & Disease Surveillance Unit, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Aamer Ikram
- Executive Director, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Nadia Nisar
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Nighat Mushtaq
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
| | - Hamza A Mirza
- Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan
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Khan A, AlBalwi MA, AlAbdulkareem I, AlMasoud A, AlAsiri A, AlHarbi W, AlSehile F, El-Saed A, Balkhy HH. Atypical influenza A(H1N1)pdm09 strains caused an influenza virus outbreak in Saudi Arabia during the 2009-2011 pandemic season. J Infect Public Health 2019; 12:557-567. [PMID: 30799182 DOI: 10.1016/j.jiph.2019.01.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/22/2019] [Accepted: 01/30/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The triple assortment influenza A(H1N1) virus emerged in spring 2009 and disseminated worldwide, including Saudi Arabia. This study was carried out to characterize Saudi influenza isolates in relation to the global strains and to evaluate the potential role of mutated residues in transmission, adaptation, and the pathogenicity of the virus. METHODS Nasopharyngeal samples (n = 6492) collected between September 2009 to March 2011 from patients with influenza-like illness were screened by PCR for influenza A(H1N1). Phylogenetic and Molecular evolutionary analysis were carried out to place the Saudi strains in relation to the global strains followed by Mutation analysis of surface and internal proteins. RESULTS Concatenated whole-genome phylogenetic analysis along with hemagglutinin (HA) signature changes, that is, Aspartic Acid (D) at position 187, P83S, S203T, and R223Q confirmed that the Saudi strains belong to the antigenic category of A/California/07/2009. However, phylogenetic analysis revealed unusual strains of A(H1N1) circulating in Saudi Arabia, not belonging to any of known clades, appearing in five distinct groups well supported by group-specific mutations and novel mutation complexes. These cases had characteristic inter- and intragroup substitution patterns while few of their closest matches showed up as sporadic cases the world over. Specific mutation patterns were detected within the functional domains of internal proteins PB2, PB1, PA, NP, NS1, and M2 having a putative role in viral fitness and virulence. Bayesian coalescent MCMC analysis revealed that Saudi strains belonged to cluster 2 of A(H1N1)pdm09 and spread a month later as compared to other strains of this cluster. CONCLUSION Influenza outbreak in Saudi Arabia during 2009-2011 was caused by atypical strains of influenza A(H1N1)pdm09, probably introduced in this community on multiple occasions. To understand the antigenic significance of these novel point mutations and mutation complexes require functional studies, which will be crucial for risk assessment of emergent strains and defining infection control measures.
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Affiliation(s)
- Anis Khan
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammed A AlBalwi
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; Department of Pathology & Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Ibraheem AlAbdulkareem
- Intramural health sciences research, Princess Nourah Bint Abdulrahman university, Riyadh, Saudi Arabia
| | - Abdulrahman AlMasoud
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulrahman AlAsiri
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Wardah AlHarbi
- Department of Medical Genomics Research, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Faisal AlSehile
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Aiman El-Saed
- Department of Infection Prevention & Control Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Hanan H Balkhy
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia; Department of Infection Prevention & Control Department, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
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Koul PA, Potdar V, Showkat M, Mir H, Chadha MS. Influenza B in a temperate region of northern India 2010-2016: co-circulation of the two lineages with northern hemispherical seasonality. Virusdisease 2018; 29:553-559. [PMID: 30539062 DOI: 10.1007/s13337-018-0487-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/10/2018] [Indexed: 11/29/2022] Open
Abstract
Scant data exist about the epidemiology of influenza B in India. We set out to address the epidemiology of influenza B in a temperate region of northern India from 2010 to 2016. Outpatient and inpatient surveillance was conducted in patients presenting with acute respiratory infection in a northern Indian hospital from September 2010 till April 2016. After recording clinical data, combined nasal/throat swabs were collected and tested for influenza viruses by real time RT-PCR. Influenza A viruses were further subtyped into A/H3N2 and A/H1N1 whereas influenza B were differentiated into B/Yamagata and B/Victoria. Virus isolation, haemaggglutination inhibition testing, sequencing and phylogenetic analysis was carried out on representative samples. Of the 6879 recruited cases, influenza B was detected in 299 (4.3%). The patients presented with respiratory symptoms of varying duration; cough, fever and nasal discharge being the most common. The peaking of the activity of the circulation showed a correlation with the onset of the winter with reduced temperatures and high dry humidity. B/Victoria lineage was detected in 35.4% (n = 106/299) whereas 53.8% (n = 161/299) were B/Yamagata. The circulation in each season was dominated by one lineage which correlated with the vaccine strain, but up to 37% consisted of a different lineage. We conclude that Influenza B exhibits a northern hemispherical seasonality in temperate northern India with co-circulation of the 2 lineages of influenza B. These findings have relevance for vaccine effectiveness and argue for vaccination with a quadrivalent influenza vaccine.
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Affiliation(s)
- Parvaiz A Koul
- 1Influenza Laboratory, Department of Internal and Pulmonary Medicine, Sheri Kashmir Institute of Medical Sciences, Srinagar, J&K 190011 India
| | - Varsha Potdar
- 2National Institute of Virology, Pune, Mahrashtra India
| | - Masooma Showkat
- 1Influenza Laboratory, Department of Internal and Pulmonary Medicine, Sheri Kashmir Institute of Medical Sciences, Srinagar, J&K 190011 India
| | - Hyder Mir
- 1Influenza Laboratory, Department of Internal and Pulmonary Medicine, Sheri Kashmir Institute of Medical Sciences, Srinagar, J&K 190011 India
| | - M S Chadha
- 2National Institute of Virology, Pune, Mahrashtra India
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15
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Comparative In Vitro and In Vivo Analysis of H1N1 and H1N2 Variant Influenza Viruses Isolated from Humans between 2011 and 2016. J Virol 2018; 92:JVI.01444-18. [PMID: 30158292 DOI: 10.1128/jvi.01444-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 08/23/2018] [Indexed: 01/08/2023] Open
Abstract
Influenza A virus pandemics are rare events caused by novel viruses which have the ability to spread in susceptible human populations. With respect to H1 subtype viruses, swine H1N1 and H1N2 viruses occasionally cross the species barrier to cause human infection. Recently isolated from humans (termed variants), swine viruses were shown to display great genetic and antigenic diversity, hence posing considerable public health risk. Here, we utilized in vitro and in vivo approaches to provide characterization of H1 subtype variant viruses isolated since the 2009 pandemic and discuss the findings in context with previously studied H1 subtype human isolates. The variant viruses were well adapted to replicate in the human respiratory cell line Calu-3 and the respiratory tracts of mice and ferrets. However, with respect to hemagglutinin (HA) activation pH, the variant viruses had fusion pH thresholds closer to that of most classical swine and triple-reassortant H1 isolates rather than viruses that had adapted to humans. Consistent with previous observations for swine isolates, the tested variant viruses were capable of efficient transmission between cohoused ferrets but could transmit via respiratory droplets to differing degrees. Overall, this investigation demonstrates that swine H1 viruses that infected humans possess adaptations required for robust replication and, in some cases, efficient respiratory droplet transmission in a mammalian model and therefore need to be closely monitored for additional molecular changes that could facilitate transmission among humans. This work highlights the need for risk assessments of emerging H1 viruses as they continue to evolve and cause human infections.IMPORTANCE Influenza A virus is a continuously evolving respiratory pathogen. Endemic in swine, H1 and H3 subtype viruses sporadically cause human infections. As each zoonotic infection represents an opportunity for human adaptation, the emergence of a transmissible influenza virus to which there is little or no preexisting immunity is an ongoing threat to public health. Recently isolated variant H1 subtype viruses were shown to display extensive genetic diversity and in many instances were antigenically distinct from seasonal vaccine strains. In this study, we provide characterization of representative H1N1v and H1N2v viruses isolated since the 2009 pandemic. Our results show that although recent variant H1 viruses possess some adaptation markers of concern, these viruses have not fully adapted to humans and require further adaptation to present a pandemic threat. This investigation highlights the need for close monitoring of emerging variant influenza viruses for molecular changes that could facilitate efficient transmission among humans.
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Mohebbi A, Fotouhi F, Jamali A, Yaghobi R, Farahmand B, Mohebbi R. Molecular epidemiology of the hemagglutinin gene of prevalent influenza virus A/H1N1/pdm09 among patient in Iran. Virus Res 2018; 259:38-45. [PMID: 30336188 DOI: 10.1016/j.virusres.2018.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/01/2018] [Accepted: 10/02/2018] [Indexed: 11/17/2022]
Abstract
In 2015, the influenza virus A/H1N1/pdm09 strain outbreak became prevalent throughout the different provinces of Iran. There are relatively limited complete genetic sequences available for this virus from Asian countries. Diagnosis and virological surveillance of influenza is essential for detecting novel genetic variants causing epidemic potential. This study describes the genetic properties of HA genome of influenza A/H1N1 pdm09 viruses circulating in Iran during the 2015/2016 season. In order to investigate the genetic pattern of influenza A/H1N1 pdm09, a total of 1758 nasopharyngeal swabs were screened by real-time RT-PCR. Of those, 510 cases were found to be positive for A/H1N1/pdm09 virus. Evolution of the approximately 100 positive specimens with high virus load was conducted via genomic phylogeny. Phylogenetic analysis of the HA genes of the A/H1N1pdm09 viruses revealed the circulation of clade 6B1, characterized by amino acid substitutions S84N, S162N and I216T, where position 162 became glycosylated. The N-glycosylation of HA protein is post or co-translational modification that affect the evolution of influenza viruses. For influenza A(H1N1) pdm09 viruses, we found more mutations in the antigenic sites than in the stem region. The results of this study confirmed the necessity of constant regular antigenic and molecular surveillance of circulating seasonal influenza viruses.
