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Qiu T, Qiu J, Yang Y, Zhang L, Mao T, Zhang X, Xu J, Cao Z. A benchmark dataset of protein antigens for antigenicity measurement. Sci Data 2020; 7:212. [PMID: 32632108 PMCID: PMC7338539 DOI: 10.1038/s41597-020-0555-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/12/2020] [Indexed: 01/03/2023] Open
Abstract
Antigenicity measurement plays a fundamental role in vaccine design, which requires antigen selection from a large number of mutants. To augment traditional cross-reactivity experiments, computational approaches for predicting the antigenic distance between multiple protein antigens are highly valuable. The performance of in silico models relies heavily on large-scale benchmark datasets, which are scattered among public databases and published articles or reports. Here, we present the first benchmark dataset of protein antigens with experimental evidence to guide in silico antigenicity calculations. This dataset includes (1) standard haemagglutination-inhibition (HI) tests for 3,867 influenza A/H3N2 strain pairs, (2) standard HI tests for 559 influenza virus B strain pairs, and (3) neutralization titres derived from 1,073 Dengue virus strain pairs. All of these datasets were collated and annotated with experimentally validated antigenicity relationships as well as sequence information for the corresponding protein antigens. We anticipate that this work will provide a benchmark dataset for in silico antigenicity prediction that could be further used to assist in epidemic surveillance and therapeutic vaccine design for viruses with variable antigenicity.
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Affiliation(s)
- Tianyi Qiu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jingxuan Qiu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Yiyan Yang
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Lu Zhang
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Tiantian Mao
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200032, China.
| | - Zhiwei Cao
- Shanghai 10th People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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Jha BK, Pandit R, Jha R, Manandhar KD. Overview of seasonal influenza and recommended vaccine during the 2016/2017 season in Nepal. Heliyon 2020; 6:e03304. [PMID: 32021940 PMCID: PMC6994851 DOI: 10.1016/j.heliyon.2020.e03304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/12/2019] [Accepted: 01/23/2020] [Indexed: 12/03/2022] Open
Abstract
Background Influenza is a highly contagious viral respiratory infection caused by influenza viruses whose epidemic and pandemic have resulted in significant morbidity and mortality. The annual epidemic of influenza results in an estimated 3–5 million cases of severe illness and about 290000–650000 deaths globally. The vaccination program has been successful to control the epidemic however, it further needs improvement. This study was aimed to investigate the types of influenza viruses prevailing in Nepal during 2016 and, to match the recommended vaccine for use during the same season. Methods A descriptive cross sectional study was carried out at National Public Health Laboratory, Kathmandu, Nepal for the period of one year (Jan–Dec 2016). A total of 1683 throat swab specimen was collected from patients of different age group referred to NPHL for influenza testing. The specimen was primarily stored at 4 °C and processed using ABI 7500 RT PCR system for the identification of influenza viruses. Results Of the total 1683 patients suspected of having influenza infection, influenza viruses were isolated from 614 (36.5%) patients with male predominance. The highest number of infection was caused by influenza A/H3 strain (51.0%) followed by influenza B (40.4%) and influenza A (H1N1) pdm09 (8.6%). Two peaks of infection were observed during the year 2016. The widely available trivalent vaccine during the season did not match the prevailing strain because of the dominance of B/Yamagata lineage over B/Victoria lineage. Conclusion We concluded that Nepal experiences semiannual cycle of influenza infection, firstly during the month of January–February and secondly during the month of July–August. The vaccine to be introduced in Nepal need to be decided by national authority based on prevailing influenza types to confer effective immunization.
