New variants and age shift to high fatality groups contribute to severe successive waves in the 2009 influenza pandemic in Taiwan

A highly efficient and accurate method of detecting and subtyping Influenza A pdm H1N1 and H3N2 viruses with newly emerging mutations in the matrix gene in Eastern Taiwan

The rapid identification of Influenza A virus and its variants, which cause severe respiratory diseases, is imperative to providing timely treatment and improving patient outcomes. Conventionally, two separate assays (total test duration of up to 6 h) are required to initially differentiate Influenza A and B viruses and subsequently distinguish the pdm H1N1 and H3N2 serotypes of Influenza A virus. In this study, we developed a multiplex real-time RT-PCR method for simultaneously detecting Influenza A and B viruses and subtyping Influenza A virus, with a substantially reduced test duration. Clinical specimens from hospitalized patients and outpatients with influenza-like symptoms in Eastern Taiwan were collected between 2011 and 2015, transported to Hualien Tzu Chi Hospital, and analyzed. Conventional RT-PCR was used to subtype the isolated Influenza A viruses. Thereafter, for rapid identification, the multiplex real-time RT-PCR method was developed and applied to identify the conserved regions that aligned with the available primers and probes. Accordingly, a multiplex RT-PCR assay with three groups of primers and probes (MAF and MAR primers and MA probe; InfAF and InfAR primers and InfA probe; and MBF and MBR primers and MB probe) was established to distinguish these viruses in the same reaction. Thus, with this multiplex RT-PCR assay, Influenza B, Influenza A pdm H1N1, and Influenza A H3N2 viruses were accurately detected and differentiated within only 2.5 h. This multiplex RT-PCR assay showed similar analytical sensitivity to the conventional singleplex assay. Further, the phylogenetic analyses of our samples revealed that the characteristics of these viruses were different from those reported previously using samples collected during 2012–2013. In conclusion, we developed a multiplex real-time RT-PCR method for highly efficient and accurate detection and differentiation of Influenza A and B viruses and subtyping Influenza A virus with a substantially reduced test duration for diagnosis.

Human infection with a reassortant swine-origin influenza A(H1N2)v virus in Taiwan, 2021

Background

Influenza A virus infections occur in different species, causing mild-to-severe symptoms that lead to a heavy disease burden. H1N1, H1N2 and H3N2 are major subtypes of swine influenza A viruses in pigs and occasionally infect humans.

Methods

A case infected by novel influenza virus was found through laboratory surveillance system for influenza viruses. Clinical specimens were tested by virus culture and/or real-time RT–PCR. The virus was identified and characterized by gene sequencing and phylogenetic analysis.

Results

In 2021, for the first time in Taiwan, an influenza A(H1N2)v virus was isolated from a 5-year old girl who was suffering from fever, runny nose and cough. The isolated virus was designated A/Taiwan/1/2021(H1N2)v. Full-genome sequencing and phylogenetic analyses revealed that A/Taiwan/1/2021(H1N2)v is a novel reassortant virus containing hemagglutinin (HA) and neuraminidase (NA) gene segments derived from swine influenza A(H1N2) viruses that may have been circulating in Taiwan for decades, and the other 6 internal genes (PB2, PB2, PA, NP, M and NS) are from human A(H1N1)pdm09 viruses.

Conclusion

Notably, the HA and NA genes of A/Taiwan/1/2021(H1N2)v separately belong to specific clades that are unique for Taiwanese swine and were proposed to be introduced from humans in different time periods. Bidirectional transmission between humans and swine contributes to influenza virus diversity and poses the next pandemic threat.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-022-01794-2.

Evaluation of Pregnancy, Younger Age, and Old Age as Independent Risk Factors for Poor Hospitalization Outcomes in Influenza A (H1N1)pdm09 Virus a Decade After the Pandemic