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Affiliation(s)
- Atefeh Mohebbi
- Department of Microbiology, College of Science Agriculture and Modern Technology, Shiraz Branch, Islamic Azad University, Shiraz, Iran.
| | - Fatemeh Fotouhi
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Abbas Jamali
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Ramin Yaghobi
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Behrokh Farahmand
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.
| | - Reza Mohebbi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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17
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Liu J, Gong LF, Xu YC, Sun ZL, Gao Q, Dong ZJ. Genetic and antigenic characterization of influenza A(H1N1)pdm09 in Yantai, China, during the 2009-2017 influenza season. J Med Virol 2018; 91:351-360. [DOI: 10.1002/jmv.25328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Juan Liu
- Yantai Center for Disease Control and Prevention; China
| | | | - Ying-chun Xu
- Yantai Center for Disease Control and Prevention; China
| | - Zhen-lu Sun
- Yantai Center for Disease Control and Prevention; China
| | - Qiao Gao
- Yantai Center for Disease Control and Prevention; China
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18
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Koul P, Potdar V, Mir H, Chadha M. The 2015 Outbreak of Severe Influenza in Kashmir, North India: Emergence of a New Clade of A/H1n1 Influenza Virus. PLOS CURRENTS 2018; 10. [PMID: 30245911 PMCID: PMC6122875 DOI: 10.1371/currents.outbreaks.519e170f2740fabd4ccd1642ff533364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Introduction: Following the initial outbreak of A/H1N1pdm09, periodic resurgences of the virus, with variable morbidity and mortality, have been reported from various parts of India including the temperate Kashmir region of northern India. An outbreak of A/H1N1 was reported in early 2015 across India with a high morbidity and mortality. We studied patients during the outbreak in Kashmir. Methods: Patients (n=1780, age 1 month to 90 years, median 35 years) presenting with acute respiratory illness to a tertiary care hospital in Srinagar, Kashmir from October 2014 to April 2015 were recruited. After clinical data recording, combined throat and nasal swabs were collected in viral transport medium and tested by real-time RT-PCR for influenza viruses. All influenza A positive samples were further subtyped using primers and probes for A/H1N1pdm09 and A/H3 whereas influenza B samples were further subtyped into B/Yamagata and B/Victoria lineages. Virus isolation, hemagglutination inhibition testing, sequencing and phylogenetic analysis was carried out using standard procedures. Testing for H275Y mutation was done to determine sensitivity to oseltamivir. All patients received symptomatic therapy and influenza positive patients were administered oseltamivir. Results: Of the 1780 patients, 540 (30%) required hospitalization and 533 tested positive for influenza [influenza A=517(A/H1N1pdm09=437, A/H3N2=78 with co-infection of both in 2 cases); influenza B=16 (B/Yamgata=15)]. About 14% (n=254) had been vaccinated against influenza, having received the NH 2014-15 vaccine, 27 (11.3%) of these testing positive for influenza. Sixteen patients, including 4 pregnant females, died due to multi-organ failure. HA sequencing depicted that 2015 isolates belonged to Clade 6B.1. No H275Y mutation was reported from A/H1N1 positives. Conclusion: Resurgent outbreak of A/H1N1pdm09, with emergence of clade 6B.1, in 2014-15 resulted in high rate of hospitalizations, morbidity and mortality. Periodic resurgences and appearance of mutants emphasize continued surveillance so as to identify newer mutations with potential for outbreaks and severe outcomes.
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Affiliation(s)
- Parvaiz Koul
- Internal & Pulmonary Medicine, Sheri Kashmir Institute of Medical Sciences, Srinagar, J&K, India
| | | | - Hyder Mir
- Internal & Pulmonary Medicine, Sheri Kashmir Institute of Medical Sciences, Srinagar, J&K, India
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Sahu M, Singh N, Shukla MK, Potdar VA, Sharma RK, Sahare LK, Ukey MJ, Barde PV. Molecular and epidemiological analysis of pandemic and post-pandemic influenza A(H1N1)pdm09 virus from central India. J Med Virol 2017; 90:447-455. [PMID: 29073730 DOI: 10.1002/jmv.24982] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/24/2017] [Indexed: 02/05/2023]
Abstract
Influenza A(H1N1)pdm09 virus pandemic struck India in 2009 and continues to cause outbreaks in its post-pandemic phase. Diminutive information is available about influenza A(H1N1)pdm09 from central India. This observational study presents epidemiological and molecular findings for the period of 6 years. Throat swab samples referred from districts of Madhya Pradesh were subjected to diagnosis of influenza A(H1N1)pdm09 following WHO guidelines. Clinical and epidemiological data were recorded and analyzed. Hemagglutinin (HA) gene sequencing and phylogenetic analysis were performed. The H275Y mutation responsible for antiviral resistance was tested using allelic real-time RT-PCR. Out of 7365 tested samples, 2406 (32.7%) were positive for influenza A(H1N1)pdm09, of which 363 (15.08%) succumbed to infection. Significant trends were observed in positivity (χ2 = 50.8; P < 0.001) and mortality (χ2 = 24.4; P < 0.001) with increasing age. Mutations having clinical and epidemiological importance were detected. Phylogenetic analysis of HA gene sequences revealed that clade 7, 6A, and 6B viruses were in circulation. Oseltamivir resistance was detected in three fatal cases. Influenza A(H1N1)pdm09 viruses having genetic diversity were detected from central India and continues to be a concern for public health. This study highlights the need of year-round monitoring by establishment of strong molecular and clinical surveillance program.
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Affiliation(s)
- Mahima Sahu
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Neeru Singh
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Mohan K Shukla
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | | | - Ravendra K Sharma
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Lalit Kumar Sahare
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Mahendra J Ukey
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
| | - Pradip V Barde
- National Institute for Research in Tribal Health (NIRTH), ICMR, Jabalpur, Madhya Prdesh, India
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20
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The high frequency of non-aspartic acid residues at HA222 in influenza A(H1N1) 2009 pandemic viruses is associated with mortality during the upsurge of 2015: a molecular and epidemiological study from central India. Epidemiol Infect 2017; 145:2656-2665. [DOI: 10.1017/s0950268817001595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
SUMMARYInfluenza A(H1N1) viruses of the 2009 pandemic (A(H1N1)pdm09) continue to cause outbreaks in the post-pandemic period. During January to May 2015, an upsurge of influenza was recorded that resulted in high fatality in central India. Genetic lineage, mutations in the hemagglutinin (HA) gene and infection by quasi-species are reported to affect disease severity. The objective of this study is to present the molecular and epidemiological trends during the 2015 influenza outbreak in central India. All the referred samples were subjected to qRT–PCR for diagnosis. HA gene sequencing (23 survivors and 24 non-survivors) and cloning were performed and analyzed using Molecular Evolutionary Genomic Analyzer (MEGA 5·05). Of the 3625 tested samples, 1607 (44·3%) were positive for influenza A(H1N1)pdm09, of which 228 (14·2%) individuals succumbed to death. A significant trend was observed in positivity (P = 0·003) and mortality (P < 0·0001) with increasing age. The circulating A(H1N1)pdm09 virus was characterized as belonging to clade-6B. Clinically significant mutations were detected. Patients infected with the quasi-species of the virus had a greater risk of death (P = 0·009). This study proposes a robust molecular and clinical surveillance program for the detection and characterization of the virus, along with prompt treatment protocols to prevent outbreaks.