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Affiliation(s)
- Bimalesh Kumar Jha
- National Public Health Laboratory, Department of Health Services, Ministry of Health and Population, Kathmandu, Nepal.,Central Department of Biotechnology, Institute of Science and Technology, Tribhuvan University, Kathmandu, Nepal
| | - Roshan Pandit
- National Public Health Laboratory, Department of Health Services, Ministry of Health and Population, Kathmandu, Nepal
| | - Runa Jha
- National Public Health Laboratory, Department of Health Services, Ministry of Health and Population, Kathmandu, Nepal
| | - Krishna Das Manandhar
- Central Department of Biotechnology, Institute of Science and Technology, Tribhuvan University, Kathmandu, Nepal
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3
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Beer K, Dai M, Howell S, Rijal P, Townsend AR, Lin Y, Wharton SA, Daniels RS, McCauley JW. Characterization of neutralizing epitopes in antigenic site B of recently circulating influenza A(H3N2) viruses. J Gen Virol 2018; 99:1001-1011. [PMID: 29944110 PMCID: PMC6171714 DOI: 10.1099/jgv.0.001101] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Influenza A(H3N2) viruses are associated with outbreaks worldwide and can cause disease with severe complications. The impact can be reduced by vaccination, which induces neutralizing antibodies that mainly target the haemagglutinin glycoprotein (HA). In this study we generated neutralizing mouse monoclonal antibodies (mAbs) against A/Victoria/361/2011 and identified their epitopes by generating and sequencing escape viruses. The epitopes are located in antigenic site B, which is near the receptor-binding site and is immunodominant in humans. Amino acid (aa) substitutions at positions 156, 158, 159, 189, 190 and 193 in antigenic site B led to reduced ability of mAbs to block receptor-binding. The majority of A(H3N2) viruses that have been circulating since 2014 are antigenically distinct from previous A(H3N2) viruses. The neutralization-sensitive epitopes in antigenic site B of currently circulating viruses were examined with these mAbs. We found that clade 3C.2a viruses, possessing an additional potential glycosylation site at HA1 position N158, were poorly recognized by some of the mAbs, but other residues, notably at position 159, also affected antibody binding. Through a mass spectrometric (MS) analysis of HA, the glycosylated sites of HA1 were established and we determined that residue 158 of HA1 was glycosylated and so modified a neutralization-sensitive epitope. Understanding and monitoring individual epitopes is likely to improve vaccine strain selection.
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Affiliation(s)
- Kerstin Beer
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mian Dai
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steven Howell
- 2Mass Spectrometry and Proteomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Pramila Rijal
- 3MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Alain R Townsend
- 3MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Yipu Lin
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen A Wharton
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Rodney S Daniels
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - John W McCauley
- 1Crick Worldwide Influenza Centre, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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Adhikari R, Thapa S. Changing Trend of Infectious Diseases in Nepal. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1052:19-38. [PMID: 29785478 PMCID: PMC7122567 DOI: 10.1007/978-981-10-7572-8_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Many infectious/communicable diseases (IDs) are endemic in Nepal. Until a decade and half ago, IDs were the major cause of both morbidity and mortality accounting 70% for both. However, as a result of various preventive measures implemented by both the state and non-state actors, the overall IDs have shown a changing (declining) trend. The most impressive decline has been seen in the intestinal helminth infection. Though the overall burden of IDs is decreasing, several newer infectious diseases (emerging infections) namely, dengue fever, scrub typhus, influenza (H5N1 and H1N1), and others are posing a great public health problem. On the other hand, though sporadic, outbreaks of endemic diseases together with HIV-TB coinfection and infection with drug resistance microbes during recent years have constituted a serious public health as well as medical problem. On the contrary, with the decline of IDs, noninfectious diseases (noncommunicable disease, NCD) namely, diabetes, cancer (and cancer therapy), and others are on the rise particularly in urban areas. Hence, currently Nepal is trapped in "double burden" of diseases. Risk of opportunistic infection has increased in immunocompromised person with NCD. To address the present situation, the multi-sectoral plan and strategies developed must be implemented effectively.
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Affiliation(s)
- Rameshwar Adhikari
- Research Center for Applied Science and Technology (RECAST), Tribhuvan University, Kathmandu, Nepal
| | - Santosh Thapa
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, Texas USA
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Jain M, Islam S, Rahman ASMZ, Akhtar S, Hasan KN, Ahsan GU, Khaleque A, Hossain M. Molecular analysis of hemagglutinin, neuraminidase, matrix genes provide insight into the genetic diversity of seasonal H3N2 human influenza a viruses in Bangladesh during July-August, 2012. Virusdisease 2018; 29:54-60. [PMID: 29607359 DOI: 10.1007/s13337-018-0431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 01/20/2018] [Indexed: 11/30/2022] Open
Abstract
Influenza A virus subtype H3 is a threat to public health and it is important to understand the evolution of the viruses for the surveillance and the selection of vaccine strains. Comparative analysis of four Bangladeshi isolates with isolates circulating other parts of the world based on three candidate genes hemagglutinin (HA), neuraminidase (NA), matrix protein (MA) showed no evidence of significant distinct subclade of viruses circulating in the country over the period of study. Despite these findings, we found N161S substitution in all four H3N2 influenza stains resulting in the gain of NSS160-162 glycosylation site. All H3N2 Influenza subtypes in the study had amino acid substitution at position 31 on the M2 protein (Aspartic acid to Asparagine) which is known to be responsible for amantadine drug resistance.