Introduction The influenza A (H1N1)pdm09 virus infection was first reported in Mexico in 2009 and quickly became the first flu pandemic of the 21st century. Statistics show that the prevalence of H1N1 infection was higher among young adults during the pandemic while the elderly were at more risk of death. However; many studies have shown a gradual change over the years, with attack rates increasing in older adults as compared to young adults. The other significant vulnerable group for this infection seems to be pregnant women. Over the years, many authors have found that pregnancy may not be a significant risk factor for increased hospitalization and poorer outcomes. This study aims to perform a comparative analysis and thereby assess pregnancy, younger age, and old age as independent risk factors for poor hospitalization outcomes. Materials and methods The hospital records of all patients with H1N1 infection admitted between January 1, 2018, to December 31, 2018, were screened. The patients included in the study were young adults (18-31 years), pregnant women, and the elderly (≥65 years). Comparative analysis was done between them. Nominal variables were compared using the chi-square test. Results A total of 379 patients were admitted to our hospital with H1N1 infection from January 1, 2018, to December 31, 2018. There were 75 elderly (19.7%), 224 (59%) middle-aged adults, 55 (14.5%) young adults, and 25 (6.5%) pregnant women. Fever (90%, 84%, and 96%) and cough with expectoration (72%, 67.3%, and 40%) were the most prevalent symptoms. The elderly reported more dyspnoea (28% vs. 5.5%, 4 %). Diabetes mellitus was found in 73.3 % of the elderly, 3.6% of the young adults, and 12% of pregnant women. Hypertension was present in 45% of the elderly, 1.8% of young adults, and 4% of pregnant women. Coronary artery disease was seen in 22.7% of the elderly and 1.8% of young adults. Chronic kidney disease (5.3%) and chronic obstructive pulmonary disease (13.3%) were seen only in the elderly group. Relative lymphopenia was prevalent in all groups and was more in pregnant women (76% vs. 61.8% and 41.8%) as compared to other groups. Serum creatinine was elevated in 38% of the elderly, 2% of young adults, and 0% of pregnant women. Abnormal chest radiograph was reported for 48% of the elderly, 30.9% of young adults, and 12% of pregnant women. Twenty-six point seven percent (26.7%) of the elderly needed more than a weeks' stay as compared to 7.3% of young adults and 20% of pregnant women. Thirty-two percent (32%) of the elderly required intensive care as compared to 1.5% of young adults and none of the pregnant women. More of the elderly (26.7%) required ventilator support than other groups (7.3% and 4%). About 25.3% of the elderly had a superinfection. Eight percent (8%) of the elderly died in the study while none died in the other groups. Conclusion Age representation and poor hospitalization outcomes due to H1N1 seem to have shifted from young adults to older age groups. The elderly are at more risk for a prolonged stay, intensive care, ventilator support, and death as compared to young adults and pregnant women. Pregnancy may not be associated with poor hospitalization outcomes for H1N1 as has been earlier thought.

Mechanistic modelling of multiple waves in an influenza epidemic or pandemic

Multiple-wave outbreaks have been documented for influenza pandemics particularly in the temperate zone, and occasionally for seasonal influenza epidemics in the tropical zone. The mechanisms shaping multiple-wave influenza outbreaks are diverse but are yet to be summarized in a systematic fashion. For this purpose, we described 12 distinct mechanistic models, among which five models were proposed for the first time, that support two waves of infection in a single influenza season, and classified them into five categories according to heterogeneities in host, pathogen, space, time and their combinations, respectively. To quantify the number of infection waves, we proposed three metrics that provide robust and intuitive results for real epidemics. Further, we performed sensitivity analyses on key parameters in each model and found that reducing the basic reproduction number or the transmission rate, limiting the addition of susceptible people who are to get the primary infection to infected areas, and limiting the probability of replenishment of people who are to be reinfected in the short term, could decrease the number of infection waves and clinical attack rate. Finally, we introduced a modelling framework to infer the mechanisms driving two-wave outbreaks. A better understanding of two-wave mechanisms could guide public health authorities to develop and implement preparedness plans and deploy control strategies.

Genetic characterisation of influenza A(H1N1)pdm09 viruses circulating in Assam, Northeast India during 2009-2015

Introduction

Influenza A(H1N1)pdm09 virus, since its identification in April 2009, has continued to cause significant outbreaks of respiratory tract infections including pandemics in humans. In the course of its evolution, the virus has acquired many mutations with an ability to cause increased disease severity. A regular molecular surveillance of the virus is essential to mark the evolutionary changes that may cause a shift to the viral behavior.

Materials and Methods

Samples of Throat/Nasal swabs were collected from a total of 3715 influenza-like illness cases and screened by Real-time Reverse Transcription-Polymerase Chain Reaction for influenza viruses. Nucleotide sequence analysis was done to identify changes in antigenicity of the virus strains.