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Genetic Characterization of Influenza A (H1N1) Pandemic 2009 Virus Isolates from Mumbai. Curr Microbiol 2017; 74:899-907. [DOI: 10.1007/s00284-017-1262-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/06/2017] [Indexed: 10/19/2022]
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Rattan A, Pawar SD, Nawadkar R, Kulkarni N, Lal G, Mullick J, Sahu A. Synergy between the classical and alternative pathways of complement is essential for conferring effective protection against the pandemic influenza A(H1N1) 2009 virus infection. PLoS Pathog 2017; 13:e1006248. [PMID: 28301559 PMCID: PMC5354441 DOI: 10.1371/journal.ppat.1006248] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 02/17/2017] [Indexed: 12/22/2022] Open
Abstract
The pandemic influenza A(H1N1) 2009 virus caused significant morbidity and mortality worldwide thus necessitating the need to understand the host factors that influence its control. Previously, the complement system has been shown to provide protection during the seasonal influenza virus infection, however, the role of individual complement pathways is not yet clear. Here, we have dissected the role of intact complement as well as of its individual activation pathways during the pandemic influenza virus infection using mouse strains deficient in various complement components. We show that the virus infection in C3-/- mice results in increased viral load and 100% mortality, which can be reversed by adoptive transfer of naïve wild-type (WT) splenocytes, purified splenic B cells, or passive transfer of immune sera from WT, but not C3-/- mice. Blocking of C3a and/or C5a receptor signaling in WT mice using receptor antagonists and use of C3aR-/- and C5aR-/- mice showed significant mortality after blocking/ablation of C3aR, with little or no effect after blocking/ablation of C5aR. Intriguingly, deficiency of C4 and FB in mice resulted in only partial mortality (24%-32%) suggesting a necessary cross-talk between the classical/lectin and alternative pathways for providing effective protection. In vitro virus neutralization experiments performed to probe the cross-talk between the various pathways indicated that activation of the classical and alternative pathways in concert, owing to coating of viral surface by antibodies, is needed for its efficient neutralization. Examination of the virus-specific complement-binding antibodies in virus positive subjects showed that their levels vary among individuals. Together these results indicate that cooperation between the classical and alternative pathways not only result in efficient direct neutralization of the pandemic influenza virus, but also lead to the optimum generation of C3a, which when sensed by the immune cells along with the antigen culminates in generation of effective protective immune responses. The pandemic influenza A(H1N1) 2009 virus is now circulating seasonally and causing a significant disease burden worldwide. Hence, it is important to delineate the immune components required for protection against its infection. Here we demonstrate that presence of intact complement is essential for clearing the pandemic influenza virus infection, wherein complement synthesized by B cells plays a major role. Further, we show that activation of the classical as well as alternative pathways is a requisite for efficient neutralization of the virus as well as the optimum generation of C3a, which is necessary for boosting the protective immune responses. Our results thus reveal that deficiencies of components of the classical and alternative pathways enhance the susceptibility to and severity of the pandemic influenza virus infection.
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Affiliation(s)
- Ajitanuj Rattan
- National Centre for Cell Science, S. P. Pune University Campus, Ganeshkhind, Pune, India
| | - Shailesh D. Pawar
- Microbial Containment Complex, National Institute of Virology, Pune, India
| | - Renuka Nawadkar
- National Centre for Cell Science, S. P. Pune University Campus, Ganeshkhind, Pune, India
| | - Neeraja Kulkarni
- National Centre for Cell Science, S. P. Pune University Campus, Ganeshkhind, Pune, India
| | - Girdhari Lal
- National Centre for Cell Science, S. P. Pune University Campus, Ganeshkhind, Pune, India
| | - Jayati Mullick
- Microbial Containment Complex, National Institute of Virology, Pune, India
| | - Arvind Sahu
- National Centre for Cell Science, S. P. Pune University Campus, Ganeshkhind, Pune, India
- * E-mail:
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Liu T, Li Z, Lin Y, Song S, Zhang S, Sun L, Wang Y, Xu A, Bi Z, Wang X. Dynamic patterns of circulating influenza virus from 2005 to 2012 in Shandong Province, China. Arch Virol 2016; 161:3047-59. [PMID: 27515172 DOI: 10.1007/s00705-016-2997-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 07/26/2016] [Indexed: 11/25/2022]
Abstract
To identify circulating emerging/reemerging viral strains and epidemiological trends, an influenza sentinel surveillance network was established in Shandong Province, China, in 2005. Nasal and/or throat swabs from patients with influenza-like-illness were collected at sentinel hospitals. Influenza viruses were detected by reverse transcription polymerase chain reaction (RT-PCR) or virus isolation. From October 2005 to March 2012, 7763 (21.44 %) of 36,209 swab samples were positive for influenza viruses, including 5221 (67.25 %) influenza A and 2542 (32.75 %) influenza B. While the influenza viruses were detected year-round, their type/subtype distribution varied significantly. Peak influenza activity was observed from November to February. The proportion of laboratory-confirmed influenza cases was highest among participants aged 0-4 years (14.97 %) in the 2005-2009 and 2010-2012 influenza seasons and the positivity rate of influenza A(H1N1)pdm09 was highest in the 15 to 24 year age group during the 2009-2010 influenza season. Genetic analysis of hemagglutinin (HA) and neuraminidase (NA) genes revealed that the viruses matched seasonal influenza vaccine strains in general, with some amino acid mutations. Influenza A(H1N1)pdm09 strains isolated in Shandong Province were characterized by an S203T mutation that is specific to clade 7 isolates. This report illustrates that the Shandong Provincial influenza surveillance system was sensitive in detecting influenza virus variability by season and by genetic composition. This system will help official public health target interventions such as education programs and vaccines.
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Affiliation(s)
- Ti Liu
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Zhong Li
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Yi Lin
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Shaoxia Song
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Shengyang Zhang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Lin Sun
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Yulu Wang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Aiqiang Xu
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China
| | - Zhenqiang Bi
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China.
| | - Xianjun Wang
- Shandong Center for Disease Control and Prevention, Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Institute for Prevention Medicine, Shandong University, Jinan, 250014, Shandong, China.
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Whole genome characterization of human influenza A(H1N1)pdm09 viruses isolated from Kenya during the 2009 pandemic. INFECTION GENETICS AND EVOLUTION 2016; 40:98-103. [DOI: 10.1016/j.meegid.2016.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/16/2016] [Accepted: 02/23/2016] [Indexed: 11/23/2022]
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25
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Koul PA, Mir H, Bhat MA, Khan UH, Khan MM, Chadha MS, Lal RB. Performance of rapid influenza diagnostic tests (QuickVue) for influenza A and B Infection in India. Indian J Med Microbiol 2015; 33 Suppl:26-31. [PMID: 25657152 DOI: 10.4103/0255-0857.148831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Rapid point-of-care (POC) tests provide an economical alternative for rapid diagnosis and treatment of influenza, especially in public health emergency situations. OBJECTIVES To test the performance of a rapid influenza diagnostic test, QuickVue (Quidel) as a POC test against a real-time polymerase chain reaction (RT-PCR) assay for detection of influenza A and B in a developing country setting. STUDY DESIGN In a prospective observational design, 600 patients with influenza-like illness (ILI) or with severe acute respiratory illness (SARI) who were referred to the Influenza Clinic of a tertiary care hospital in Srinagar, India from September 2012 to April 2013, were enrolled for diagnostic testing for influenza using QuickVue or RT-PCR. All influenza A-positive patients by RT-PCR were further subtyped using primers and probes for A/H1pdm09 and A/H3. RESULTS Of the 600 patients, 186 tested positive for influenza A or B by RT-PCR (90 A/H1N1pdm09, 7 A/H3 and 89 influenza B), whereas only 43 tested positive for influenza (influenza A=22 and influenza B=21) by QuickVue. Thus, the sensitivity of the QuickVue was only 23% (95% confidence interval, CI: 17.3-29.8) and specificity was 100% (95% CI: 99.1-100) with a positive predictive value (PPV) of 100% (95% CI 91.8-100) and a negative predictive value (NPV) of 74.3% (95% CI: 70.5-77.9) as compared to RT-PCR. CONCLUSIONS The high specificity of QuickVue suggest that this POC test can be a useful tool for patient management or triaging during a public health crisis but a low sensitivity suggests that a negative test result need to be further tested using RT-PCR.
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Affiliation(s)
- P A Koul
- Department of Internal and Pulmonary Medicine and MSM Project for Influenza, Sher I Kashmir Institute of Medical Sciences, Soura, Srinagar, Jammu and Kashmir, India
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Resende PC, Motta FC, Born PS, Machado D, Caetano BC, Brown D, Siqueira MM. Phylogenetic analyses of influenza A (H1N1)pdm09 hemagglutinin gene during and after the pandemic event in Brazil. INFECTION GENETICS AND EVOLUTION 2015; 36:147-155. [PMID: 26371065 DOI: 10.1016/j.meegid.2015.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/20/2015] [Accepted: 09/04/2015] [Indexed: 12/17/2022]
Abstract
Pandemic influenza A H1N1 [A(H1N1)pdm09] was first detected in Brazil in May 2009, and spread extensively throughout the country causing a peak of infection during June to August 2009. Since then, it has continued to circulate with a seasonal pattern, causing high rates of morbidity and mortality. Over this period, the virus has continually evolved with the accumulation of new mutations. In this study we analyze the phylogenetic relationship in a collection of 220 A(H1N1)pdm09 hemagglutinin (HA) gene sequences collected during and after the pandemic period (2009 to 2014) in Brazil. In addition, we have looked for evidence of viral polymorphisms associated with severe disease and compared the range of viral variants with the vaccine strain (A/California/7/2009) used throughout this period. The phylogenetic analyses in this study revealed the circulation of at least eight genetic groups in Brazil. Two (G6-pdm and G7-pdm) co-circulated during the pandemic period, showing an early pattern of viral diversification with a low genetic distance from vaccine strain. Other phylogenetic groups, G5, G6 (including 6B, 6C and 6D subgroups), and G7 were found in the subsequent epidemic seasons from 2011 to 2014. These viruses exhibited more amino acid differences from the vaccine strain with several substitutions at the antigenic sites. This is associated with a theoretical decrease in the vaccine efficacy. Furthermore, we observed that the presence of any polymorphism at residue 222 of the HA gene was significantly associated with severe/fatal cases, reinforcing previous reports that described this residue as a potential virulence marker. This study provides new information about the circulation of some viral variants in Brazil, follows up potential genetic markers associated with virulence and allows infer if the efficacy of the current vaccine against more recent A(H1N1)pdm09 strains may be reduced.