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Affiliation(s)
- Mukesh Jain
- 1Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Sohidul Islam
- 1Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - A S M Zisanur Rahman
- 1Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Sharmin Akhtar
- 1Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Kazi Nadim Hasan
- 1Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Gias Uddin Ahsan
- 2Department of Public Health, North South University, Dhaka, 1229 Bangladesh.,3NSU Genome Research Institute (NGRI), North South University, Dhaka, 1229 Bangladesh
| | - Abdul Khaleque
- 1Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh
| | - Maqsud Hossain
- 1Department of Biochemistry and Microbiology, North South University, Dhaka, 1229 Bangladesh.,3NSU Genome Research Institute (NGRI), North South University, Dhaka, 1229 Bangladesh
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6
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Liu F, Veguilla V, Gross FL, Gillis E, Rowe T, Xu X, Tumpey TM, Katz JM, Levine MZ, Lu X. Effect of Priming With Seasonal Influenza A(H3N2) Virus on the Prevalence of Cross-Reactive Hemagglutination-Inhibition Antibodies to Swine-Origin A(H3N2) Variants. J Infect Dis 2017; 216:S539-S547. [PMID: 28934461 DOI: 10.1093/infdis/jix093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Recent outbreaks of swine-origin influenza A(H3N2) variant (H3N2v) viruses have raised public health concerns. Previous studies indicated that older children and young adults had the highest levels of hemagglutination-inhibition (HI) antibodies to 2010-2011 H3N2v viruses. However, newly emerging 2013 H3N2v have acquired antigenic mutations in the hemagglutinin at amino acid position 145 (N145K/R). We estimated the levels of serologic cross-reactivity among humans primed with seasonal influenza A(H3N2) (sH3N2), using postinfection ferret antisera. We also explored age-related HI antibody responses to 2012-2013 H3N2v viruses. Methods Human and ferret antisera were tested in HI assays against 1 representative 2012 H3N2v (145N) and 2 2013 H3N2v (145K/R) viruses, together with 9 sH3N2 viruses circulating since 1968. Results Low levels of cross-reactivity between the H3N2v and sH3N2 viruses from the 1970s-1990s were observed using postinfection ferret antisera. The overall seroprevalence among the sH3N2-primed population against 2012-2013 H3N2v viruses was >50%, and age-related seroprevalence was observed. Seroprevalence was significantly higher to 2013 H3N2v than to 2012 H3N2v viruses among some children likely to have been primed with A/Sydney/5/97-like (145K) or A/Wuhan/359/95-like viruses (145K). Conclusions A single substitution (N145K/R) was sufficient to affect seropositivity to H3N2v viruses in some individuals. Insight into age-related antibody responses to newly emerging H3N2v viruses is critical for risk assessment and pandemic preparedness.
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Affiliation(s)
- Feng Liu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Vic Veguilla
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - F Liaini Gross
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Eric Gillis
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas Rowe
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Xiyan Xu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Terrence M Tumpey
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jacqueline M Katz
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Min Z Levine
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Xiuhua Lu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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Escalera-Zamudio M, Nelson MI, Cobián Güemes AG, López-Martínez I, Cruz-Ortiz N, Iguala-Vidales M, García ER, Barrera-Badillo G, Díaz-Quiñonez JA, López S, Arias CF, Isa P. Molecular epidemiology of influenza A/H3N2 viruses circulating in Mexico from 2003 to 2012. PLoS One 2014; 9:e102453. [PMID: 25075517 PMCID: PMC4116128 DOI: 10.1371/journal.pone.0102453] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/16/2014] [Indexed: 11/18/2022] Open
Abstract
In this work, nineteen influenza A/H3N2 viruses isolated in Mexico between 2003 and 2012 were studied. Our findings show that different human A/H3N2 viral lineages co-circulate within a same season and can also persist locally in between different influenza seasons, increasing the chance for genetic reassortment events. A novel minor cluster was also identified, named here as Korea, that circulated worldwide during 2003. Frequently, phylogenetic characterization did not correlate with the determined antigenic identity, supporting the need for the use of molecular evolutionary tools additionally to antigenic data for the surveillance and characterization of viral diversity during each flu season. This work represents the first long-term molecular epidemiology study of influenza A/H3N2 viruses in Mexico based on the complete genomic sequences and contributes to the monitoring of evolutionary trends of A/H3N2 influenza viruses within North and Central America.
