Evolution-informed forecasting of seasonal influenza A (H3N2)

2017 ◽  
Author(s):  
Xiangjun Du ◽  
Aaron A. King ◽  
Robert J. Woods ◽  
Mercedes Pascual
Keyword(s):  
Influenza A ◽  
Seasonal Influenza ◽  
The United States ◽  
Evolutionary Change ◽  
Amino Acid Sequences ◽  
Epidemiological Surveillance ◽  
Transmission Model ◽  
Genetic Sequences ◽  
Antigenic Evolution ◽  
H3n2 Influenza

ABSTRACTInter-pandemic or seasonal influenza exacts an enormous annual burden both in terms of human health and economic impact. Incidence prediction ahead of season remains a challenge largely because of the virus’ antigenic evolution. We propose here a forecasting approach that incorporates evolutionary change into a mechanistic epidemiological model. The proposed models are simple enough that their parameters can be estimated from retrospective surveillance data. These models link amino-acid sequences of hemagglutinin epitopes with a transmission model for seasonal H3N2 influenza, also informed by H1N1 levels. With a monthly time series of H3N2 incidence in the United States over 10 years, we demonstrate the feasibility of prediction ahead of season and an accurate real-time forecast for the 2016/2017 influenza season.SUMMARYSkillful forecasting of seasonal (H3N2) influenza incidence ahead of the season is shown to be possible by means of a transmission model that explicitly tracks evolutionary change in the virus, integrating information from both epidemiological surveillance and readily available genetic sequences.

scholarly journals Antigenic evolution of H3N2 influenza A viruses in swine in the United States from 2012 to 2016

2018 ◽  
Vol 13 (1) ◽  
pp. 83-90 ◽  
Author(s):  
Marcus J. Bolton ◽  
Eugenio J. Abente ◽  
Divya Venkatesh ◽  
Jered A. Stratton ◽  
Michael Zeller ◽  
...  
Keyword(s):  
United States ◽  
Influenza A ◽  
The United States ◽  
Influenza A Viruses ◽  
Antigenic Evolution ◽  
H3n2 Influenza

scholarly journals Competitive evolution of H1N1 and H3N2 influenza viruses in the United States

2021 ◽  
Author(s):  
Chaiwat Wilasang ◽  
Pikkanet Suttirat ◽  
Anuwat Wiratsudakul ◽  
Sudarat Chadsuthi ◽  
Charin Modchang
Keyword(s):  
United States ◽  
Amino Acid ◽  
Disease Transmission ◽  
The United States ◽  
Evolutionary Change ◽  
Amino Acid Sequences ◽  
Influenza Viruses ◽  
Time Varying ◽  
Competitive Evolution ◽  
H3n2 Influenza

Seasonal influenza causes vast public health and economic impact globally. The prevention and control of the annual epidemics remain a challenge due to the antigenic evolution of the viruses. Here, we presented a novel modeling framework based on changes in amino acid sequences and relevant epidemiological data to retrospectively investigate the competitive evolution and transmission of H1N1 and H3N2 influenza viruses in the United States during October 2002 and April 2019. To do so, we estimated the time-varying disease transmission rate from the reported influenza cases and the time-varying evolutionary rate of the viruses from the changes in amino acid sequences. By incorporating these time-varying rates into the transmission models, we found that the models could accurately capture the evolutionary transmission dynamics of influenza viruses in the United States. Our modeling results also showed that models incorporating evolutionary change of the virus could provide better modeling performance suggesting the critical role of the evolutionary change of virus on the disease transmission.

scholarly journals Next generation methodology for updating HA vaccines against emerging human seasonal influenza A(H3N2) viruses

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
James D. Allen ◽  
Ted M. Ross
Keyword(s):  
Influenza Virus ◽  
Immune Responses ◽  
Influenza A ◽  
Seasonal Influenza ◽  
Influenza Viruses ◽  
Next Generation ◽  
Virus Infections ◽  
Wild Type ◽  
Influenza Hemagglutinin ◽  
H3n2 Influenza