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Affiliation(s)
- Paola Cristina Resende
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Fernando Couto Motta
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Priscila Silva Born
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Daniela Machado
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil; Fondation Mérieux, Emerging Pathogens Laboratory, Centre International de Recherche en Infectologie (CIRI), Lyon, France
| | - Braulia Costa Caetano
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - David Brown
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Marilda Mendonça Siqueira
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
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27
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Koul PA, Broor S, Saha S, Barnes J, Smith C, Shaw M, Chadha M, Lal RB. Differences in influenza seasonality by latitude, northern India. Emerg Infect Dis 2015; 20:1723-6. [PMID: 25279651 PMCID: PMC4193176 DOI: 10.3201/eid2010.140431] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The seasonality of influenza in the tropics complicates vaccination timing. We investigated influenza seasonality in northern India and found influenza positivity peaked in Srinagar (34.09°N) in January–March but peaked in New Delhi (28.66°N) in July–September. Srinagar should consider influenza vaccination in October–November, but New Delhi should vaccinate in May–June.
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28
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Carbone V, Schneider EK, Rockman S, Baker M, Huang JX, Ong C, Cooper MA, Yuriev E, Li J, Velkov T. Molecular Characterisation of the Haemagglutinin Glycan-Binding Specificity of Egg-Adapted Vaccine Strains of the Pandemic 2009 H1N1 Swine Influenza A Virus. Molecules 2015; 20:10415-34. [PMID: 26056814 PMCID: PMC6272818 DOI: 10.3390/molecules200610415] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/01/2015] [Indexed: 12/14/2022] Open
Abstract
The haemagglutinin (HA) glycan binding selectivity of H1N1 influenza viruses is an important determinant for the host range of the virus and egg-adaption during vaccine production. This study integrates glycan binding data with structure-recognition models to examine the impact of the K123N, D225G and Q226R mutations (as seen in the HA of vaccine strains of the pandemic 2009 H1N1 swine influenza A virus). The glycan-binding selectivity of three A/California/07/09 vaccine production strains, and purified recombinant A/California/07/09 HAs harboring these mutations was examined via a solid-phase ELISA assay. Wild-type A/California/07/09 recombinant HA bound specifically to α2,6-linked sialyl-glycans, with no affinity for the α2,3-linked sialyl-glycans in the array. In contrast, the vaccine virus strains and recombinant HA harboring the Q226R HA mutation displayed a comparable pattern of highly specific binding to α2,3-linked sialyl-glycans, with a negligible affinity for α2,6-linked sialyl-glycans. The D225G A/California/07/09 recombinant HA displayed an enhanced binding affinity for both α2,6- and α2,3-linked sialyl-glycans in the array. Notably its α2,6-glycan affinity was generally higher compared to its α2,3-glycan affinity, which may explain why the double mutant was not naturally selected during egg-adaption of the virus. The K123N mutation which introduces a glycosylation site proximal to the receptor binding site, did not impact the α2,3/α2,6 glycan selectivity, however, it lowered the overall glycan binding affinity of the HA; suggesting glycosylation may interfere with receptor binding. Docking models and 'per residues' scoring were employed to provide a structure-recognition rational for the experimental glycan binding data. Collectively, the glycan binding data inform future vaccine design strategies to introduce the D225G or Q226R amino acid substitutions into recombinant H1N1 viruses.
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Affiliation(s)
- Vincenzo Carbone
- AgResearch Limited, Grasslands Research Centre, Tennent Drive, Private Bag 11008, Palmerston North 4442, New Zealand.
| | - Elena K Schneider
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia.
| | - Steve Rockman
- CSL Limited Poplar Road, Parkville 3052, Victoria, Australia.
| | - Mark Baker
- Priority Research Centre in Reproductive Science, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia.
| | - Johnny X Huang
- Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road St Lucia, QLD 4072, Brisbane, Australia.
| | - Chi Ong
- CSL Limited Poplar Road, Parkville 3052, Victoria, Australia.
| | - Matthew A Cooper
- Institute for Molecular Bioscience, University of Queensland, 306 Carmody Road St Lucia, QLD 4072, Brisbane, Australia.
| | - Elizabeth Yuriev
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia.
| | - Jian Li
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia.
| | - Tony Velkov
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria, Australia.
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Chadha MS, Potdar VA, Saha S, Koul PA, Broor S, Dar L, Chawla-Sarkar M, Biswas D, Gunasekaran P, Abraham AM, Shrikhande S, Jain A, Anukumar B, Lal RB, Mishra AC. Dynamics of influenza seasonality at sub-regional levels in India and implications for vaccination timing. PLoS One 2015; 10:e0124122. [PMID: 25938466 PMCID: PMC4418715 DOI: 10.1371/journal.pone.0124122] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/26/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Influenza surveillance is an important tool to identify emerging/reemerging strains, and defining seasonality. We describe the distinct patterns of circulating strains of the virus in different areas in India from 2009 to 2013. METHODS Patients in ten cities presenting with influenza like illness in out-patient departments of dispensaries/hospitals and hospitalized patients with severe acute respiratory infections were enrolled. Nasopharangeal swabs were tested for influenza viruses by real-time RT-PCR, and subtyping; antigenic and genetic analysis were carried out using standard assays. RESULTS Of the 44,127 ILI/SARI cases, 6,193 (14.0%) were positive for influenza virus. Peaks of influenza were observed during July-September coinciding with monsoon in cities Delhi and Lucknow (north), Pune (west), Allaphuza (southwest), Nagpur (central), Kolkata (east) and Dibrugarh (northeast), whereas Chennai and Vellore (southeast) revealed peaks in October-November, coinciding with the monsoon months in these cities. In Srinagar (Northern most city at 34°N latitude) influenza circulation peaked in January-March in winter months. The patterns of circulating strains varied over the years: whereas A/H1N1pdm09 and type B co-circulated in 2009 and 2010, H3N2 was the predominant circulating strain in 2011, followed by circulation of A/H1N1pdm09 and influenza B in 2012 and return of A/H3N2 in 2013. Antigenic analysis revealed that most circulating viruses were close to vaccine selected viral strains. CONCLUSIONS Our data shows that India, though physically located in northern hemisphere, has distinct seasonality that might be related to latitude and environmental factors. While cities with temperate seasonality will benefit from vaccination in September-October, cities with peaks in the monsoon season in July-September will benefit from vaccination in April-May. Continued surveillance is critical to understand regional differences in influenza seasonality at regional and sub-regional level, especially in countries with large latitude span.
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Affiliation(s)
| | | | | | - Parvaiz A. Koul
- Sheri-Kashmir Institute of Medical Sciences, Srinagar, India
| | - Shobha Broor
- All India Institute of Medical Sciences, New Delhi, India
| | - Lalit Dar
- All India Institute of Medical Sciences, New Delhi, India
| | | | | | | | | | | | - Amita Jain
- King George Medical University (KGMU), Lucknow, India
| | | | - Renu B. Lal
- Centers for Disease Control and Prevention, Atlanta, USA
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Neumann G, Kawaoka Y. Transmission of influenza A viruses. Virology 2015; 479-480:234-46. [PMID: 25812763 PMCID: PMC4424116 DOI: 10.1016/j.virol.2015.03.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 02/10/2015] [Accepted: 03/02/2015] [Indexed: 12/25/2022]
Abstract
Influenza A viruses cause respiratory infections that range from asymptomatic to deadly in humans. Widespread outbreaks (pandemics) are attributable to 'novel' viruses that possess a viral hemagglutinin (HA) gene to which humans lack immunity. After a pandemic, these novel viruses form stable virus lineages in humans and circulate until they are replaced by other novel viruses. The factors and mechanisms that facilitate virus transmission among hosts and the establishment of novel lineages are not completely understood, but the HA and basic polymerase 2 (PB2) proteins are thought to play essential roles in these processes by enabling avian influenza viruses to infect mammals and replicate efficiently in their new host. Here, we summarize our current knowledge of the contributions of HA, PB2, and other viral components to virus transmission and the formation of new virus lineages.