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Affiliation(s)
- Marina Escalera-Zamudio
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha I. Nelson
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | | | | | | | | | | | | | | | - Susana López
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Carlos F. Arias
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Pavel Isa
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- * E-mail:
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8
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Wong KKY, Bull RA, Rockman S, Scott G, Stelzer-Braid S, Rawlinson W. Correlation of polymerase replication fidelity with genetic evolution of influenza A/Fujian/411/02(H3N2) viruses. J Med Virol 2011; 83:510-6. [PMID: 21264873 DOI: 10.1002/jmv.21991] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Influenza virus evolves continuously through mutations presumed to result from evolutionary pressure driving viral replication. This study examined the relationship between the genetic evolution and replication fidelity of influenza viruses. Analysis of influenza sequences from National Centre for Biotechnology Information (NCBI) database revealed a gradual decrease in the rate of genetic evolution of A/Fujian/411/02(H3N2)-like variants after the emergence and predominance of the A/H3N2 Fujian strain in 2002. This decrease may be related to an increase in replication fidelity, which was investigated by assessing mutation frequencies of reassortant viruses carrying the PB1 segment of Fujian variants isolated between 2003 and 2005 in a sequencing-based plaque assay. The data revealed a threefold decrease in substitution per site of the reassortant viruses carrying the Fujian PB1 segments isolated in 2004-2005 compared with those circulating in 2003. The decrease in mutation frequency paralleled a decrease in genetic evolution of the Fujian variants from the NCBI database. This correlation implicates changes in the polymerase replication fidelity as contributing to altered genetic evolution of influenza viruses.
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Affiliation(s)
- Karen Ka Yin Wong
- Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney, Australia
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9
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Lin JH, Chiu SC, Cheng JC, Chang HW, Hsiao KL, Lin YC, Wu HS, Liu HF. Molecular epidemiology and antigenic analyses of influenza A viruses H3N2 in Taiwan. Clin Microbiol Infect 2011; 17:214-22. [PMID: 20370800 DOI: 10.1111/j.1469-0691.2010.03228.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The severity of an influenza epidemic season may be influenced not only by variability in the surface glycoproteins, but also by differences in the internal proteins of circulating influenza viruses. To better understand viral antigenic evolution, all eight gene segments from 44 human H3N2 epidemic strains isolated during 2004-2008 in Taiwan were analyzed to provide a profile of protein variability. Comparison of the evolutionary profiles of the HA, NA and PB2 genes of influenza A (H3N2) viruses indicated that they were derived from a group of H3N2 isolates first seen in 2004. However, the PA, M and PB1 genes were derived from a different group of H3N2 isolates from 2004. Tree topology revealed the NP and NS genes could each be segregated into two groups similar to those for the polymerase genes. In addition, new genetic variants occurred during the non-epidemic period and become the dominant strain after one or two seasons. Comparison of evolutionary patterns in consecutive years is necessary to correlate viral genetic changes with antigenic changes as multiple lineages co-circulate.
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Affiliation(s)
- J-H Lin
- Center for Research and Diagnostics, Centers for Disease Control, Taipei, Taiwan
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10
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Department of Defense Global Laboratory-Based Influenza Surveillance: 1998-2005. Am J Prev Med 2009; 37:235-41. [PMID: 19666159 DOI: 10.1016/j.amepre.2009.04.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 03/12/2009] [Accepted: 04/29/2009] [Indexed: 11/23/2022]
Abstract
The Department of Defense (DoD) Global Laboratory-Based Influenza Surveillance Program was initiated in 1997 to formally consolidate and expand existing influenza surveillance programs within the DoD and in areas where DoD was working. Substantial changes in 2008 provided an opportunity to review the operation of the surveillance program as it existed during seven complete influenza seasons (1998-2005); the review was conducted in 2008. A unique aspect of the DoD program was the global reach for specimen collection and the ability to rapidly ship, process, and evaluate specimens from 27 countries. The resulting epidemiologic data combined with the culture results from >46,000 patients provided information that was shared with similar national and international programs, such as those of the CDC. Likewise, selected influenza isolates were molecularly characterized and shared with the CDC to be compared with other surveillance programs. Timeliness of the samples contributed to the information available for annual influenza vaccine selection.