Results

The present study describes the molecular characteristics of influenza A(H1N1)pdm09 viruses detected in Assam of Northeast India during 2009-2015. Influenza A viruses were detected in 11.4% (425/3715), of which influenza A(H1N1)pdm09 viruses were detected in 41.4% (176/425). The nucleotide sequencing of influenza A(H1N1)pdm09 viruses revealed a total of 17 and 22 amino acid substitutions in haemagglutinin (HA) and neuraminidase (NA) genes of the virus, respectively, compared to contemporary vaccine strain A/California/07/2009. The important mutations detected in HA genes of A/Assam(H1N1)pdm09 strains included E391K, K180Q and S202T. Mutation 'N248D' which has an ability to develop oseltamivir resistance was also detected in NA gene of A/Assam(H1N1)pdm09 strains.

Conclusions

Regular molecular surveillance of influenza A(H1N1)pdm09 is important to monitor the viral behavior in terms of increase virulence, drug resistance pattern and emergence of novel strains.

Seasonal dynamics of influenza viruses and age distribution of infected individuals across nine seasons covering 2009-2018 in Taiwan

BACKGROUND/PURPOSE

A swine-origin influenza A/H1N1 virus (termed A/H1N1pdm) caused a pandemic in 2009 and has continuously circulated in the human population. To investigate its possible ecological effects on circulating influenza strains, the seasonal patterns of influenza viruses and the respective age distribution of infected patients were studies.

METHODS

The data obtained from national influenza surveillance systems in Taiwan from July 2009 to June 2018 were analyzed.

RESULTS

The A/H1N1pdm and A/H3N2 strains usually caused a higher ratio of severe to mild cases than influenza B. New variants of A/H1N1pdm and A/H3N2 emerged accompanied by a large epidemic peak. However, the new influenza B variants intended to circulate for several seasons before causing a large epidemic. The major group of outpatients affected by A/H1N1pdm were aged 13-23 years in the pandemic wave, and the age range of infected individuals gradually shifted to 24-49 and 0-6 years across seasons; A/H1N1pdm-infected inpatients were aged 24-49 years in 2009-2011, and the age range gradually switched to older groups aged 50-65 and >65 years. Individuals aged 0-6 or 24-49 years accounted for the majority of A/H3N2-infected outpatients across seasons, whereas most of the inpatients affected by A/H3N2 were aged >65 years.

CONCLUSION

Understanding the effects of new variants and changes in dominant circulating viral strains on the age distribution of the affected human population, disease severity and epidemic levels is useful for the establishment of fine-tuned strategies for further improvement of influenza control.

Clinical characteristics of patients with laboratory-confirmed influenza A(H1N1)pdm09 during the 2013/2014 and 2015/2016 clade 6B/6B.1/6B.2-predominant outbreaks

A novel pandemic influenza A(H1N1)pdm09 virus emerged in 2009 globally, and it continues to circulate in humans. The National Influenza Surveillance Network in Taiwan identified five A(H1N1)pdm09-predominant seasons, representing the 2009/2010, 2010/2011, 2012/2013, 2013/2014, and 2015/2016 outbreaks from 2009 to 2016. Independently, a retrospective cohort study (which enrolled 639 infected patients during the five seasons) was conducted at Chang Gung Memorial Hospital to explore the risk factors associated with influenza A(H1N1)pdm09-related complications. A phylogenetic analysis of hemagglutinin (HA) sequences showed that the circulating A(H1N1)pdm09 virus belonged to clades 1, 2, and 8 in 2009/2010; clades 3, 4, 5, and 7 in 2010/2011; clades 7 and 6C in 2012/2013; clades 6B in 2013/2014; and 6B/6B.1/6B.2 in 2015/2016. Compared to individuals infected in non-6B/6B.1/6B.2 seasons (2009/2010, 2010/2011, and 2012/2013), those infected in 6B/6B.1/6B.2 seasons (2013/2014 and 2015/2016) were at higher risk for influenza-related complications (adjusted odds ratio [aOR]: 1.6, 95% confidence interval [CI]: 1.0–2.8), pneumonia (aOR: 1.78, 95% CI: 1.04–3.04), mechanical ventilation (aOR: 2.6, 95% CI: 1.2–5.6), and acute respiratory distress syndrome (aOR: 5.5, 95% CI: 1.9–15.9). For the increased severity of infection during the influenza A(H1N1)pdm09 clade 6B/6B.1/6B.2 seasons, aspects related to the antigenic change of A(H1N1)pdm09 virus, immune response of the host, and environmental factors required further investigation.