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Affiliation(s)
- Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, 575 Science Drive, Madison, WI 53711, USA; Division of Virology, Department of Microbiology and Immunology and International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
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31
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Jain A, Dangi T, Jain B, Singh AK, Singh JV, Kumar R. Genetic changes in influenza A(H3N2) viruses circulating during 2011 to 2013 in northern India (Lucknow). J Med Virol 2015; 87:1268-75. [PMID: 25914198 DOI: 10.1002/jmv.24096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2014] [Indexed: 11/07/2022]
Abstract
Genetic variability in the hemagglutinin (HA1) and the neuraminidase (NA) genes of influenza viruses results in the emergence of new strains which differ in pathogenicity and severity. The present study was undertaken for genotypic characterization of the HA1 and NA genes of the influenza A(H3N2) strains, detected during the 2011-2013. A total of fifty five influenza A(H3N2) positive samples [2011 (n = 20), 2012 (n = 4) and 2013 (n = 31)] were studied. The 824 bp segment of HA1 gene and 931 bp segment of NA gene were amplified and sequenced by Big-Dye terminator kit on ABI3130, Genetic analyzer. Molecular and phylogenetic analysis was done by MEGA 5.05 software and PhyML program (v3.0). Mutations were determined by comparing the deduced amino acid sequences of study strains with that of 2009-2013 vaccine strains. The studied influenza A(H3N2) strains showed 98.1-99.6% similarity in HA1 and NA amino acid sequences with the influenza A/Victoria/361/2011 vaccine strain. Four mutations in the HA1 amino acid sequences (T128A, R142G, L157S and N278K) and three unique mutations in the NA amino acid sequences [D251V, S315G and V313A] were found. These mutations were observed only in strains from the year 2013 (cluster II). None of the strains showed the presence of mutations, N294S and R292K, markers of oseltamivir resistance. In conclusion, Lucknow strains have accumulated the significant number of mutations in the antigenic sites of the HA and the NA coding sequences and continue to be evolving from the 2013 vaccine strain [A/Victoria/361/2011], however, mutations specific for oseltamivir resistance were not detected.
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Affiliation(s)
- Amita Jain
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Tanushree Dangi
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Bhawana Jain
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - Ajay Kumar Singh
- Department of Microbiology, King George's Medical University, Lucknow, India
| | - J V Singh
- Department of Community, Medicine King George's Medical University, Lucknow, India
| | - Rashmi Kumar
- Department of Paediatrics, King George's Medical University, Lucknow, India
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32
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Horm SV, Mardy S, Rith S, Ly S, Heng S, Vong S, Kitsutani P, Ieng V, Tarantola A, Ly S, Sar B, Chea N, Sokhal B, Barr I, Kelso A, Horwood PF, Timmermans A, Hurt A, Lon C, Saunders D, Ung SA, Asgari N, Roces MC, Touch S, Komadina N, Buchy P. Epidemiological and virological characteristics of influenza viruses circulating in Cambodia from 2009 to 2011. PLoS One 2014; 9:e110713. [PMID: 25340711 PMCID: PMC4207757 DOI: 10.1371/journal.pone.0110713] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/16/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The Cambodian National Influenza Center (NIC) monitored and characterized circulating influenza strains from 2009 to 2011. METHODOLOGY/PRINCIPAL FINDINGS Sentinel and study sites collected nasopharyngeal specimens for diagnostic detection, virus isolation, antigenic characterization, sequencing and antiviral susceptibility analysis from patients who fulfilled case definitions for influenza-like illness, acute lower respiratory infections and event-based surveillance. Each year in Cambodia, influenza viruses were detected mainly from June to November, during the rainy season. Antigenic analysis show that A/H1N1pdm09 isolates belonged to the A/California/7/2009-like group. Circulating A/H3N2 strains were A/Brisbane/10/2007-like in 2009 before drifting to A/Perth/16/2009-like in 2010 and 2011. The Cambodian influenza B isolates from 2009 to 2011 all belonged to the B/Victoria lineage represented by the vaccine strains B/Brisbane/60/2008 and B/Malaysia/2506/2004. Sequences of the M2 gene obtained from representative 2009-2011 A/H3N2 and A/H1N1pdm09 strains all contained the S31N mutation associated with adamantanes resistance except for one A/H1N1pdm09 strain isolated in 2011 that lacked this mutation. No reduction in the susceptibility to neuraminidase inhibitors was observed among the influenza viruses circulating from 2009 to 2011. Phylogenetic analysis revealed that A/H3N2 strains clustered each year to a distinct group while most A/H1N1pdm09 isolates belonged to the S203T clade. CONCLUSIONS/SIGNIFICANCE In Cambodia, from 2009 to 2011, influenza activity occurred throughout the year with peak seasonality during the rainy season from June to November. Seasonal influenza epidemics were due to multiple genetically distinct viruses, even though all of the isolates were antigenically similar to the reference vaccine strains. The drug susceptibility profile of Cambodian influenza strains revealed that neuraminidase inhibitors would be the drug of choice for influenza treatment and chemoprophylaxis in Cambodia, as adamantanes are no longer expected to be effective.
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MESH Headings
- Animals
- Antigens, Viral/immunology
- Cambodia/epidemiology
- Dogs
- Drug Resistance, Viral
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Humans
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/isolation & purification
- Influenza A Virus, H3N2 Subtype/genetics
- Influenza A Virus, H3N2 Subtype/isolation & purification
- Influenza B virus/genetics
- Influenza B virus/isolation & purification
- Influenza Vaccines/immunology
- Influenza, Human/epidemiology
- Influenza, Human/immunology
- Influenza, Human/virology
- Madin Darby Canine Kidney Cells
- Orthomyxoviridae/immunology
- Orthomyxoviridae/isolation & purification
- Orthomyxoviridae/physiology
- Phylogeny
- Seasons
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Affiliation(s)
- Srey Viseth Horm
- Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Sek Mardy
- Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
- World Health Organization, Phnom Penh, Cambodia
| | - Sareth Rith
- Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Sovann Ly
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Seng Heng
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Sirenda Vong
- Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Paul Kitsutani
- Influenza Division, National Center for Immunization and Respiratory Disease, Center for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Vannra Ieng
- World Health Organization, Phnom Penh, Cambodia
| | - Arnaud Tarantola
- Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Sowath Ly
- Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Borann Sar
- Centers for Disease Control and Prevention, Cambodia Office, Phnom Penh, Cambodia
| | - Nora Chea
- Centers for Disease Control and Prevention, Cambodia Office, Phnom Penh, Cambodia
| | - Buth Sokhal
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Ian Barr
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
| | - Anne Kelso
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
| | - Paul F. Horwood
- Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
| | - Ans Timmermans
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Aeron Hurt
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - David Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Sam An Ung
- National Institute of Public Health, Phnom Penh, Cambodia
| | - Nima Asgari
- World Health Organization, Phnom Penh, Cambodia
| | | | - Sok Touch
- Communicable Disease Control Department, Ministry of Health, Phnom Penh, Cambodia
| | - Naomi Komadina
- WHO Collaborating Centre for Reference and Research on Influenza, Melbourne, Australia
| | - Philippe Buchy
- Institut Pasteur du Cambodge, Réseau International des Instituts Pasteur, Phnom Penh, Cambodia
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Oliveira MJC, Motta FDC, Siqueira MM, Resende PC, Born PDS, Souza TML, Mesquita M, Oliveira MDLA, Carney S, Mello WAD, Magalhães V. Molecular findings from influenza A(H1N1)pdm09 detected in patients from a Brazilian equatorial region during the pandemic period. Mem Inst Oswaldo Cruz 2014; 109:912-7. [PMID: 25410995 PMCID: PMC4296496 DOI: 10.1590/0074-0276140210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/08/2014] [Indexed: 12/16/2022] Open
Abstract
After the World Health Organization officially declared the end of the first pandemic
of the XXI century in August 2010, the influenza A(H1N1)pdm09 virus has been
disseminated in the human population. In spite of its sustained circulation, very
little on phylogenetic data or oseltamivir (OST) resistance is available for the
virus in equatorial regions of South America. In order to shed more light on this
topic, we analysed the haemagglutinin (HA) and neuraminidase (NA) genes of influenza
A(H1N1)pdm09 positive samples collected during the pandemic period in the Pernambuco
(PE), a northeastern Brazilian state. Complete HA sequences were compared and amino
acid changes were related to clinical outcome. In addition, the H275Y substitution in
NA, associated with OST resistance, was investigated by pyrosequencing. Samples from
PE were grouped in phylogenetic clades 6 and 7, being clustered together with
sequences from South and Southeast Brazil. The D222N/G HA gene mutation, associated
with severity, was found in one deceased patient that was pregnant. Additionally, the
HA mutation K308E, which appeared in Brazil in 2010 and was only detected worldwide
the following year, was identified in samples from hospitalised cases. The resistance
marker H275Y was not identified in samples tested. However, broader studies are
needed to establish the real frequency of resistance in this Brazilian region.
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Affiliation(s)
| | - Fernando do Couto Motta
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Marilda M Siqueira
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Paola Cristina Resende
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Priscilla da Silva Born
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Thiago Moreno L Souza
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | - Milene Mesquita
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
| | | | - Sharon Carney
- Laboratório de Vírus Respiratórios e do Sarampo, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, RJ, Brasil
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Analyzing the interaction of a herbal compound Andrographolide from Andrographis paniculata as a folklore against swine flu (H1N1). ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2014; 4:S624-S630. [PMID: 32289026 PMCID: PMC7129870 DOI: 10.1016/s2222-1808(14)60692-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 06/05/2014] [Accepted: 08/05/2014] [Indexed: 11/24/2022]
Abstract
Objective To find new bioactive molecules for the treatment of swine flu. Methods The present study is an attempt to elucidate inhibition potential of andrographolide and its derivatives along with an associated binding mechanism through virtual screening and molecular docking simulation studies. Results Our findings revealed structural conformation changes in 150 loop, secondary sialic acid binding site residues of ACZ97474 {Neuraminidase (A/Blore/NIV236/2009(H1N1)}. Andrographolide have been identified as the highest binging energy of -10.88 Kcal/mol, 3 hydrogen bond interactions (Arg152, Lys150, and Gly197), total intermolecular energy of -12.07 Kcal/mol with bioactivity value (Ki) of 10.59 nmol/L, while the Food and Drug Admistraton approved drug Oseltamivir and Zanamivir have shown 2 and 4 hydrogen bond interactions with binding energies of -6.28 Kcal/mol and -7.73Kcal/mol, respectively, which is higher than andrographolide. The guanidine group of Arg152 has binding affinities to the hydrophilic nature of the inhibitors (-OH and =O groups), as identified by docking of andrographolide (CID: 5318517) on neuraminidase. Conclusions Hence, andrographolide has the potential to inhibit neuraminidase activity of H1N1 and may be used as an alternative medicinal therapy for swine flu positive patient. With potent antiviral activity and a potentially new mechanism of action, andrographolide may warrant further evaluation as a possible therapy for influenza.