AbstractWhile vaccines remain the best tool for preventing influenza virus infections, they have demonstrated low to moderate effectiveness in recent years. Seasonal influenza vaccines typically consist of wild-type influenza A and B viruses that are limited in their ability to elicit protective immune responses against co-circulating influenza virus variant strains. Improved influenza virus vaccines need to elicit protective immune responses against multiple influenza virus drift variants within each season. Broadly reactive vaccine candidates potentially provide a solution to this problem, but their efficacy may begin to wane as influenza viruses naturally mutate through processes that mediates drift. Thus, it is necessary to develop a method that commercial vaccine manufacturers can use to update broadly reactive vaccine antigens to better protect against future and currently circulating viral variants. Building upon the COBRA technology, nine next-generation H3N2 influenza hemagglutinin (HA) vaccines were designed using a next generation algorithm and design methodology. These next-generation broadly reactive COBRA H3 HA vaccines were superior to wild-type HA vaccines at eliciting antibodies with high HAI activity against a panel of historical and co-circulating H3N2 influenza viruses isolated over the last 15 years, as well as the ability to neutralize future emerging H3N2 isolates.

scholarly journals Unseasonal Transmission of H3N2 Influenza A Virus During the Swine-Origin H1N1 Pandemic

2010 ◽  
Vol 84 (11) ◽  
pp. 5715-5718 ◽  
Author(s):  
Elodie Ghedin ◽  
David E. Wentworth ◽  
Rebecca A. Halpin ◽  
Xudong Lin ◽  
Jayati Bera ◽  
...  
Keyword(s):  
New York ◽  
Influenza A Virus ◽  
Influenza A ◽  
New York State ◽  
The United States ◽  
Influenza Viruses ◽  
Influenza A Viruses ◽  
York State ◽  
Low Incidence ◽  
H3n2 Influenza

ABSTRACT The initial wave of swine-origin influenza A virus (pandemic H1N1/09) in the United States during the spring and summer of 2009 also resulted in an increased vigilance and sampling of seasonal influenza viruses (H1N1 and H3N2), even though they are normally characterized by very low incidence outside of the winter months. To explore the nature of virus evolution during this influenza “off-season,” we conducted a phylogenetic analysis of H1N1 and H3N2 sequences sampled during April to June 2009 in New York State. Our analysis revealed that multiple lineages of both viruses were introduced and cocirculated during this time, as is typical of influenza virus during the winter. Strikingly, however, we also found strong evidence for the presence of a large transmission chain of H3N2 viruses centered on the south-east of New York State and which continued until at least 1 June 2009. These results suggest that the unseasonal transmission of influenza A viruses may be more widespread than is usually supposed.

scholarly journals Genetic and Antigenic Evolution of European Swine Influenza A Viruses of HA-1C (Avian-Like) and HA-1B (Human-Like) Lineages in France from 2000 to 2018

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1304
Author(s):  
Amélie Chastagner ◽  
Séverine Hervé ◽  
Stéphane Quéguiner ◽  
Edouard Hirchaud ◽  
Pierrick Lucas ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Phylogenetic Analyses ◽  
Swine Influenza ◽  
Amino Acid Sequences ◽  
Antigenic Drift ◽  
Influenza A Viruses ◽  
Double Deletion ◽  
Antigenic Evolution ◽  
Amino Acid Mutations

This study evaluated the genetic and antigenic evolution of swine influenza A viruses (swIAV) of the two main enzootic H1 lineages, i.e., HA-1C (H1av) and -1B (H1hu), circulating in France between 2000 and 2018. SwIAV RNAs extracted from 1220 swine nasal swabs were hemagglutinin/neuraminidase (HA/NA) subtyped by RT-qPCRs, and 293 virus isolates were sequenced. In addition, 146 H1avNy and 105 H1huNy strains were submitted to hemagglutination inhibition tests. H1avN1 (66.5%) and H1huN2 (25.4%) subtypes were predominant. Most H1 strains belonged to HA-1C.2.1 or -1B.1.2.3 clades, but HA-1C.2, -1C.2.2, -1C.2.3, -1B.1.1, and -1B.1.2.1 clades were also detected sporadically. Within HA-1B.1.2.3 clade, a group of strains named “Δ146-147” harbored several amino acid mutations and a double deletion in HA, that led to a marked antigenic drift. Phylogenetic analyses revealed that internal segments belonged mainly to the “Eurasian avian-like lineage”, with two distinct genogroups for the M segment. In total, 17 distinct genotypes were identified within the study period. Reassortments of H1av/H1hu strains with H1N1pdm virus were rarely evidenced until 2018. Analysis of amino acid sequences predicted a variability in length of PB1-F2 and PA-X proteins and identified the appearance of several mutations in PB1, PB1-F2, PA, NP and NS1 proteins that could be linked to virulence, while markers for antiviral resistance were identified in N1 and N2. Altogether, diversity and evolution of swIAV recall the importance of disrupting the spreading of swIAV within and between pig herds, as well as IAV inter-species transmissions.

