Genetic drift of influenza A(H3N2) viruses during two consecutive seasons in 2011-2013 in Corsica, France

Protein Microarray Analysis of the Specificity and Cross-Reactivity of Influenza Virus Hemagglutinin-Specific Antibodies

Current seasonal influenza virus vaccines engender antibody-mediated protection that is hemagglutinin (HA) subtype specific and relatively short-lived. Coverage for other subtypes or even variants within a subtype could be improved from a better understanding of the factors that promote HA-specific antibody cross-reactivity. Current assays to evaluate cross-reactivity, such as the ELISA, require a separate test for each antigen and are neither high-throughput nor sample-sparing. To address this need, we produced an array of 283 purified HA proteins from influenza A virus subtypes H1 to H16 and H18 and influenza B virus. To evaluate performance, arrays were probed with sera from individuals before and after a booster dose of inactivated heterologous H5N1 vaccine and naturally infected cases at presentation and follow-up during the 2010 to 2011 influenza season, when H3N2 was prevalent. The response to the H5 vaccine boost was IgG only and confined to H5 variants. The response to natural H3N2 infection consisted of IgG and IgA and was reactive with all H3 variants displayed, as well as against other group 2 HA subtypes. In both groups, responses to HA1 proteins were subtype specific. In contrast, baseline signals were higher, and responses broader, against full-length HA proteins (HA1+HA2) compared to HA1 alone. We propose that these elevated baseline signals and breadth come from the recognition of conserved epitopes in the stalk domain by cross-reactive antibodies accumulated from previous exposure(s) to seasonal influenza virus. This array is a valuable high-throughput alternative to the ELISA for monitoring specificity and cross-reactivity of HA antibodies and has many applications in vaccine development.IMPORTANCE Seasonal influenza is a serious public health problem because the viral infection spreads easily from person to person and because of antigenic drift in neutralizing epitopes. Influenza vaccination is the most effective way to prevent the disease, although challenging because of the constant evolution of influenza virus subtypes. Our high-throughput protein microarrays allow for interrogation of subunit-specific IgG and IgA responses to 283 different HA proteins comprised of HA1 and HA2 domains as well as full-length HA proteins. This provides a tool that allows for novel insights into the response to exposure to influenza virus antigens. Data generated with our technology will enhance our understanding of the factors that improve the strength, breadth, and durability of vaccine-mediated immune responses and develop more effective vaccines.

Semi-quantitative Influenza A population averages from a multiplex respiratory viral panel (RVP): potential for reflecting target sequence changes affecting the assay

Background

Yearly influenza virus mutations potentially affect the performance of molecular assays, if nucleic acid changes involve the sequences in the assay. Because individual patient viral loads depend on variables such as duration of illness, specimen type, age, and immunosuppression, we examined seasonal population averages of positive tests to smooth inherent variability.

Methods

We studied the population seasonal averages of the semi-quantitative nAMPs for the influenza matrix and hemagglutinin genes in the GenMark (Carlsbad, CA) Respiratory Viral Panel assay between 3 institutions over 3 Influenza seasons.

Results

Population average nAMPs were strikingly consistent between separate institutions, but differed substantially between H3N2 and H1N1 seasons. In the 2012–2013 and 2014–2015 influenza seasons, matrix gene H3N2 nAMP averages were 50–70% less than those of the same assay in the 2013–2014 H1N1 season. Influenza strains representative of these seasons were grown in tissue culture and when the supernatant virus was adjusted to the same copy number using a TaqMan assay, the same relative differences were reproduced in the RVP assay. Because the sequences for the PCR and PCR product detection in the GenMark assay are proprietary, the manufacturer provided single stranded DNA matching the capture probe for the representative H3N2 (3 mismatches) and H1N1 strains (2 different mismatches). Equimolar concentrations of these synthetic DNA sequences gave average nAMP values that closely correlated with the average nAMPS of the representative strains and their respective seasonal averages.

Conclusions

Seasonal averages of semi-quantitative data may provide a means to follow assay performance as a reflection of the effects of molecular drift.