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Mathisen M, Strand TA, Sharma BN, Chandyo RK, Valentiner-Branth P, Basnet S, Adhikari RK, Hvidsten D, Shrestha PS, Sommerfelt H. RNA viruses in community-acquired childhood pneumonia in semi-urban Nepal; a cross-sectional study. BMC Med 2009; 7:35. [PMID: 19635124 PMCID: PMC2727531 DOI: 10.1186/1741-7015-7-35] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Accepted: 07/27/2009] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Pneumonia is among the main causes of illness and death in children <5 years of age. There is a need to better describe the epidemiology of viral community-acquired pneumonia (CAP) in developing countries. METHODS From July 2004 to June 2007, we examined nasopharyngeal aspirates (NPA) from 2,230 cases of pneumonia (World Health Organization criteria) in children 2 to 35 months old recruited in a randomized trial of zinc supplementation at a field clinic in Bhaktapur, Nepal. The specimens were examined for respiratory syncytial virus (RSV), influenza virus type A (InfA) and B (InfB), parainfluenza virus types 1, 2 and 3 (PIV1, PIV2, and PIV3), and human metapneumovirus (hMPV) using a multiplex reverse transcriptase polymerase chain reaction (PCR) assay. RESULTS We identified 919 virus isolates in 887 (40.0%) of the 2,219 NPA specimens with a valid PCR result, of which 334 (15.1%) yielded RSV, 164 (7.4%) InfA, 129 (5.8%) PIV3, 98 (4.4%) PIV1, 93 (4.2%) hMPV, 84 (3.8%) InfB, and 17 (0.8%) PIV2. CAP occurred in an epidemic pattern with substantial temporal variation during the three years of study. The largest peaks of pneumonia occurrence coincided with peaks of RSV infection, which occurred in epidemics during the rainy season and in winter. The monthly number of RSV infections was positively correlated with relative humidity (rs = 0.40, P = 0.01), but not with temperature or rainfall. An hMPV epidemic occurred during one of the three winter seasons and the monthly number of hMPV cases was also associated with relative humidity (rs = 0.55, P = 0.0005). CONCLUSION Respiratory RNA viruses were detected from NPA in 40% of CAP cases in our study. The most commonly isolated viruses were RSV, InfA, and PIV3. RSV infections contributed substantially to the observed CAP epidemics. The occurrence of viral CAP in this community seemed to reflect more or less overlapping micro-epidemics with several respiratory viruses, highlighting the challenges of developing and implementing effective public health control measures.
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Affiliation(s)
- Maria Mathisen
- Centre for International Health, University of Bergen, PO Box 7804, N-5020 Bergen, Norway
| | - Tor A Strand
- Centre for International Health, University of Bergen, PO Box 7804, N-5020 Bergen, Norway
- Medical Microbiology, Department of Laboratory Medicine, Sykehuset Innlandet Lillehammer, Norway
| | - Biswa N Sharma
- Department of Microbiology, Tribhuvan University Teaching Hospital, Kathmandu, Nepal
| | - Ram K Chandyo
- Centre for International Health, University of Bergen, PO Box 7804, N-5020 Bergen, Norway
- Child Health Department, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Palle Valentiner-Branth
- Department of Epidemiology, Division of Epidemiology, Statens Serum Institut, Copenhagen, Denmark
| | - Sudha Basnet
- Child Health Department, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Ramesh K Adhikari
- Child Health Department, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Dag Hvidsten
- Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Prakash S Shrestha
- Child Health Department, Institute of Medicine, Tribhuvan University, Kathmandu, Nepal
| | - Halvor Sommerfelt
- Centre for International Health, University of Bergen, PO Box 7804, N-5020 Bergen, Norway
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
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Daum LT, Canas LC, Arulanandam BP, Niemeyer D, Valdes JJ, Chambers JP. Real-time RT-PCR assays for type and subtype detection of influenza A and B viruses. Influenza Other Respir Viruses 2009; 1:167-75. [PMID: 19432632 PMCID: PMC4634535 DOI: 10.1111/j.1750-2659.2007.00024.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Influenza viruses type A (H3N2 and H1N1 subtypes) and B are the most prevalently circulating human influenza viruses. However, an increase in several confirmed cases of high pathogenic H5N1 in humans has raised concerns of a potential pandemic underscoring the need for rapid, point of contact detection. In this report, we describe development and evaluation of ‘type,’ i.e., influenza virus A and B, and ‘subtype,’ i.e., H1, H3, and H5, specific, single‐step/reaction vessel format, real‐time RT‐PCR assays using total RNA from archived reference strains, shell‐vial cultured and uncultured primary (throat swab/nasal wash) clinical samples. The type A and B specific assays detected all 16 influenza type A viruses and both currently circulating influenza B lineages (Yamagata and Victoria), respectively. ‘Type’ and ‘subtype’ specific assays utilize one common set of thermocycling conditions, are specific and highly sensitive (detection threshold of approximately 100 target template molecules). All clinical specimens and samples were evaluated using both the unconventional portable Ruggedized Advanced Pathogen Identification Device (RAPID) and standard laboratory bench LightCycler instruments. These potentially field‐deployable assays could offer significant utility for rapid, point of care screening needs arising from a pandemic influenza outbreak.