An epidemic surge of influenza A(H3N2) virus at the end of the 2016-2017 season in Taiwan with an increased viral genetic heterogeneity

BACKGROUND

The epidemic of the 2016-2017 influenza season in Taiwan started early with moderate activity and was predominated by the influenza A(H3N2) virus. However, the influenza activity increased dramatically during the late stage of the 2016-2017 season.

OBJECTIVES

The genetic and antigenic characteristics of the influenza A(H3N2) virus circulating in Taiwan during the 2016-2017 season were investigated. The relationship between virus clades and the patients' 2016-2017 vaccination histories was determined.

STUDY DESIGN

Respiratory samples from patients with influenza-like illness in the community, clustered outbreaks, and inpatients with severe complications were tested for influenza virus. Influenza gene sequencing, phylogenetic analysis and hemagglutination inhibition assay were performed.

RESULTS

A total of 1185, 690 and 353 cases of outpatients, inpatients and cluster events were tested positive for the A(H3N2) virus in this report. Multiple clades of the H3N2 virus co-circulated. New genetic variants were detected, including clade 3C.2a.1 with additional N121 K, K92R or T135 K mutations, 3C.2a.3a with T135 K and R150 K mutations and 3C.2a.4. The proportions of N121 K and T135 K mutations were continuously increasing. Most of the viruses (85.4%, 111/130) were antigenically related to the current vaccine strain. Infection by different clade H3N2 viruses did not correlate with immunization with the 2016-2017 vaccine.

CONCLUSIONS

The data in this study indicate that antigenic drift is not the primary determinant of the epidemic wave at the end of the 2016-2017 season. The fitness changes in new variants, waning immunity and climatic changes are considered as possible contributors to the resurgence of the influenza A(H3N2) virus.

Taiwan's Public Health National Laboratory System: Success in Influenza Diagnosis and Surveillance

Taiwan's National Laboratory System is one of the action packages of the Global Health Security Agenda, which was launched by the World Health Organization (WHO) to promote health security as an international priority and to encourage progress toward full implementation of the WHO International Health Regulations (IHR) 2005. The mission of each national laboratory system is to conduct real-time biosurveillance and effective laboratory-based diagnostics, as measured by a nationwide laboratory system able to reliably conduct diagnoses on specimens transported properly to designated laboratories from at least 80% of the regions in the country. In Taiwan, the national laboratory system for public health is well-established and coordinated by the Taiwan Centers for Disease Control (CDC), which is the government authority in charge of infectious disease prevention and intervention. Through the national laboratory system, Taiwan CDC effectively detects and characterizes pathogens that cause communicable diseases across the entire country, including both known and novel threats, and also conducts epidemiologic analyses of infectious diseases. In this article, we describe the national laboratory system for public health in Taiwan. We provide additional information on the national influenza laboratory surveillance network to demonstrate how our national laboratory systems work in practice, including descriptions of long-term seasonal influenza characterization and successful experiences identifying novel H7N9 and H6N1 influenza viruses.

Cost-effectiveness analysis of the direct and indirect impact of intranasal live attenuated influenza vaccination strategies in children: alternative country profiles

BACKGROUND

Influenza poses a significant burden on healthcare systems and society, with under-recognition in the paediatric population. Existing vaccination policies (largely) target the elderly and other risk groups where complications may arise.

OBJECTIVE

The goal of this study was to evaluate the cost-effectiveness of annual paediatric vaccination (in 2-17-year-olds) with live attenuated influenza vaccination (LAIV), as well as the protective effect on the wider population in England and Wales (base). The study aimed to demonstrate broad applications of the model in countries where epidemiological and transmission data is limited and that have sophisticated vaccination policies (Brazil, Spain, and Taiwan).

METHODS

The direct and indirect impact of LAIV in the paediatric cohort was simulated using an age-stratified dynamic transmission model over a 5-year time horizon of daily cycles and applying discounting of 3.5% in the base case. Pre-existing immunity structure was based on a 1-year model run. Sensitivity analyses were conducted.

RESULTS

In the base case for England and Wales, the annual paediatric strategy with LAIV was associated with improvements in influenza-related events and quality-adjusted life years (QALYs) lost, yielding an incremental cost per QALY of £6,208. The model was robust to change in the key input parameters. The probabilistic analysis demonstrated LAIV to be cost effective in more than 99% of iterations, assuming a willingness-to-pay threshold of £30,000. Incremental costs per QALY for Brazil were £2,817, and for the cases of Spain and Taiwan the proposed strategy was dominant over the current practice.