Age-specific genetic and antigenic variations of influenza A viruses in Hong Kong, 2013-2014

Age-specific genetic and antigenic variations of influenza viruses have not been documented in tropical and subtropical regions. We implemented a systematic surveillance program in two tertiary hospitals in Hong Kong Island, to collect 112 A(H1N1)pdm09 and 254 A(H3N2) positive specimens from 2013 to 2014. Of these, 56 and 72 were identified as genetic variants of the WHO recommended vaccine composition strains, respectively. A subset of these genetic variants was selected for hemagglutination-inhibition (HI) tests, but none appeared to be antigenic variants of the vaccine composition strains. We also found that genetic and antigenicity variations were similar across sex and age groups of ≤18 yrs, 18 to 65 yrs, and ≥65 yrs. Our findings suggest that none of the age groups led other age groups in genetic evolution of influenza virus A strains. Future studies from different regions and longer study periods are needed to further investigate the age and sex heterogeneity of influenza viruses.

Assessing Antigenic Drift of Seasonal Influenza A(H3N2) and A(H1N1)pdm09 Viruses

Under selective pressure from the host immune system, antigenic epitopes of influenza virus hemagglutinin (HA) have continually evolved to escape antibody recognition, termed antigenic drift. We analyzed the genomes of influenza A(H3N2) and A(H1N1)pdm09 virus strains circulating in Thailand between 2010 and 2014 and assessed how well the yearly vaccine strains recommended for the southern hemisphere matched them. We amplified and sequenced the HA gene of 120 A(H3N2) and 81 A(H1N1)pdm09 influenza virus samples obtained from respiratory specimens and calculated the perfect-match vaccine efficacy using the p_epitope model, which quantitated the antigenic drift in the dominant epitope of HA. Phylogenetic analysis of the A(H3N2) HA1 genes classified most strains into genetic clades 1, 3A, 3B, and 3C. The A(H3N2) strains from the 2013 and 2014 seasons showed very low to moderate vaccine efficacy and demonstrated antigenic drift from epitopes C and A to epitope B. Meanwhile, most A(H1N1)pdm09 strains from the 2012–2014 seasons belonged to genetic clades 6A, 6B, and 6C and displayed the dominant epitope mutations at epitopes B and E. Finally, the vaccine efficacy for A(H1N1)pdm09 (79.6–93.4%) was generally higher than that of A(H3N2). These findings further confirmed the accelerating antigenic drift of the circulating influenza A(H3N2) in recent years.

Predicting clinical severity based on substitutions near epitope A of influenza A/H3N2

Epitopes are the main targets for specific antibodies in the host defense systems. Recent studies have shown that amino acid (aa) substitutions located within the influenza A/H3N2 hemagglutinin 1 (HA1) epitopes A-E, particularly in A and B, result in antigenic drift. Viruses with such drift mutations may have resulted in more severe influenza-related illness during influenza epidemics between late 2012 and early 2015. We sought to quantify vaccine mismatches in epitopes A-E of the HA1 protein, and correlate these with the severity of the patient's illness. The influenza A/H3N2 clinical samples were collected between April 2009 and November 2013 (n=206). Patients were clinically stratified into groups with mild, moderate, and severe influenza-like illness (ILI). The impact of the number of aa mismatches in each of epitopes A-E, gender, age groups (⩽18, 19-64, ⩾65 years), and comorbidities on the likelihood that patients would suffer moderate and/or severe ILI due to influenza A/H3N2 infection were assessed. A higher number of aa mismatches in epitope A between the vaccine and locally circulating viruses correlated with more severe influenza infection, although this correlation was most significant with pre-existing comorbidities. A practical application of this finding would be to monitor patients (especially those in high-risk groups) infected with such viruses more closely, as they are at increased risk of developing more serious disease. Epidemiologically, it was of interest to note that viruses from subclade 3A of Victoria/208 strain were not detected in Singapore between 2009 and 2012. By contrast, these viruses were detected at a prevalence of up to 40% in the 2011-2012 influenza seasons in other regions of the Northern and Southern hemispheres. Such findings support the rationale for more regionally customized seasonal influenza vaccine compositions to optimize the protection of the population against locally circulating virus strains.

Determining drug efficacy parameters for mathematical models of influenza

Antivirals are the first line of defence against influenza, so drug efficacy should be re-evaluated for each new strain. However, due to the time and expense involved in assessing the efficacy of drug treatments both in vitro and in vivo, treatment regimens are largely not re-evaluated even when strains are found to be resistant to antivirals. Mathematical models of the infection process can help in this assessment, but for accurate model predictions, we need to measure model parameters characterizing the efficacy of antivirals. We use computer simulations to explore whether in vitro experiments can be used to extract drug efficacy parameters for use in viral kinetics models. We find that the efficacy of neuraminidase inhibitors can be determined by measuring viral load during a single cycle assay, while the efficacy of adamantanes can be determined by measuring infected cells during the preparation stage for the single cycle assay.