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Affiliation(s)
- Luke T Daum
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX 78249, USA
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Xiu W, Wen Y, Shen X, Xie J, Yang S, Wu B, Wang M. Molecular evolution of influenza A (H3N2) viruses circulated in Fujian Province, China during the 1996–2004 period. ACTA ACUST UNITED AC 2008; 51:373-80. [DOI: 10.1007/s11427-008-0050-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2007] [Accepted: 01/07/2008] [Indexed: 01/19/2023]
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14
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Lin JH, Chiu SC, Lee CH, Su YJ, Tsai HC, Peng YT, Wu HS. Genetic and antigenic analysis of epidemic influenza viruses isolated during 2006-2007 season in Taiwan. J Med Virol 2008; 80:316-22. [PMID: 18098164 DOI: 10.1002/jmv.21074] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Influenza viruses are some of the most active pathogens in Taiwan. The monitoring influenza activity has been coordinated by the Centers for Diseases Control, Taiwan, and the surveillance is based on integrated clinical and virological surveillance components. Data from sentinel physician networks and other sources, mainly hospitals were collected. During 2006-07 season, a total of 1724 cases of laboratory-confirmed influenza were reported by collaborating laboratories and sentinels, which was five fold higher than during the corresponding part of the 2005-06 season. Of the Taiwan isolates analyzed using post-infection ferret antisera, 1.5% were H1N1 (A/Hi), 21.5% H3N2 (A/H3), and 77.0% influenza B viruses. This reflects the predominance of influenza B viruses during 2006-07 season. In addition, continued antigenic drift was seen with the A/I-B viruses compared with the previous season's reference strains. However, an increasing number of recent A/H3 isolates characterized in our report were amantadine sensitive. Preparation for an influenza pandemic is presently a high priority in Taiwan. Laboratory-based surveillance systems must be timely in order to be effective. The data presented here highlights the need to characterize the circulating strains both antigenically and genetically during regular surveillance. Any contribution of individual genes or gene combinations to usual or unusual epidemic characteristics might thus be identified ensuring that virus strains can be selected for vaccine formulation that will most closely match the circulating viruses.
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Affiliation(s)
- Jih-Hui Lin
- Research and Diagnostic Center, Centers for Disease Control, Taipei, Taiwan.
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15
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Liao YC, Lee MS, Ko CY, Hsiung CA. Bioinformatics models for predicting antigenic variants of influenza A/H3N2 virus. ACTA ACUST UNITED AC 2008; 24:505-12. [PMID: 18187440 DOI: 10.1093/bioinformatics/btm638] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
MOTIVATION Continual and accumulated mutations in hemagglutinin (HA) protein of influenza A virus generate novel antigenic strains that cause annual epidemics. RESULTS We propose a model by incorporating scoring and regression methods to predict antigenic variants. Based on collected sequences of influenza A/H3N2 viruses isolated between 1971 and 2002, our model can be used to accurately predict the antigenic variants in 1999-2004 (agreement rate = 91.67%). Twenty amino acid positions identified in our model contribute significantly to antigenic difference and are potential immunodominant positions.
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Affiliation(s)
- Yu-Chieh Liao
- Division of Biostatistics and Bioinformatics, National Health Research Institutes, Zhunan 350, Taiwan
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16
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Genetic analysis of influenza A/H3N2 and A/H1N1 viruses circulating in Vietnam from 2001 to 2006. J Clin Microbiol 2007; 46:399-405. [PMID: 17942644 DOI: 10.1128/jcm.01549-07] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza A virus has the ability to overcome immunity from previous infections through the acquisition of genetic changes. Thus, understanding the evolution of the viruses in humans is important for the surveillance and the selection of vaccine strains. A total of 30 influenza A/H3N2 viruses and 35 influenza A/H1N1 viruses that were collected in Vietnam from 2001 to 2006 were used to analyze the evolution of the hemagglutinin (HA), neuraminidase (NA), and matrix protein (M) genes. Phylogenetic analysis of individual gene segments revealed that the HA and the NA genes of the influenza A viruses evolved in a sequential way. However, the evolutionary pattern of the M gene proved to be nonlinear and was not linked with that of the HA and NA genes. Genetic drift in HA1 segments, especially in the antigenic sites of A/H3N2 viruses, occurred more frequently in A/H3N2 viruses than it did in A/H1N1 viruses. Two reassortants, one influenza A/H3N2 strain and one A/H1N1 strain, were found on the basis of the phylogenetic analysis of the three genes. While both genetic mutation and reassortment contributed to their evolution, the frequency of genetic changes and reassortment events differs between the two subtypes. As influenza viruses circulate throughout the year, we emphasize the importance of surveillance in tropical and subtropical zones, where the emergence of new strains may be detected earlier than it is in temperate zones.
