scholarly journals Real-time characterization of the molecular epidemiology of an influenza pandemic

2013 ◽  
Vol 9 (5) ◽  
pp. 20130331 ◽  
Author(s):  
J. Hedge ◽  
S. J. Lycett ◽  
A. Rambaut
Keyword(s):  
Real Time ◽  
Influenza A ◽  
Sequence Data ◽  
Influenza Pandemic ◽  
H1n1 Influenza ◽  
Accurate Estimation ◽  
Time Estimates ◽  
Dataset Size ◽  
2009 H1n1

Early characterization of the epidemiology and evolution of a pandemic is essential for determining the most appropriate interventions. During the 2009 H1N1 influenza A pandemic, public databases facilitated widespread sharing of genetic sequence data from the outset. We use Bayesian phylogenetics to simulate real-time estimates of the evolutionary rate, date of emergence and intrinsic growth rate ( r 0 ) of the pandemic from whole-genome sequences. We investigate the effects of temporal range of sampling and dataset size on the precision and accuracy of parameter estimation. Parameters can be accurately estimated as early as two months after the first reported case, from 100 genomes and the choice of growth model is important for accurate estimation of r 0 . This demonstrates the utility of simple coalescent models to rapidly inform intervention strategies during a pandemic.

scholarly journals Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Ignacio Mena ◽  
Martha I Nelson ◽  
Francisco Quezada-Monroy ◽  
Jayeeta Dutta ◽  
Refugio Cortes-Fernández ◽  
...  
Keyword(s):  
Influenza A ◽  
Influenza Pandemic ◽  
H1n1 Influenza ◽  
Central Mexico ◽  
Genome Sequences ◽  
Viral Reservoirs ◽  
Long Distance ◽  
Conflicting Evidence ◽  
2009 H1n1 ◽  
H1n1 Influenza Pandemic

Asia is considered an important source of influenza A virus (IAV) pandemics, owing to large, diverse viral reservoirs in poultry and swine. However, the zoonotic origins of the 2009 A/H1N1 influenza pandemic virus (pdmH1N1) remain unclear, due to conflicting evidence from swine and humans. There is strong evidence that the first human outbreak of pdmH1N1 occurred in Mexico in early 2009. However, no related swine viruses have been detected in Mexico or any part of the Americas, and to date the most closely related ancestor viruses were identified in Asian swine. Here, we use 58 new whole-genome sequences from IAVs collected in Mexican swine to establish that the swine virus responsible for the 2009 pandemic evolved in central Mexico. This finding highlights how the 2009 pandemic arose from a region not considered a pandemic risk, owing to an expansion of IAV diversity in swine resulting from long-distance live swine trade.

scholarly journals Phylogeographic reconstruction using air transportation data and its application to the 2009 H1N1 influenza A pandemic

2019 ◽  
Author(s):  
Susanne Reimering ◽  
Sebastian Muñoz ◽  
Alice C. McHardy
Keyword(s):  
Influenza A ◽  
State Of The Art ◽  
Sequence Data ◽  
Air Transportation ◽  
H1n1 Influenza ◽  
Real Sequence ◽  
Influenza A Viruses ◽  
Geographic Spread ◽  
2009 H1n1 ◽  
Genetic Sequences

AbstractInfluenza A viruses cause seasonal epidemics and occasional pandemics in the human population. While the worldwide circulation of seasonal influenza is at least partly understood, the exact migration patterns between countries, states or cities are not well studied. Here, we use the Sankoff algorithm for parsimonious phylogeographic reconstruction together with effective distances based on a worldwide air transportation network. By first simulating geographic spread and then phylogenetic trees and genetic sequences, we confirmed that reconstructions with effective distances inferred phylogeographic spread more accurately than reconstructions with geographic distances and Bayesian reconstructions with BEAST, the current state-of-the-art. Our method extends the state-of-the-art by using fine-grained locations like airports and inferring intermediate locations not observed among sampled isolates. When applied to sequence data of the pandemic H1N1 influenza A virus in 2009, our approach correctly inferred the origin and proposed airports mainly involved in the spread of the virus. In case of a novel outbreak, this approach allows to rapidly analyze sequence data and infer origin and spread routes to improve disease surveillance and control.Author summaryInfluenza A viruses infect up to 5 million people in recurring epidemics every year. Further, viruses of zoonotic origin constantly pose a pandemic risk. Understanding the geographical spread of these viruses, including the origin and the main spread routes between cities, states or countries, could help to monitor or contain novel outbreaks. Based on genetic sequences and sampling locations, the geographic spread can be reconstructed along a phylogenetic tree. Our approach uses a parsimonious reconstruction with air transportation data and was verified using a simulation of the 2009 H1N1 influenza A pandemic. Applied to real sequence data of the outbreak, our analysis gave detailed insights into spread patterns of influenza A viruses, highlighting the origin as well as airports mainly involved in the spread.