Role of Preschool and Primary School Children in Epidemics of Influenza A in a Local Community in Japan during Two Consecutive Seasons with A(H3N2) as a Predominant Subtype

Enhanced influenza surveillance was implemented to analyze transmission dynamics particularly driving force of influenza transmission in a community during 2011/12 and 2012/13 seasons in Odate City, Japan. In these two consecutive seasons, influenza A(H3N2) was the predominant influenza A subtype. Suspected influenza cases were tested by commercial rapid test kits. Demographic and epidemiological information of influenza positive cases were recorded using a standardized questionnaire, which included age or age group, date of visit, date of fever onset, and the result of rapid test kit. Epidemiological parameters including epidemic midpoint (EM) and growth rate (GR) were analyzed. In 2012/13 season, numbers of influenza A positive cases were significantly lower among preschool (212 cases) and primary school (224 cases) children than in 2011/12 season (461 and 538 cases, respectively). Simultaneously, total influenza A cases were also reduced from 2,092 in 2011/12 season to 1,846 in 2012/13 season. The EMs in preschool and primary school children were earlier than EMs for adult and all age group in both 2011/12 and 2012/13 seasons. The GR in 2012/13 season was significantly lower than that in 2011/12 season (0.11 and 0.18, respectively, p = 0.003). Multiple linear regression analysis by school districts revealed that GRs in both seasons were significantly correlated with the incidence of school age children. Our findings suggest that preschool and primary school children played an important role as a driving force of epidemics in the community in both 2011/12 and 2012/13 seasons. The reduction of total influenza A cases in 2012/13 season can be explained by decreased susceptible population in these age groups due to immunity acquired by infections in 2011/12 season. Further investigations are needed to investigate the effect of pre-existing immunity on influenza transmission in the community.

Epidemiology and viral etiology of the influenza-like illness in corsica during the 2012-2013 Winter: an analysis of several sentinel surveillance systems

Influenza-like illness (ILI) surveillance is important to identify circulating and emerging/reemerging strains and unusual epidemiological trends. The present study aimed to give an accurate picture of the 2012-2013 ILI outbreak in Corsica by combining data from several surveillance systems: general practice, emergency general practice, hospital emergency units, intensive care units, and nursing homes. Twenty-eight respiratory viruses were retrospectively investigated from patients in general practice with ILI. Sequence analysis of the genetic changes in the hemagglutinin gene of influenza viruses (A(H1N1)pdm2009, A(H3N2) and B) was performed. The trends in ILI/influenza consultation rates and the relative illness ratios (RIRs) of having an ILI consultation were estimated by age group for the different surveillance systems analyzed. Of the 182 ILI patients enrolled by general practitioners, 57.7% tested positive for influenza viruses. Phylogenetic analyses suggested a genetic drift for influenza B and A(H3N2) viruses. The ILI/influenza surveillance systems showed similar trends and were well correlated. In accordance with virological data, the RIRs of having an ILI consultation were highest among the young (<15 years old) and decreased with age. No clusters of acute respiratory illness were declared by the sentinel nursing homes. This study is noteworthy in that it is the first extensive description of the 2012-2013 ILI outbreak in Corsica as monitored through several surveillance systems. To improve ILI surveillance in Corsica, a consortium that links together the complementary regional surveillance ILI systems described here is being implemented.

Effectiveness of 2012-2013 influenza vaccine against influenza-like illness in general population: estimation in a French web-based cohort

Most of the methods used for estimating the influenza vaccine effectiveness (IVE) target the individuals who have an influenza-like illness (ILI) rather than virologically-proven influenza and access the healthcare system. The objective of this study was to estimate the 2012-2013 IVE in general French population, using a cohort of volunteers registered on GrippeNet.fr, an online surveillance system for ILI. The IVE estimations were obtained through a logistic regression, and analyses were also performed by focusing on at-risk population of severe influenza, and by varying inclusion period and ILI definition. Overall, 1996 individuals were included in the analyses. The corrected IVE was estimated to 49% (20 to 67) for the overall population, and 32% (0 to 58) for the at-risk population. Three covariables appeared with a significant effect on the occurrence of at least one ILI during the epidemic: the age (P = 0.045), the presence of a child in the household (P<10(-3)), and the frequency of cold/flu (P<10(-3)). Comparable results were found at epidemic peak time in the hypothesis of real-time feed of data. In this study, we proposed a novel, follow-up, web-based method to reveal seasonal vaccine effectiveness, which enables analysis in a portion of the population that is not tracked by the health care system in most VE studies.