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17
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Shahidi M, Kheiri MT, Amini-Bavil-Olyaee S, Hosseini M, Moattari A, Tabatabaeian M, Bashar R, Sarrami-Forooshani R, Mahboudi F. Molecular and phylogenetic analysis of human influenza virus among Iranian patients in Shiraz, Iran. J Med Virol 2007; 79:803-10. [PMID: 17457914 DOI: 10.1002/jmv.20890] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Influenza is a viral respiratory pathogen responsible for frequent seasonal epidemics. There are currently three major human influenza viruses in global circulation namely A/H1N1, A/H3N2, and B. The objective of this study was to determine the human influenza virus genotypes in Shiraz, the capital of the Fars province of Iran. Three hundred patients suspected with human influenza virus infection were enrolled in this survey (2004-2005). The throat samples were cultured and titrated by hemagglutination (HA) assay. Typing and subtyping were performed by an in-house developed multiplex RT-PCR. Moreover, the phylogenetic analysis was carried out for HA gene. A total of 24 samples were found to be positive for human influenza virus infection, 17 H1N1 and 7 H3N2. These results were in agreement with the HI assay. The phylogenetic analysis results revealed that the Iranian H1N1 isolated were close to the A/New Caledonia/20/99 vaccine strain genetically and the Iranian H3N2 isolates were also related closely to the Fujian/411/021 and California/7/2004 vaccine strains. However, a slight genetic drift was found in these isolates. In conclusion, it was demonstrated that both influenza A subtypes A/H1N1 and A/H3N2 were dominant among Iranian patients in Shiraz during the 2004/5 winter season.
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Affiliation(s)
- Mahsa Shahidi
- Influenza Unit, Pasteur Institute of Iran, Tehran, Iran
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18
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Lin B, Blaney KM, Malanoski AP, Ligler AG, Schnur JM, Metzgar D, Russell KL, Stenger DA. Using a resequencing microarray as a multiple respiratory pathogen detection assay. J Clin Microbiol 2006; 45:443-52. [PMID: 17135438 PMCID: PMC1829030 DOI: 10.1128/jcm.01870-06] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simultaneous testing for detection of infectious pathogens that cause similar symptoms (e.g., acute respiratory infections) is invaluable for patient treatment, outbreak prevention, and efficient use of antibiotic and antiviral agents. In addition, such testing may provide information regarding possible coinfections or induced secondary infections, such as virally induced bacterial infections. Furthermore, in many cases, detection of a pathogen requires more than genus/species-level resolution, since harmful agents (e.g., avian influenza virus) are grouped with other, relatively benign common agents, and for every pathogen, finer resolution is useful to allow tracking of the location and nature of mutations leading to strain variations. In this study, a previously developed resequencing microarray that has been demonstrated to have these capabilities was further developed to provide individual detection sensitivity ranging from 10(1) to 10(3) genomic copies for more than 26 respiratory pathogens while still retaining the ability to detect and differentiate between close genetic neighbors. In addition, the study demonstrated that this system allows unambiguous and reproducible sequence-based strain identification of the mixed pathogens. Successful proof-of-concept experiments using clinical specimens show that this approach is potentially very useful for both diagnostics and epidemic surveillance.
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Affiliation(s)
- Baochuan Lin
- Center for Bio/Molecular Science and Engineering, Code 6900, Naval Research Laboratory, Washington, DC 20375, USA.
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19
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Mak A, Rahmanian R, Lei V, Lawrence D, Krajden M, Brunham RC, Skowronski D, Li Y, Booth T, Goh SH, Petric M. Longitudinal analysis of genotype distribution of influenza A virus from 2003 to 2005. J Clin Microbiol 2006; 44:3583-8. [PMID: 17021086 PMCID: PMC1594783 DOI: 10.1128/jcm.02601-05] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Influenza A viruses cause yearly epidemics, in part, due to their ability to overcome immunity from previous infections through acquisition of mutations. Amino acid sequences encoded by genes 4 (HA), 6 (NA), 7 (M), and 8 (NS) from 77 H3N2 influenza A isolates, collected between November 2003 and March 2005, were analyzed to determine the extent to which the viruses mutated within epidemic periods and between the epidemics. Nucleotide and amino acid sequences were stable throughout the epidemics but experienced substantial changes between epidemics. Major changes occurred in the HA gene in 5 to 7 amino acids and the NA gene in 11 to 13 amino acids and changes of 5 amino acids occurred in the M and NS genes. In the HA gene, changes occurred in sites known to be epitopes that determine the hemagglutination inhibition reactivity, and these were shown to be associated with a change of strain from A/Fujian/411/2002-like to A/California/7/2004-like viruses. Our findings indicate that genotype determination promises to be a rapid approach for detecting new strains of influenza A viruses in a population.
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Affiliation(s)
- Annie Mak
- BC Centre for Disease Control, 655 W12th Ave., Vancouver, BC V5Z 4R4, Canada.