CONCLUSION

In addition to existing policies, annual paediatric vaccination using LAIV provides a cost-effective strategy that offers direct and indirect protection in the wider community. Paediatric vaccination strategies using LAIV demonstrated clinical and economic benefits over alternative (current vaccination) strategies in England and Wales as well as Brazil, Spain, and Taiwan.

A molecular modelling approach to understand the effect of co-evolutionary mutations (V344M, I354L) identified in the PB2 subunit of influenza A 2009 pandemic H1N1 virus on m7GTP ligand binding

The cap binding domain of the polymerase basic 2 (PB2) subunit of influenza polymerases plays a critical role in mediating the 'cap-snatching' mechanism by binding the 5' cap of host pre-mRNAs during viral mRNA transcription. Monitoring variations in the PB2 protein is thus vital for evaluating the pathogenic potential of the virus. Based on selection pressure analysis of PB2 gene sequences of the pandemic H1N1 (pH1N1) viruses of the period 2009-2014, we identified a site, 344V/M, in the vicinity of the cap binding pocket showing evidence of adaptive evolution and another co-evolving residue, 354I/L, in close vicinity. Modelling of the three-dimensional structure of the pH1N1 PB2 cap binding domain, docking of the pre-mRNA cap analogue m7GTP and molecular dynamics simulation studies of the docked complexes performed for four PB2 variants observed showed that the complex possessing V344M with I354L possessed better ligand binding affinity due to additional hydrogen bond contacts between m7GTP and the key residues His432 and Arg355 that was attributed to a displacement of the 424 loop and a flip of the side chain of Arg355, respectively. The co-evolutionary mutations identified (V344M, I354L) were found to be established in the PB2 gene of the pH1N1 viral population over the period 2010-2014. The study demonstrates the molecular basis for the enhanced m7GTP ligand binding affinity with the 344M-354L synergistic combination in PB2. Furthermore, the insight gained into understanding the molecular mechanism of cap binding in pH1N1 viruses may be useful for designing novel drugs targeting the PB2 cap binding domain.

Comparison of age-specific hospitalization during pandemic and seasonal influenza periods from 2009 to 2012 in Taiwan: a nationwide population-based study

Background

Determining the age-specific hospitalization burden associated with seasonal influenza and the (H1N1) 2009 pandemic is important for the development of effective vaccine strategies and clinical management. The aim of this study was to investigate age-specific differences in hospitalization rates during the pandemic and seasonal periods.

Methods

Using the Taiwan National Health Insurance Research Database (NHIRD), we identified hospitalized patients with a principle discharge diagnosis of influenza-related infection (ICD-9-CM 487) between 2009 and 2012.

Results

Based on the time distribution of influenza-related hospitalizations and previously reported epidemic periods, the first and second waves of the (H1N1) 2009 pandemic (p1 is known as 2009.07-2010.01, and p2 is known as 2010.12-2011.03) and three seasonal periods (s1 is known as 2010.03-2010.11, s2 is known as 2011.10-2012.03, and s3 is known as 2012.04-2012.10) were found. During these five periods, children younger than 7 years of age consistently had the highest hospitalization rate of the studied age groups. In individuals younger than 50 years of age, the seasonal periods were associated with a significantly lower risk of hospitalization than that of p1 (Relative risk (RR) range = 0.18–0.85); however, they had a significantly higher hospitalization risk for adults over 50 years of age (RR = 1.51–3.22). Individuals over 50 years of age also had a higher intensive care unit admission rate and case fatality ratio than individuals under than 50 years of age during the seasonal periods and especially during the pandemic periods.

Conclusions

In both pandemic and seasonal periods, the highest hospitalization rate was observed for children younger than 7 years of age. Adults over 50 years of age had a higher hospitalization risk during the seasonal periods and a higher clinical severity during the pandemic periods. Those results emphasize that the importance of influenza-related prevention strategies in the younger and older age groups, either seasonal or pandemic periods.