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Hirve S, Krishnan A, Dawood FS, Lele P, Saha S, Rai S, Gupta V, Lafond KE, Juvekar S, Potdar V, Broor S, Lal RB, Chadha M. Incidence of influenza-associated hospitalization in rural communities in western and northern India, 2010-2012: a multi-site population-based study. J Infect 2014; 70:160-70. [PMID: 25218056 DOI: 10.1016/j.jinf.2014.08.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/02/2014] [Accepted: 08/05/2014] [Indexed: 11/16/2022]
Abstract
BACKGROUND The global burden of influenza is increasingly recognized, but data from India remain sparse. We conducted a multi-site population-based surveillance study to estimate and compare rates of influenza-associated hospitalization at two rural Indian health and demographic surveillance system (HDSS) sites at Ballabgarh and Vadu during 2010-2012. METHODS Prospective facility-based surveillance for all hospitalizations (excluding those for trauma, elective surgery and obstetric, ophthalmic or psychiatric reasons) was conducted at 72 health facilities. After collection of clinical details, patients had nasopharyngeal swabs taken and tested by reverse transcription polymerase chain reaction for influenza viruses. Annual healthcare utilization surveys (HUS) were conducted in HDSS households to identify proportion of hospitalizations occurring at non-study facilities to adjust for hospitalizations missed through facility-based surveillance. RESULTS HUS showed that 69% and 67% of hospitalizations occurred at study facilities at Ballabgarh and Vadu, respectively. Overall, 6004 patients hospitalized with acute medical illness at participating facilities were enrolled (1717 from Ballabgarh; 4287 from Vadu). The proportion of patients with influenza was higher at Vadu than Ballabgarh annually (2010: 21% vs. 5%, p < 0.05; 2011: 18% vs. 5%, p < 0.05; 2012: 23% vs. 5%, p < 0.05). Annual adjusted influenza-associated hospitalization rates were 5-11 fold higher in Vadu (20.3-51.6 per 10,000) vs Ballabgarh (4.4-6.3 per 10,000). At both sites, influenza A/H1N1pdm09 and B predominated during 2010, A/H3N2 and B during 2011, and A/H1N1pdm09 and B during 2012. CONCLUSION The markedly different influenza hospitalization rates by season and across communities in India highlight the need for sustained multi-site surveillance system for estimating national influenza disease burden. That would be the first step for initiating discussions around Influenza prevention and control strategies in the country.
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Affiliation(s)
- Siddhivinayak Hirve
- Vadu Rural Health Program, King Edward Memorial Hospital Research Center, Pune, India
| | - Anand Krishnan
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Fatimah S Dawood
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, USA
| | - Pallavi Lele
- Vadu Rural Health Program, King Edward Memorial Hospital Research Center, Pune, India
| | - Siddhartha Saha
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, USA
| | - Sanjay Rai
- Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Vivek Gupta
- National Institute of Mental Health and Allied Sciences, Bangalore, India
| | - Kathryn E Lafond
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, USA
| | - Sanjay Juvekar
- Vadu Rural Health Program, King Edward Memorial Hospital Research Center, Pune, India
| | - Varsha Potdar
- National Institute of Virology, Indian Council of Medical Research, 20-A, Dr Ambedkar Road, Pune 411001, India
| | | | - Renu B Lal
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, USA
| | - Mandeep Chadha
- National Institute of Virology, Indian Council of Medical Research, 20-A, Dr Ambedkar Road, Pune 411001, India.
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Singh AK, Jain A, Jain B, Singh KP, Dangi T, Mohan M, Dwivedi M, Kumar R, Kushwaha RAS, Singh JV, Mishra AC, Chhaddha MS. Viral aetiology of acute lower respiratory tract illness in hospitalised paediatric patients of a tertiary hospital: one year prospective study. Indian J Med Microbiol 2014; 32:13-8. [PMID: 24399381 DOI: 10.4103/0255-0857.124288] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
CONTEXT Acute lower respiratory tract infections (ALRI), ranked as the second leading cause of death are the primary cause of hospitalisation in children. Viruses are the most important causative agents of ALRI. AIM To study the viral aetiology of ALRI in children at a tertiary care hospital. SETTING AND DESIGN One year prospective observational study in a tertiary care hospital of King George's Medical University, Lucknow. MATERIAL AND METHODS Nasopharyngeal aspirate (NPA) was collected from children admitted with signs and symptoms of ALRI who were aged 0-14 years. Samples were transported to the laboratory at 4°C in viral transport media and processed for detection of respiratory syncytial virus (RSV) A and B, influenza virus A and B, adenovirus (ADV), human Boca virus (HBoV), human metapneumo virus (hMPV) and parainfluenzavirus 1, 2, 3 and 4 using mono/multiplex real-time polymerase chain reaction (RT-PCR). STATA was used for statistical analysis. RESULTS In one year, 188 NPAs were screened for respiratory viruses, of which 45.7% tested positive. RSV was most commonly detected with 21.3% positivity followed by measles virus (8.5%), influenza A virus (7.4%), ADV (5.3%), influenza B virus (1.6%), hMPV (1.1%) and HBoV (0.5%). Month wise maximum positivity was seen in December and January. Positivity rate of RSV was highest in children aged < 1 year, which decreased with increase in age, while positive rate of influenza virus increased with increasing age. CONCLUSION The occurrence of viral predominance in ALRI is highlighted.
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Affiliation(s)
| | - A Jain
- Department of Microbiology, NIV, Infl uenza division, King George's Medical University, Lucknow, Uttar Pradesh, India
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Goka EA, Vallely PJ, Mutton KJ, Klapper PE. Mutations associated with severity of the pandemic influenza A(H1N1)pdm09 in humans: a systematic review and meta-analysis of epidemiological evidence. Arch Virol 2014; 159:3167-83. [PMID: 25078388 DOI: 10.1007/s00705-014-2179-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 07/12/2014] [Indexed: 10/25/2022]
Abstract
Mutations in the haemagglutinin (HA), non-structural protein 1 (NS1) and polymerase basic protein 2 (PB2) of influenza viruses have been associated with virulence. This study investigated the association between mutations in these genes in influenza A(H1N1)pdm09 virus and the risk of severe or fatal disease. Searches were conducted on the MEDLINE, EMBASE and Web of Science electronic databases and the reference lists of published studies. The PRISMA and STROBE guidelines were followed in assessing the quality of studies and writing-up. Eighteen (18) studies, from all continents, were included in the systematic review (recruiting patients 0 - 77 years old). The mutation D222G was associated with a significant increase in severe disease (pooled RD: 11 %, 95 % CI: 3.0 % - 18.0 %, p = 0.004) and the risk of fatality (RD: 23 %, 95 % CI: 14.0 %-31.0 %, p = < 0.0001). No association was observed between the mutations HA-D222N, D222E, PB2-E627K and NS1-T123V and severe/fatal disease. The results suggest that no virus quasispecies bearing virulence-conferring mutations in the HA, PB2 and NS1 predominated. However issues of sampling bias, and bias due to uncontrolled confounders such as comorbidities, and viral and bacterial coinfection, should be born in mind. Influenza A viruses should continue to be monitored for the occurrence of virulence-conferring mutations in HA, PB2 and NS1. There are suggestions that respiratory virus coinfections also affect virus virulence. Studies investigating the role of genetic mutations on disease outcome should make efforts to also investigate the role of respiratory virus coinfections.