scholarly journals Structural Characterization of the Hemagglutinin Receptor Specificity from the 2009 H1N1 Influenza Pandemic

2011 ◽  
Vol 86 (2) ◽  
pp. 982-990 ◽  
Author(s):  
R. Xu ◽  
R. McBride ◽  
C. M. Nycholat ◽  
J. C. Paulson ◽  
I. A. Wilson
Keyword(s):  
Structural Characterization ◽  
Influenza Pandemic ◽  
H1n1 Influenza ◽  
Receptor Specificity ◽  
2009 H1n1 ◽  
H1n1 Influenza Pandemic

scholarly journals The PB2-E627K Mutation Attenuates Viruses Containing the 2009 H1N1 Influenza Pandemic Polymerase

mBio ◽  
2010 ◽  
Vol 1 (1) ◽  
Author(s):  
Brett W. Jagger ◽  
Matthew J. Memoli ◽  
Zong-Mei Sheng ◽  
Li Qi ◽  
Rachel J. Hrabal ◽  
...  
Keyword(s):  
Influenza A Virus ◽  
Influenza A ◽  
H1n1 Virus ◽  
Influenza Pandemic ◽  
Influenza Infection ◽  
H1n1 Influenza ◽  
Influenza Viruses ◽  
Pandemic Virus ◽  
2009 H1n1 ◽  
Animal Reservoirs

ABSTRACTThe swine-origin H1N1 influenza A virus emerged in early 2009 and caused the first influenza pandemic in 41 years. The virus has spread efficiently to both the Northern and the Southern Hemispheres and has been associated with over 16,000 deaths. Given the virus’s recent zoonotic origin, there is concern that the virus could acquire signature mutations associated with the enhanced pathogenicity of previous pandemic viruses or H5N1 viruses with pandemic potential. We tested the hypothesis that mutations in the polymerase PB2 gene at residues 627 and 701 would enhance virulence but found that influenza viruses containing these mutations in the context of the pandemic virus polymerase complex are attenuated in cell culture and mice.IMPORTANCEInfluenza A virus (IAV) evolution is characterized by host-specific lineages, and IAVs derived in whole or in part from animal reservoirs have caused pandemics in humans. Because IAVs are known to acquire host-adaptive genome mutations, and since the PB2 gene of the 2009 H1N1 virus is of recent avian derivation, there exists concern that the pathogenicity of the 2009 H1N1 influenza A pandemic virus could be potentiated by acquisition of the host-adaptive PB2-E627K or -D701N mutations, which have been shown to enhance the virulence of other influenza viruses. We present data from a mouse model of influenza infection showing that such mutations do not increase the virulence of viruses containing the 2009 H1N1 viral polymerase.

scholarly journals Seroincidence of Influenza Among HIV-infected and HIV-uninfected Men During the 2009 H1N1 Influenza Pandemic, Bangkok, Thailand

2014 ◽  
Vol 1 (3) ◽  
Author(s):  
Shikha Garg ◽  
Sonja J. Olsen ◽  
Stefan Fernandez ◽  
Charung Muangchana ◽  
Kamonthip Rungrojcharoenkit ◽  
...  
Keyword(s):  
Influenza A ◽  
Influenza Pandemic ◽  
H1n1 Influenza ◽  
First Year ◽  
Serum Samples ◽  
Influenza A H1n1 ◽  
2009 H1n1 ◽  
Paired Serum ◽  
Sex With Men ◽  
H1n1 Influenza Pandemic