Prior population immunity reduces the expected impact of CTL-inducing vaccines for pandemic influenza control

Vaccines that trigger an influenza-specific cytotoxic T cell (CTL) response may aid pandemic control by limiting the transmission of novel influenza A viruses (IAV). We consider interventions with hypothetical CTL-inducing vaccines in a range of epidemiologically plausible pandemic scenarios. We estimate the achievable reduction in the attack rate, and, by adopting a model linking epidemic progression to the emergence of IAV variants, the opportunity for antigenic drift. We demonstrate that CTL-inducing vaccines have limited utility for modifying population-level outcomes if influenza-specific T cells found widely in adults already suppress transmission and prove difficult to enhance. Administration of CTL-inducing vaccines that are efficacious in "influenza-experienced" and "influenza-naive" hosts can likely slow transmission sufficiently to mitigate a moderate IAV pandemic. However if neutralising cross-reactive antibody to an emerging IAV are common in influenza-experienced hosts, as for the swine-variant H3N2v, boosting CTL immunity may be ineffective at reducing population spread, indicating that CTL-inducing vaccines are best used against novel subtypes such as H7N9. Unless vaccines cannot readily suppress transmission from infected hosts with naive T cell pools, targeting influenza-naive hosts is preferable. Such strategies are of enhanced benefit if naive hosts are typically intensively mixing children and when a subset of experienced hosts have pre-existing neutralising cross-reactive antibody. We show that CTL-inducing vaccination campaigns may have greater power to suppress antigenic drift than previously suggested, and targeting adults may be the optimal strategy to achieve this when the vaccination campaign does not have the power to curtail the attack rate. Our results highlight the need to design interventions based on pre-existing cellular immunity and knowledge of the host determinants of vaccine efficacy, and provide a framework for assessing the performance requirements of high-impact CTL-inducing vaccines.

Epidemiological and viral genome characteristics of the first human H7N9 influenza infection in Guangdong Province, China

BACKGROUND

The first H7N9 human case in south of China was confirmed in Guangdong Province on August 2013, outside of the typical influenza season. For investigating the H7N9 virus source and transmission in the local community, we analyze the epidemiology and genome features of the virus isolated from the first human infection detected in Guangdong Province.

METHODS

The data including medical records, exposure history and time line of events for the H7N9 patient and close contacts was collected. Variation and genetic signatures of H7N9 virus in Guangdong was analyzed using ClustalW algorithm and comparison with mutations associated with changes in biological characteristics of the virus.

RESULTS

The female patient had a history of poultry exposure, and she was transferred from a local primary hospital to an intensive care unit (ICU) upon deterioration. No additional cases were reported. Similar to previous infections with avian influenza A (H7N9) virus, the patient presented with both upper and lower respiratory tract symptoms. Respiratory failure progressed quickly, and the patient recovered 4 weeks after the onset of symptoms. Genome analysis of the virus indicated that the predicted antigen city and internal genes of the virus are similar to previously reported H7N9 viruses. The isolated virus is susceptible to neuraminidase (NA) inhibitors but resistant to adamantine. Although this virus contains some unique mutations that were only detected in avian or environment-origin avian influenza A (H7N9) viruses, it is still quite similar to other human H7N9 isolates.

CONCLUSIONS

The epidemiological features and genome of the first H7N9 virus in Guangdong Province are similar to other human H7N9 infections. This virus may have existed in the environment and live poultry locally; therefore, it is important to be alert of the risk of H7N9 re-emergence in China, including emergence outside the typical influenza season.

Survival analysis of infected mice reveals pathogenic variations in the genome of avian H1N1 viruses

Most influenza pandemics have been caused by H1N1 viruses of purely or partially avian origin. Here, using Cox proportional hazard model, we attempt to identify the genetic variations in the whole genome of wild-type North American avian H1N1 influenza A viruses that are associated with their virulence in mice by residue variations, host origins of virus (Anseriformes-ducks or Charadriiformes-shorebirds), and host-residue interactions. In addition, through structural modeling, we predicted that several polymorphic sites associated with pathogenicity were located in structurally important sites, especially in the polymerase complex and NS genes. Our study introduces a new approach to identify pathogenic variations in wild-type viruses circulating in the natural reservoirs and ultimately to understand their infectious risks to humans as part of risk assessment efforts towards the emergence of future pandemic strains.