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Affiliation(s)
- E A Goka
- Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, University of Manchester, 1st Floor Stopford building, Oxford Road, Manchester, M13 9PL, UK,
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Dangi T, Jain B, Singh AK, Singh J, Kumar R, Dwivedi M, Verma AK, Chadha MS, Jain A. Molecular characterization of circulating pandemic strains of influenza A virus during 2012 to 2013 in Lucknow (India). J Med Virol 2014; 86:2134-41. [DOI: 10.1002/jmv.23946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 01/24/2023]
Affiliation(s)
- Tanushree Dangi
- Department of Microbiology; King George's Medical University; Lucknow India
| | - Bhawana Jain
- Department of Microbiology; King George's Medical University; Lucknow India
| | - Ajay Kumar Singh
- Department of Microbiology; King George's Medical University; Lucknow India
| | - J.V. Singh
- Department of Community Medicine; King George's Medical University; Lucknow India
| | - Rashmi Kumar
- Department of Paediatrics; King George's Medical University; Lucknow India
| | - Mukesh Dwivedi
- Department of Microbiology; King George's Medical University; Lucknow India
| | - Anil Kumar Verma
- Department of Microbiology; King George's Medical University; Lucknow India
| | | | - Amita Jain
- Department of Microbiology; King George's Medical University; Lucknow India
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Mesquita M, Resende P, Marttorelli A, Machado V, Sacramento CQ, Fintelman-Rodrigues N, Abrantes JL, Tavares R, Schirmer M, Siqueira MM, Souza TML. Detection of the influenza A(H1N1)pdm09 virus carrying the K-15E, P83S and Q293H mutations in patients who have undergone bone marrow transplant. PLoS One 2014; 9:e94822. [PMID: 24740088 PMCID: PMC3989246 DOI: 10.1371/journal.pone.0094822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 03/20/2014] [Indexed: 12/17/2022] Open
Abstract
The 2009 pandemic influenza A(H1N1)pdm09 virus emerged and caused considerable morbidity and mortality in the third world, especially in Brazil. Although circulating strains of A(H1N1)pdm09 are A/California/04/2009-like (CA-04-like) viruses, various studies have suggested that some mutations in the viral hemagglutinin (HA) may be associated with enhanced severity and fatality. This phenomenon is particularly challenging for immunocompromised individuals, such as those who have undergone bone marrow transplant (BMT), because they are more likely to display worse clinical outcomes to influenza infection than non-immunocompromised individuals. We studied the clinical and viral aspects of post-BMT patients with confirmed A(H1N1)pdm09 diagnosis in the largest cancer hospital in Brazil. We found a viral strain with K-15E, P83S and Q293H polymorphisms in the HA, which is presumably more virulent, in these individuals. Despite that, these patients showed only mild symptoms of infection. Our findings complement the discovery of mild cases of infection with the A(H1N1)pdm09 virus with the K-15E, P83S and Q293H mutations in Brazil and oppose other studies that have linked these changes with increased disease severity. These results could be important for a better comprehension of the impact of the pandemic influenza in the context of BMT.
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Affiliation(s)
- Milene Mesquita
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Paola Resende
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Andressa Marttorelli
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Viviane Machado
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Carolina Q. Sacramento
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Natalia Fintelman-Rodrigues
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Juliana L. Abrantes
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Rita Tavares
- Center for Bone Marrow Transplantation (CEMO), National Cancer Institute (INCa), Rio de Janeiro, RJ, Brazil
| | - Marcelo Schirmer
- Center for Bone Marrow Transplantation (CEMO), National Cancer Institute (INCa), Rio de Janeiro, RJ, Brazil
| | - Marilda M. Siqueira
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Thiago Moreno L. Souza
- Measles and Respiratory viruses Laboratory, WHO/NIC, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil
- * E-mail:
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Singh AK, Jain B, Verma AK, Kumar A, Dangi T, Dwivedi M, Singh KP, Jain A. Hospital outbreak of human respiratory syncytial virus (HRSV) illness in immunocompromised hospitalized children during summer. CLINICAL RESPIRATORY JOURNAL 2014; 9:180-4. [DOI: 10.1111/crj.12121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/09/2014] [Accepted: 02/06/2014] [Indexed: 11/26/2022]
Affiliation(s)
- Ajay K. Singh
- Department of Microbiology; King George Medical University; Lucknow India
| | - Bhawana Jain
- Department of Microbiology; King George Medical University; Lucknow India
| | - Anil K. Verma
- Department of Microbiology; King George Medical University; Lucknow India
| | - Archana Kumar
- Department of Pediatrics; King George Medical University; Lucknow India
| | - Tanushree Dangi
- Department of Microbiology; King George Medical University; Lucknow India
| | - Mukesh Dwivedi
- Department of Microbiology; King George Medical University; Lucknow India
| | - Kaleshwar P. Singh
- Department of Microbiology; King George Medical University; Lucknow India
| | - Amita Jain
- Department of Microbiology; King George Medical University; Lucknow India
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Evolution trends of the 2009 pandemic influenza A (H1N1) viruses in different continents from March 2009 to April 2012. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0341-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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42
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Jain B, Singh AK, Dangi T, Agarwal A, Verma AK, Dwivedi M, Singh KP, Jain A. High prevalence of human metapneumovirus subtype B in cases presenting as severe acute respiratory illness: an experience at tertiary care hospital. CLINICAL RESPIRATORY JOURNAL 2014; 8:225-33. [DOI: 10.1111/crj.12064] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Revised: 09/25/2013] [Accepted: 10/13/2013] [Indexed: 01/09/2023]
Affiliation(s)
- Bhawana Jain
- Department of Microbiology; King George Medical University; Lucknow India
| | - Ajay Kr Singh
- Department of Microbiology; King George Medical University; Lucknow India
| | - Tanushree Dangi
- Department of Microbiology; King George Medical University; Lucknow India
| | - Anjali Agarwal
- Department of Microbiology; King George Medical University; Lucknow India
| | - Anil Kumar Verma
- Department of Microbiology; King George Medical University; Lucknow India
| | - Mukesh Dwivedi
- Department of Microbiology; King George Medical University; Lucknow India
| | - Kaleshwar P. Singh
- Department of Microbiology; King George Medical University; Lucknow India
| | - Amita Jain
- Department of Microbiology; King George Medical University; Lucknow India
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Purakayastha DR, Gupta V, Broor S, Sullender W, Fowler K, Widdowson MA, Lal RB, Krishnan A. Clinical differences between influenza A (H1N1) pdm09 & influenza B infections identified through active community surveillance in North India. Indian J Med Res 2013; 138:962-8. [PMID: 24521643 PMCID: PMC3978989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND & OBJECTIVES Most studies on the clinical presentation with influenza viruses have been conducted in outpatient or inpatient medical facilities with only a few studies in community settings. Clinical differences between influenza A (H1N1) pdm 09 and influenza B virus infections have importance for community-based public health surveillance. An active community surveillance at the time of emergence of pandemic influenza provided us with an opportunity to compare the clinical features among patients infected with influenza A (H1N1) pdm09 virus and those with influenza B virus co-circulating in an active community-based weekly surveillance in three villages in Faridabad, Haryana, north India. METHODS Active surveillance for febrile acute respiratory infection (FARI) was carried out in a rural community (n=16,182) in the context of an inactivated trivalent influenza vaccine trial (among children <11 yr). Individuals with FARI were assessed clinically by nurses and respiratory samples collected and tested for influenza viruses by real time RT-PCR from November 2009 to August 2010. Clinical symptoms of patients with influenza A (H1N1) pdm 09 and influenza B infection were compared. RESULTS Of the 4796 samples tested, 822 (17%) were positive for influenza virus. Of these, 443 (54%) were influenza A (H1N1) pdm09, 373 (45%) were influenza B and six were other subtypes/mixed infections. The mean age was lower for patients with influenza B (16.4 yr) than influenza A (H1N1) pdm09 infection (18.7 yr; P=0.04). Among children aged 5-18 yr, chills/rigours (OR 4.0; CI 2.2, 7.4), sore throat (OR 6.8; CI 2.3, 27.3) and headache (OR2.0; CI 1.3, 3.3) were more common in influenza A (H1N1) pdm09 infection than in influenza B cases. Chills/rigours (OR 2.4; CI 1.4, 4.0) and headache (OR 1.7; CI 1.0, 2.7) were associated with influenza A (H1N1) pdm09 infection in those >18 yr. No significant differences were seen in children <5 yr. CONCLUSION Our findings show that the differences in the clinical presentation of influenza A(H1N1)pdm09 and influenza B infections are not likely to be of clinical or public health significance.
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Affiliation(s)
| | | | | | | | | | | | | | - Anand Krishnan
- Department of Microbiology, Centre for Community Medicine, All India Institute of Medical Sciences, New Delhi, India
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El Rhaffouli H, El Fahime EM, Laraqui A, Bajjou T, Melloul M, Obeid S, Fathallah L, Lahlou-Amine I. Evolution of the hemagglutinin gene of the influenza A(H1N1)pdm09 virus in Morocco during two influenza seasons 2009-2011. Curr Microbiol 2013; 68:372-80. [PMID: 24212335 DOI: 10.1007/s00284-013-0463-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/15/2013] [Indexed: 11/30/2022]
Abstract
To study genetic evolution of Moroccan influenza A(H1N1)pdm09 virus strains, we conducted a molecular characterization of the hemagglutinin gene subunit 1 (HA1) of 36 influenza A(H1N1)pdm09 virus strains. The stains were collected from patients in Rabat and Casablanca during two influenza seasons 2009-2010 and 2010-2011. Nucleotide and amino acid sequences of 14 influenza A(H1N1)pdm09 virus strains from 2009 to 2010 were ~97 and 99 %, respectively, similar to the reference strain A/California/07/2009 (H1N1). Phylogenetic analysis of 22 influenza A(H1N1)pdm09 virus strains from 2010 to 2011 revealed a co-circulation of three well-described different genetic groups. Most important, none of the identified groups showed significant changes at the antigenic site of the virus HA1 subunit which may alter the efficacy of California/07/2009 (H1N1) vaccine.