scholarly journals Risk Factors and Outcomes for Pandemic H1N1 Influenza Compared with Seasonal Influenza in Hospitalized Children in China

2012 ◽  
Vol 23 (4) ◽  
pp. 199-203 ◽  
Author(s):  
Qingli Zhang ◽  
Wei Ji ◽  
Zhongqin Guo ◽  
Zhenjiang Bai ◽  
Noni E MacDonald
Keyword(s):  
Influenza A ◽  
Seasonal Influenza ◽  
Case Series ◽  
H1n1 Influenza ◽  
The United States ◽  
Intensive Care Unit Care ◽  
Hospitalized Children ◽  
Pandemic H1n1 Influenza ◽  
The Mean ◽  
Secondary Bacterial Pneumonia

OBJECTIVE: To compare clinical features and outcomes of children hospitalized in China with pandemic (p)H1N1 between 2009 and 2010 versus seasonal influenza A between 2008 and 2009.METHODS: Systematic review of laboratory-confirmed admissions to the Children’s Hospital, Soochow University (Suzhou, China).RESULTS: Seventy-five children younger than 14 years of age were admitted with pH1N1, 70 with H3N2 and three with seasonal H1N1. With pH1N1, the mean age was older (36 months versus seven months), the length of stay was longer (nine days versus seven days), underlying conditions were more common (29% versus 15%), anemia was more common (11% versus 0%) (P<0.05), with trends toward more secondary bacterial pneumonia and intensive care unit care, compared with seasonal influenza. Two of the 75 children with pH1N1 died versus no deaths in children with seasonal influenza. None of the children had received pH1N1, seasonal influenza, conjugated pneumococal orHaemophilus influenzaeb vaccines.CONCLUSION: In China, children hospitalized with pH1N1 influenza differed from case series in Canada, Argentina and the United States, suggesting that locale, background and health care system influenced the presentation and outcomes of pandemic and seasonal influenza.

scholarly journals The Geographic Synchrony of Seasonal Influenza: A Waves across Canada and the United States

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e21471 ◽  
Author(s):  
Dena L. Schanzer ◽  
Joanne M. Langley ◽  
Trevor Dummer ◽  
Samina Aziz
Keyword(s):  
United States ◽  
Influenza A ◽  
Seasonal Influenza ◽  
The United States

scholarly journals Lessons from the Past: Comparison of the Disease Burden of the Influenza A (H1N1) Pandemic 2009-10 and Seasonal Influenza 2010-2019 in the United States

2021 ◽  
Author(s):  
James A Koziol
Keyword(s):  
United States ◽  
Influenza A ◽  
Disease Burden ◽  
Seasonal Influenza ◽  
The United States ◽  
H1n1 Pandemic ◽  
Elderly Adults ◽  
The Past ◽  
Medical Visits ◽  
Influenza A H1n1

Abstract Background Annual influenza outbreaks constitute a major public health concern, both in the United States and worldwide. Comparisons of the health burdens of outbreaks might lead to the identification of specific at-risk populations, for whom public health resources should be marshaled appropriately and equitably. Methods We examined the disease burden of the 2009-10 influenza A (H1N1) pandemic relating to illnesses, medical visits, hospitalizations, and mortality, compared to influenza seasons 2010 to 2019, in the United States, as compiled by the Centers for Disease Control. Results With regard to seasonal influenza, rates of illnesses and medical visits were highest in infants aged 0–4 years, followed by adults aged 50–64 years. Rates of hospitalizations and deaths evinced a starkly different pattern, both dominated by elderly adults aged 65 and over. Youths aged 0 to 17 years were especially adversely affected by the H1N1 pandemic relative to hospitalizations and mortality compared to seasonal influenza; but curiously the opposite pattern was observed in elderly adults (aged 65 and older). Conclusions The disease burden of the 2009-10 influenza A pandemic was strikingly unlike that observed in the subsequent influenza seasons 2010 to 2019, in the United States: the past did not predict the future.