The influence of changing host immunity on 1918-19 pandemic dynamics

The sociological and biological factors which gave rise to the three pandemic waves of Spanish influenza in England during 1918-19 are still poorly understood. Symptom reporting data available for a limited set of locations in England indicates that reinfection in multiple waves occurred, suggesting a role for loss of infection-acquired immunity. Here we explore the role that changes in host immunity, driven by a combination of within-host factors and viral evolution, may play in explaining weekly mortality data and wave-by-wave symptomatic attack-rates available for a subset of English cities. Our results indicate that changes in the phenotype of the pandemic virus are likely required to explain the closely spaced waves of infection, but distinguishing between the detailed contributions of viral evolution and changing adaptive immune responses to transmission rates is difficult given the dearth of sero-epidemiological and virological data available even for more contemporary pandemics. We find that a dynamical model in which pre-pandemic protection in older "influenza-experienced" cohorts is lost rapidly prior to the second wave provides the best fit to the mortality and symptom reporting data. Best fitting parameter estimates for such a model indicate that post-infection protection lasted of order months, while other statistical analyses indicate that population-age was inversely correlated with overall mortality during the herald wave. Our results suggest that severe secondary waves of pandemic influenza may be triggered by viral escape from pre-pandemic immunity, and thus that understanding the role of heterosubtypic or cross-protective immune responses to pandemic influenza may be key to controlling the severity of future influenza pandemics.

Newly emerging mutations in the matrix genes of the human influenza A(H1N1)pdm09 and A(H3N2) viruses reduce the detection sensitivity of real-time reverse transcription-PCR

New variants of the influenza A(H1N1)pdm09 and A(H3N2) viruses were detected in Taiwan between 2012 and 2013. Some of these variants were not detected in clinical specimens using a common real-time reverse transcription-PCR (RT-PCR) assay that targeted the conserved regions of the viral matrix (M) genes. An analysis of the M gene sequences of the new variants revealed that several newly emerging mutations were located in the regions where the primers or probes of the real-time RT-PCR assay bind; these included three mutations (G225A, T228C, and G238A) in the A(H1N1)pdm09 virus, as well as one mutation (C163T) in the A(H3N2) virus. These accumulated mismatch mutations, together with the previously identified C154T mutation of the A(H1N1)pdm09 virus and the C153T and G189T mutations of the A(H3N2) virus, result in a reduced detection sensitivity for the real-time RT-PCR assay. To overcome the loss of assay sensitivity due to mismatch mutations, we established a real-time RT-PCR assay using degenerate nucleotide bases in both the primers and probe and successfully increased the sensitivity of the assay to detect circulating variants of the human influenza A viruses. Our observations highlight the importance of the simultaneous use of different gene-targeting real-time RT-PCR assays for the clinical diagnosis of influenza.

Increased transmissibility explains the third wave of infection by the 2009 H1N1 pandemic virus in England

In the 2009 H1N1 pandemic, the United Kingdom experienced two waves of infection, the first in the late spring and the second in the autumn. Given the low level of susceptibility to the pandemic virus expected to be remaining in the population after the second wave, it was a surprise that a substantial third epidemic occurred in the UK population between November 2010 and February 2011, despite no evidence for any significant antigenic evolution of the pandemic virus. Here, we use a mathematical model of influenza transmission embedded within a Bayesian synthesis inferential framework to jointly analyze syndromic, virological, and serological surveillance data collected in England in 2009-2011 and thereby assess epidemiological mechanisms which might have generated the third wave. We find that substantially increased transmissibility of the H1N1pdm09 virus is required to reproduce the third wave, suggesting that the virus evolved and increased fitness in the human host by the end of 2010, or that the very cold weather experienced in the United Kingdom at that time enhanced transmission rates. We also find some evidence that the preexisting heterologous immunity which reduced attack rates in adults during 2009 had substantially decayed by the winter of 2010, thus increasing the susceptibility of the adult population to infection. Finally, our analysis suggests that a pandemic vaccination campaign targeting adults and school-age children could have mitigated or prevented the third wave even at moderate levels of coverage.

Characterization of oseltamivir-resistant influenza A(H1N1)pdm09 viruses in Taiwan in 2009-2011

The early isolated swine-origin influenza A(H1N1)pdm09 viruses were susceptible to oseltamivir; however, there is a concern about whether oseltamivir-resistant influenza A(H1N1)pdm09 viruses will spread worldwide as did the oseltamivir-resistant seasonal influenza A(H1N1) viruses in 2007-2008. In this study, the frequency of oseltamivir resistance in influenza A(H1N1)pdm09 viruses was determined in Taiwan. From May 2009 to April 2011, 1,335 A(H1N1)pdm09-positive cases in Taiwan were tested for the H275Y mutation in the neuraminidase (NA) gene that confers resistance to oseltamivir. Among these, 15 patients (1.1%) were found to be infected with H275Y virus. All the resistant viruses were detected after the patients have received the oseltamivir. The overall monthly ratio of H275Y-harboring viruses ranged between 0% and 2.88%, and the peak was correlated with influenza epidemics. The genetic analysis revealed that the oseltamivir-resistant A(H1N1)pdm09 viruses can emerged from different variants with a great diversity under drug pressure. The ratio of NA/HA activities in different clades of oseltamivir-resistant viruses was reduced compared to those in the wild-type viruses, indicating that the balance of NA/HA in the current oseltamivir-resistant influenza A(H1N1)pdm09 viruses was interfered. It is possible that H275Y-bearing A(H1N1)pdm09 virus has not yet spread globally because it lacks the essential permissive mutations that can compensate for the negative impact on fitness by the H275Y amino acid substitution in NA. Continuous monitoring the evolution patterns of sensitive and resistant viruses is required to respond to possible emergence of resistant viruses with permissive genetic background which enable the wide spread of resistance.