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Affiliation(s)
- Hicham El Rhaffouli
- Biosafety Level 3 and Research Laboratory (LRB-P3), Faculty of Medicine and Pharmacy, Mohammed V Military Teaching Hospital, University Mohammed V-Souissi, Hay Ryade, BP 190, Rabat, Morocco,
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Genomic analysis of pandemic and post-pandemic influenza A pH1N1 viruses isolated in Rio Grande do Sul, Brazil. Arch Virol 2013; 159:621-30. [PMID: 24114147 DOI: 10.1007/s00705-013-1855-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 09/14/2013] [Indexed: 01/23/2023]
Abstract
During the 2009 influenza A pH1N1 pandemics in Brazil, the state that was most affected was Rio Grande do Sul (RS), with over 3,000 confirmed cases, including 298 deaths. While no cases were confirmed in 2010, 103 infections with 14 deaths by pH1N1 were reported in 2011. Genomic analysis of the circulating viruses is fundamental for understanding viral evolution and supporting vaccine development against these pathogens. This study investigated whole genomes of six pH1N1 virus isolates from pandemic and post-pandemic periods in RS, Brazil. Phylogenetic analysis using the concatenated genome segments demonstrated that at least two lineages of the virus co-circulated in RS during the 2009 pandemic period. Moreover, our analysis showed that the post-pandemic pH1N1 virus from 2011 constitutes a distinct clade whose ancestor belongs to clade 7. All six isolates contained amino acid substitutions in their proteins when compared to the archetype strains California/04/2009 and California/07/2009. The 2011 isolates contained more amino acid substitutions, and most of their genes were under purifying selection. Based on the amino acid substitutions in HA epitopes from strains isolated in RS, Brazil, in silico analysis predicted a decrease in vaccine efficacy against post-pandemic strains (median 31.562 %) in relation to pandemic ones (median 39.735 %).
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The Frequency Distribution of Cases Affected by Influenza A (H1N1) Based on Demographic Characteristics During2008 – 2009 in Yazd Province (Iran). Jundishapur J Microbiol 2013. [DOI: 10.5812/jjm.7471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Koul P, Khan U, Bhat K, Saha S, Broor S, Lal R, Chadha M. Recrudescent Wave of A/H1N1pdm09 Influenza Viruses in Winter 2012-2013 in Kashmir, India. PLOS CURRENTS 2013; 5. [PMID: 24818063 PMCID: PMC4011547 DOI: 10.1371/currents.outbreaks.f1241c3a2625fc7a81bf25eea81f66e6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Some parts of world, including India observed a recrudescent wave of influenza A/H1N1pdm09 in 2012. We undertook a study to examine the circulating influenza strains, their clinical association and antigenic characteristics to understand the recrudescent wave of A/H1N1pdm09 from November 26, 2012 to Feb 28, 2013 in Kashmir, India. Of the 751 patients (545 outpatient and 206 hospitalized) presenting with acute respiratory infection at a tertiary care hospital in Srinagar; 184 (24.5%) tested positive for influenza. Further type and subtype analysis revealed that 106 (58%) were influenza A (H1N1pdm09 =105, H3N2=1) and 78 (42%) were influenza B. The influenza positive cases had a higher frequency of chills, nasal discharge, sore throat, body aches and headache, compared to influenza negative cases. Of the 206 patients hospitalized for pneumonia/acute respiratory distress syndrome or an exacerbation of an underlying lung disease, 34 (16.5%) tested positive for influenza (22 for H1N1pdm09, 11 for influenza B). All influenza-positive patients received oseltamivir and while most patients responded well to antiviral therapy and supportive care, 6 patients (4 with H1N1pdm09 and 2 with influenza B) patients died of progressive respiratory failure and multi-organ dysfunction. Following a period of minimal circulation, H1N1pdm09 re-emerged in Kashmir in 2012-2013, causing serious illness and fatalities. As such the healthcare administrators and policy planners need to be wary and monitor the situation closely.
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Affiliation(s)
| | - Umar Khan
- Internal & Pulmonary Medicine, SKIMS, Srinagar, J&K
| | - Khursheed Bhat
- Department of Internal and Pulmonary Medicine, SKIMS, Srinagar
| | | | - Shobha Broor
- Director Inclen Laboratory, Inclen trust International, New Delhi
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Chen J, Yan B, Chen Q, Yao Y, Wang H, Liu Q, Zhang S, Wang H, Chen Z. Evaluation of neutralizing efficacy of monoclonal antibodies specific for 2009 pandemic H1N1 influenza A virus in vitro and in vivo. Arch Virol 2013; 159:471-83. [PMID: 24057757 DOI: 10.1007/s00705-013-1852-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 08/07/2013] [Indexed: 12/20/2022]
Abstract
Pandemic influenza A virus (H1N1) 2009 poses a serious public-health challenge worldwide. To characterize the neutralizing epitopes of this virus, we generated a panel of eight monoclonal antibodies (mAbs) against the HA of the A/California/07/2009 virus. The antibodies were specific for the 2009 pdm H1N1 HA, as the antibodies displayed HA-specific ELISA, hemagglutination inhibition (HAI) and neutralization activity. One mAb (mAb12) showed significantly higher HAI and neutralizing titers than the other mAbs. We mapped the antigenic epitopes of the HA by characterizing escape mutants of a 2009 H1N1 vaccine strain (NYMC X-179A). The amino acid changes suggested that these eight mAbs recognized HA antigenic epitopes located in the Sa, Sb, Ca1 and Ca2 sites. Passive immunization with mAbs showed that mAb12 displayed more efficient neutralizing activity in vivo than the other mAbs. mAb12 was also found to be protective, both prophylactically and therapeutically, against a lethal viral challenge in mice. In addition, a single injection of 10 mg/kg mAb12 outperformed a 5-day course of treatment with oseltamivir (10 mg/kg/day by gavage) with respect to both prophylaxis and treatment of lethal viral infection. Taken together, our results showed that mouse-origin mAbs displayed neutralizing effectiveness in vitro and in vivo. One mAb in particular (mAb12) recognized an epitope within the Sb site and demonstrated outstanding neutralizing effectiveness.
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Affiliation(s)
- Jianjun Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China,
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Whole-Genome Sequence Analysis of Postpandemic Influenza A(H1N1)pdm09 Virus Isolates from India. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00727-13. [PMID: 24051317 PMCID: PMC3778200 DOI: 10.1128/genomea.00727-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The pandemic influenza A(H1N1)pdm09 virus was first detected in India in May 2009 and continued to circulate in the postpandemic period. Whole-genome sequence analysis of postpandemic A(H1N1)pdm09 viruses showed the circulation of clade 6 and clade 7 viruses. The hemagglutinin (HA) gene showed increased diversity compared with that in the pandemic phase.
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Ruggiero T, De Rosa F, Cerutti F, Pagani N, Allice T, Stella ML, Milia MG, Calcagno A, Burdino E, Gregori G, Urbino R, Di Perri G, Ranieri MV, Ghisetti V. A(H1N1)pdm09 hemagglutinin D222G and D222N variants are frequently harbored by patients requiring extracorporeal membrane oxygenation and advanced respiratory assistance for severe A(H1N1)pdm09 infection. Influenza Other Respir Viruses 2013; 7:1416-26. [PMID: 23927713 PMCID: PMC4634302 DOI: 10.1111/irv.12146] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2013] [Indexed: 12/31/2022] Open
Abstract
Background In patients with A(H1N1)pdm09 infection, severe lung involvement requiring admission to intensive care units (ICU) has been reported. Mutations at the hemagglutinin (HA) receptor binding site (RBS) have been associated with increased virulence and disease severity, representing a potential marker of critical illness. Objectives To assess the contribution of HA‐RBS variability in critically ill patients, A(H1N1)pdm09 virus from adult patients with severe infection admitted to ICU for extracorporeal membrane oxygenation support (ECMO) during influenza season 2009–2011 in Piemonte (4·2 million inhabitants), northwestern Italy, was studied. Patients and methods We retrospectively analyzed HA‐RBS polymorphisms in ICU patients and compared with those from randomly selected inpatients with mild A(H1N1)pdm09 disease and outpatients with influenza from the local surveillance program. Results By HA‐RBS direct sequencing of respiratory specimens, D222G and D222N viral variants were identified in a higher proportion in ICU patients (n = 8/24, 33·3%) than in patients with mild disease (n = 2/34, 6%) or in outpatients (n = 0/44) (Fisher's exact test P < 0·0001; OR 38·5; CI 95% 4·494–329·9). Eleven ICU patients died (42%), three of them carrying the D222G variant, which was associated with RBS mutation S183P in two. D222G and D222N mutants were identified in upper and lower respiratory samples. Conclusions A(H1N1)pdm09 HA substitutions D222G and D222N were harbored in a significantly higher proportion by patients with acute respiratory distress for A(H1N1)pdm09 severe infection requiring ICU admission and ECMO. These data emphasize the importance of monitoring viral evolution for understanding virus–host adaptation aimed at the surveillance of strain circulation and the study of viral correlates of disease severity.
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Affiliation(s)
- Tina Ruggiero
- Department of Infectious Diseases, Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, Turin, Italy
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