Abstract Among 368 Thai men who have sex with men with paired serum samples collected before and during the 2009 H1N1 influenza pandemic, we determined influenza A (H1N1)pdm09 seroconversion rates (≥4-fold rise in antibody titers by hemagglutination inhibition or microneutralization assays). Overall, 66 of 232 (28%) participants seroconverted after the first year of A(H1N1)pdm09 activity, and 83 of 234 (35%) participants seroconverted after the second year. Influenza A(H1N1)pdm09 seroconversion did not differ between human immunodeficiency virus (HIV)-infected (55 of 2157 [35%]) and HIV-uninfected (71 of 2211 [34%]) participants (P = .78). Influenza A(H1N1)pdm09 seroconversion occurred in approximately one third of our Thai study population and was similar among HIV-infected and HIV-uninfected participants.

A Survey-Based Assessment of United States Clinical Laboratory Response to the 2009 H1N1 Influenza Outbreak

2010 ◽  
Vol 134 (11) ◽  
pp. 1671-1678
Author(s):  
Randall T. Hayden ◽  
Megan T. Wick ◽  
Alicia B. Rodriguez ◽  
Angela M. Caliendo ◽  
Michael J. Mitchell ◽  
...  
Keyword(s):  
United States ◽  
Influenza A ◽  
Clinical Laboratory ◽  
Influenza Pandemic ◽  
H1n1 Influenza ◽  
The United States ◽  
Critical Element ◽  
Emerging Infections ◽  
Influenza Outbreak ◽  
2009 H1n1

Abstract Context.—The recent outbreak of pandemic influenza created enormous economic, logistical, and analytical challenges for clinical laboratories. Laboratory response represented a critical element in the care of affected patients, but little has been published regarding this aspect of the pandemic. Objective.—To assess the overall response of clinical diagnostic laboratories across the United States to the initial phase of the 2009 H1N1 influenza A pandemic. Design.—A 24-question survey was developed and distributed by e-mail to determine current influenza testing practices and how those practices were changed in response to the outbreak of 2009 H1N1 influenza. The survey was distributed to participants in the College of American Pathologists proficiency testing programs related to viral diagnostics. Survey questions focused on laboratory safety, communication of results, testing volume and resources, and whether changes in resource allocation or laboratory practice were anticipated in preparation for the 2009–2010 influenza season. Results.—A total of 24.3% (931) of laboratories responded to the survey. Overall, few laboratories reported changes in methodology in response to the 2009 H1N1 influenza outbreak, although, notably, the number of centers using molecular amplification methods more than doubled, from 41 to 91. Turn-around time for result reporting and safety methods used were largely as expected for individual testing modalities. Shortages in staffing, testing supplies, and personal protective equipment were reported, but most sites were able to maintain operations and did not feel that patient care was negatively affected. Conclusion.—This report provides a comprehensive picture of clinical laboratory responses in the early stages of the 2009 H1N1 influenza pandemic. These data should assist in the continued laboratory management of this outbreak and in planning for future emerging infections.

Pandemic influenza A (H1N1) virus infection and avian influenza A (H5N1) virus infection: a comparative analysisThis paper is one of a selection of papers published in this special issue entitled “Second International Symposium on Recent Advances in Basic, Clinical, and Social Medicine” and has undergone the Journal's usual peer review process.

2010 ◽  
Vol 88 (4) ◽  
pp. 575-587 ◽  
Author(s):  
Christine Korteweg ◽  
Jiang Gu
Keyword(s):  
Virus Infection ◽  
Influenza A ◽  
Peer Review Process ◽  
Influenza Pandemic ◽  
H1n1 Influenza ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
H5n1 Influenza ◽  
Influenza A H1n1 ◽  
2009 H1n1