Whole genome characterization, phylogenetic and genome signature analysis of human pandemic H1N1 virus in Thailand, 2009-2012

BACKGROUND

Three waves of human pandemic influenza occurred in Thailand in 2009-2012. The genome signature features and evolution of pH1N1 need to be characterized to elucidate the aspects responsible for the multiple waves of pandemic.

METHODOLOGY/FINDINGS

Forty whole genome sequences and 584 partial sequences of pH1N1 circulating in Thailand, divided into 1(st), 2(nd) and 3(rd) wave and post-pandemic were characterized and 77 genome signatures were analyzed. Phylogenetic trees of concatenated whole genome and HA gene sequences were constructed calculating substitution rate and d(N)/d(S) of each gene. Phylogenetic analysis showed a distinct pattern of pH1N1 circulation in Thailand, with the first two isolates from May, 2009 belonging to clade 5 while clades 5, 6 and 7 co-circulated during the first wave of pH1N1 pandemic in Thailand. Clade 8 predominated during the second wave and different proportions of the pH1N1 viruses circulating during the third wave and post pandemic period belonged to clades 8, 11.1 and 11.2. The mutation analysis of pH1N1 revealed many adaptive mutations which have become the signature of each clade and may be responsible for the multiple pandemic waves in Thailand, especially with regard to clades 11.1 and 11.2 as evidenced with V731I, G154D of PB1 gene, PA I330V, HA A214T S160G and S202T. The substitution rate of pH1N1 in Thailand ranged from 2.53×10(-3)±0.02 (M2 genes) to 5.27×10(-3)±0.03 per site per year (NA gene).

CONCLUSIONS

All results suggested that this virus is still adaptive, maybe to evade the host's immune response and tends to remain in the human host although the d(N)/d(S) were under purifying selection in all 8 genes. Due to the gradual evolution of pH1N1 in Thailand, continuous monitoring is essential for evaluation and surveillance to be prepared for and able to control future influenza activities.

Amino acids transitioning of 2009 H1N1pdm in Taiwan from 2009 to 2011

A swine-origin influenza A was detected in April 2009 and soon became the 2009 H1N1 pandemic strain (H1N1pdm). The current study revealed the genetic diversity of H1N1pdm, based on 77 and 70 isolates which we collected, respectively, during the 2009/2010 and 2010/2011 influenza seasons in Taiwan. We focused on tracking the amino acid transitioning of hemagglutinin (HA) and neuraminidase (NA) genes in the early diversification of the virus and compared them with H1N1pdm strains reported worldwide. We identified newly emerged mutation markers based on A/California/04/2009, described how these markers shifted from the first H1N1pdm season to the one that immediately followed, and discussed how these observations may relate to antigenicity, receptor-binding, and drug susceptibility. It was found that the amino acid mutation rates of H1N1pdm were elevated, from 9.29×10⁻³ substitutions per site in the first season to 1.46×10⁻² in the second season in HA, and from 5.23×10⁻³ to 1.10×10⁻² in NA. Many mutation markers were newly detected in the second season, including 11 in HA and 8 in NA, and some were found having statistical correlation to disease severity. There were five noticeable HA mutations made to antigenic sites. No significant titer changes, however, were detected based on hemagglutination inhibition tests. Only one isolate with H275Y mutation known to reduce susceptibility to NA inhibitors was detected. As limited Taiwanese H1N1pdm viruses were isolated after our sampling period, we gathered 8,876 HA and 6,017 NA H1N1pdm sequences up to April 2012 from NCBI to follow up the dynamics of mentioned HA mutations. While some mutations described in this study seemed to either settle in or die out in the 2011–2012 season, a number of them still showed signs of transitioning, prompting the importance of continuous monitoring of this virus for more seasons to come.