scholarly journals Optimizing antiviral treatment for seasonal influenza in the United States: A Mathematical Modeling Analysis

2020 ◽  
Author(s):  
Matan Yechezkel ◽  
Martial Ndeffo-Mba ◽  
Dan Yamin
Keyword(s):  
United States ◽  
High Risk ◽  
Seasonal Influenza ◽  
Antiviral Treatment ◽  
Social Contact ◽  
Population Level ◽  
The United States ◽  
Transmission Model ◽  
High Risk Patients ◽  
Risk Patients

Seasonal influenza remains a major health burden in the United States. Despite recommendations of early antiviral treatment of high-risk patients, the effective treatment coverage remains very low. We developed an influenza transmission model that incorporates data on infectious viral load, social contact, and healthcare-seeking behavior, to evaluate the population-level impact of increasing antiviral treatment timeliness and coverage among high-risk patients in the US. We found that increasing the rate of early treatment among high-risk patients who received treatment more than 48 hours after symptoms onset, would substantially avert infections and influenza-induced hospitalizations. We found that treatment of the elderly has the highest impact on reducing hospitalizations, whereas treating high-risk individuals aged 5-19 years old has the highest impact on transmission. The population-level impact of increased timeliness and coverage of treatment among high-risk patients was observed regardless of seasonal influenza vaccination coverage and the severity of the influenza season.

scholarly journals Pathogenesis and Transmission of Genetically Diverse Swine-Origin H3N2 Variant Influenza A Viruses from Multiple Lineages Isolated in the United States, 2011–2016

2018 ◽  
Vol 92 (16) ◽  
Author(s):  
Xiangjie Sun ◽  
Joanna A. Pulit-Penaloza ◽  
Jessica A. Belser ◽  
Claudia Pappas ◽  
Melissa B. Pearce ◽  
...  
Keyword(s):  
United States ◽  
Respiratory Tract ◽  
Influenza A ◽  
Seasonal Influenza ◽  
The United States ◽  
Influenza Viruses ◽  
Upper Respiratory Tract ◽  
Pandemic Preparedness

ABSTRACTWhile several swine-origin influenza A H3N2 variant (H3N2v) viruses isolated from humans prior to 2011 have been previously characterized for their virulence and transmissibility in ferrets, the recent genetic and antigenic divergence of H3N2v viruses warrants an updated assessment of their pandemic potential. Here, four contemporary H3N2v viruses isolated during 2011 to 2016 were evaluated for their replicative ability in bothin vitroandin vivoin mammalian models as well as their transmissibility among ferrets. We found that all four H3N2v viruses possessed similar or enhanced replication capacities in a human bronchial epithelium cell line (Calu-3) compared to a human seasonal influenza virus, suggestive of strong fitness in human respiratory tract cells. The majority of H3N2v viruses examined in our study were mildly virulent in mice and capable of replicating in mouse lungs with different degrees of efficiency. In ferrets, all four H3N2v viruses caused moderate morbidity and exhibited comparable titers in the upper respiratory tract, but only 2 of the 4 viruses replicated in the lower respiratory tract in this model. Furthermore, despite efficient transmission among cohoused ferrets, recently isolated H3N2v viruses displayed considerable variance in their ability to transmit by respiratory droplets. The lack of a full understanding of the molecular correlates of virulence and transmission underscores the need for close genotypic and phenotypic monitoring of H3N2v viruses and the importance of continued surveillance to improve pandemic preparedness.IMPORTANCESwine-origin influenza viruses of the H3N2 subtype, with the hemagglutinin (HA) and neuraminidase (NA) derived from historic human seasonal influenza viruses, continue to cross species barriers and cause human infections, posing an indelible threat to public health. To help us better understand the potential risk associated with swine-origin H3N2v viruses that emerged in the United States during the 2011-2016 influenza seasons, we use bothin vitroandin vivomodels to characterize the abilities of these viruses to replicate, cause disease, and transmit in mammalian hosts. The efficient respiratory droplet transmission exhibited by some of the H3N2v viruses in the ferret model combined with the existing evidence of low immunity against such viruses in young children and older adults highlight their pandemic potential. Extensive surveillance and risk assessment of H3N2v viruses should continue to be an essential component of our pandemic preparedness strategy.

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