The 2009 H1N1 and H5N1 influenza viruses are newly (re-) emerged influenza A viruses (2009 A(H1N1) and A(H5N1), respectively) that have recently posed tremendous health threats in many regions worldwide. With the 2009 outbreak of H1N1 influenza A, the world witnessed the first influenza pandemic of the 21st century. The disease has rapidly spread across the entire globe, and has resulted in hundreds of thousands of cases with confirmed infection. Although characterized by high transmissibility, the virulence and fatality of the 2009 A(H1N1) influenza virus have thus far remained relatively low. The reverse holds true for A(H5N1) influenza; at a fatality rate that exceeds 60%, it is known to cause severe damage to the human respiratory system, but is not presently capable of efficient transmission from human to human. Apart from the clear differences between the two types of influenza, there are some significant similarities that warrant attention. In particular, the more severe and fatal 2009 A(H1N1) influenza cases have shown symptoms similar to those reported in cases of A(H5N1) influenza. Histopathological findings for these cases, to the extent available, also appear to have similarities for both diseases in terms of damage and severity. Here we review important recent publications in this area, and we discuss some of the key commonalities and contrasts between the two influenza A types in terms of their biology, origins, clinical features, pathology and pathogenesis, and receptors and transmissibility.

Development of a multiplex real-time RT-PCR assay for detection of influenza A, influenza B, RSV and typing of the 2009-H1N1 influenza virus

2010 ◽  
Vol 167 (2) ◽  
pp. 113-118 ◽  
Author(s):  
Weston C. Hymas ◽  
Alan Mills ◽  
Sheri Ferguson ◽  
Janine Langer ◽  
Rosemary C. She ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Real Time ◽  
Influenza A ◽  
H1n1 Influenza ◽  
Influenza B ◽  
Rt Pcr ◽  
H1n1 Influenza Virus ◽  
Pcr Assay ◽  
2009 H1n1

Epidemiological analysis of critically ill adult patients with pandemic influenza A(H1N1) in South Korea

2012 ◽  
Vol 141 (5) ◽  
pp. 1070-1079 ◽  
Author(s):  
S. B. HONG ◽  
E. Y. CHOI ◽  
S. H. KIM ◽  
G. Y. SUH ◽  
M. S. PARK ◽  
...  
Keyword(s):  
South Korea ◽  
Influenza A ◽  
Multivariate Logistic Regression Analysis ◽  
H1n1 Influenza ◽  
Epidemiological Analysis ◽  
Influenza A H1n1 ◽  
Failure Assessment ◽  
2009 H1n1 ◽  
Independent Risk Factors ◽  
Chronic Comorbidities

SUMMARYA total of 245 patients with confirmed 2009 H1N1 influenza were admitted to the intensive-care units of 28 hospitals (South Korea). Their mean age was 55·3 years with 68·6% aged >50 years, and 54·7% male. Nine were obese and three were pregnant. One or more comorbidities were present in 83·7%, and nosocomial acquisition occurred in 14·3%. In total, 107 (43·7%) patients received corticosteroids and 66·1% required mechanical ventilation. Eighty (32·7%) patients died within 30 days after onset of symptoms and 99 (40·4%) within 90 days. Multivariate logistic regression analysis showed that the clinician's decision to prescribe corticosteroids, older age, Sequential Organ Failure Assessment score and nosocomial bacterial pneumonia were independent risk factors for 90-day mortality. In contrast with Western countries, critical illness in Korea in relation to 2009 H1N1 was most common in older patients with chronic comorbidities; nosocomial acquisition occurred occasionally but disease in obese or pregnant patients was uncommon.

scholarly journals Subcutaneous Immunization with Baculovirus Surface-Displayed Hemagglutinin of Pandemic H1N1 Influenza A Virus Induces Protective Immunity in Mice

2011 ◽  
Vol 18 (9) ◽  
pp. 1582-1585 ◽  
Author(s):  
Mookkan Prabakaran ◽  
Tao Meng ◽  
Fang He ◽  
Tan YunRui ◽  
Jia Qiang ◽  
...  
Keyword(s):  
Virus Infection ◽  
Protective Immunity ◽  
Influenza A ◽  
H1n1 Virus ◽  
H1n1 Influenza ◽  
Influenza Virus Hemagglutinin ◽  
Inactive Form ◽  
2009 H1n1 ◽  
Subcutaneous Immunization ◽  
H1n1 Virus Infection

ABSTRACTThe protective immunity of baculovirus displaying influenza virus hemagglutinin (BacHA) against influenza 2009 H1N1 virus infection in a murine model was investigated. The results showed that mice vaccinated with live BacHA or an inactive form of adjuvanted BacHA had enhanced specific antibody responses and induced protective immunity against 2009 H1N1 virus infection, suggesting the potential of baculovirus as a live or inactivated vaccine.

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