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20
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Wang Z, Daum LT, Vora GJ, Metzgar D, Walter EA, Canas LC, Malanoski AP, Lin B, Stenger DA. Identifying influenza viruses with resequencing microarrays. Emerg Infect Dis 2006; 12:638-46. [PMID: 16704813 PMCID: PMC3294710 DOI: 10.3201/eid1204.051441] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Resequencing microarrays rapidly identify influenza viruses. Identification of genetic variations of influenza viruses is essential for epidemic and pandemic outbreak surveillance and determination of vaccine strain selection. In this study, we combined a random amplification strategy with high-density resequencing microarray technology to demonstrate simultaneous detection and sequence-based typing of 25 geographically distributed human influenza virus strains collected in 2004 and 2005. In addition to identification, this method provided primary sequence information, which suggested that distinct lineages of influenza viruses co-circulated during the 2004–2005 season, and simultaneously identified and typed all component strains of the trivalent FluMist intranasal vaccine. The results demonstrate a novel, timely, and unbiased method for the molecular epidemiologic surveillance of influenza viruses.
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Affiliation(s)
- Zheng Wang
- Naval Research Laboratory, Washington, DC, USA
- NOVA Research Inc., Alexandria, Virginia, USA
| | - Luke T. Daum
- Air Force Institute for Operational Health, Brooks City Base, San Antonio, Texas, USA
| | | | - David Metzgar
- Naval Health Research Center, San Diego, California, USA
| | | | - Linda C. Canas
- Air Force Institute for Operational Health, Brooks City Base, San Antonio, Texas, USA
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21
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Daum LT, Canas LC, Klimov AI, Shaw MW, Gibbons RV, Shrestha SK, Myint KS, Acharya RP, Rimal N, Reese F, Niemeyer DM, Arulanandam BP, Chambers JP. Molecular analysis of isolates from influenza B outbreaks in the U.S. and Nepal, 2005. Arch Virol 2006; 151:1863-74. [PMID: 16736092 DOI: 10.1007/s00705-006-0777-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2006] [Accepted: 04/06/2006] [Indexed: 10/24/2022]
Abstract
Currently circulating influenza B viruses can be divided into two antigenically and genetically distinct lineages referred to by their respective prototype strains, B/Yamagata/16/88 and B/Victoria/2/87, based on amino acid differences in the hemagglutinin surface glycoprotein. During May and July 2005, clinical specimens from two early season influenza B outbreaks in Arizona and southeastern Nepal were subjected to antigenic (hemagglutinin inhibition) and nucleotide sequence analysis of hemagglutinin (HA1), neuraminidase (NA), and NB genes. All isolates exhibited little reactivity with the B/Shanghai/361/2002 (B/Yamagata-like) vaccine strain and significantly reduced reactivity with the previous 2003/04 B/Hong Kong/330/2001 (B/Victoria-like) vaccine strain. The majority of isolates were antigenically similar to B/Hawaii/33/2004, a B/Victoria-like reference strain. Sequence analysis indicated that 33 of 34 isolates contained B/Victoria-like HA and B/Yamagata-like NA and NB proteins. Thus, these outbreak isolates are both antigenically and genetically distinct from the current Northern Hemisphere vaccine virus strain as well as the previous 2003-04 B/Hong Kong/330/2001 (B/Victoria lineage) vaccine virus strain but are genetically similar to B/Malaysia/2506/2004, the vaccine strain proposed for the coming seasons in the Northern and Southern Hemispheres. Since these influenza B outbreaks occurred in two very distant geographical locations, these viruses may continue to circulate during the 2006 season, underscoring the importance of rapid molecular monitoring of HA, NA and NB for drift and reassortment.
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Affiliation(s)
- L T Daum
- Air Force Institute for Operational Health, Brooks City Base, TX 78235, USA.
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22
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Ansaldi F, Bacilieri S, Banfi F, Durando P, Sticchi L, Icardi G, Gasparini R. Neutralizing and hemagglutination-inhibiting activities of antibodies elicited by the 2004-2005 influenza vaccine against drifted viruses. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2006; 13:162-4. [PMID: 16426017 PMCID: PMC1356628 DOI: 10.1128/cvi.13.1.162-164.2006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 10/18/2005] [Accepted: 11/01/2005] [Indexed: 11/20/2022]
Abstract
Evaluation of the antibody responses induced by the 2004-2005 influenza vaccine strain against the homologous variant, the 2004-2005 field isolates, and a previous circulating strain showed that a correlation between neutralizing and hemagglutination-inhibiting activities exists only when the antigen is very close to the vaccine strain.
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Affiliation(s)
- Filippo Ansaldi
- Department of Health Sciences, University of Genoa, Via Pastore 1, 16100 Genoa, Italy.
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23
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Potter P. Ancient Myths and Avian Pestilence. Emerg Infect Dis 2005; 11:1332-3. [PMID: 16102301 PMCID: PMC3320490 DOI: 10.3201/eid1108.ac1108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Polyxeni Potter
- Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA.
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