Date Published: November 30, 2011
Publisher: Public Library of Science
Author(s): Ji-Rong Yang, Yuan-Pin Huang, Feng-Yee Chang, Li-Ching Hsu, Yu-Cheng Lin, Chun-Hui Su, Pei-Jer Chen, Ho-Sheng Wu, Ming-Tsan Liu, Thomas F. Schulz. http://doi.org/10.1371/journal.pone.0028288
Past influenza pandemics have been characterized by the signature feature of multiple waves. However, the reasons for multiple waves in a pandemic are not understood. Successive waves in the 2009 influenza pandemic, with a sharp increase in hospitalized and fatal cases, occurred in Taiwan during the winter of 2010. In this study, we sought to discover possible contributors to the multiple waves in this influenza pandemic. We conducted a large-scale analysis of 4703 isolates in an unbiased manner to monitor the emergence, dominance and replacement of various variants. Based on the data from influenza surveillance and epidemic curves of each variant clade, we defined virologically and temporally distinct waves of the 2009 pandemic in Taiwan from May 2009 to April 2011 as waves 1 and 2, an interwave period and wave 3. Except for wave 3, each wave was dominated by one distinct variant. In wave 3, three variants emerged and co-circulated, and formed distinct phylogenetic clades, based on the hemagglutinin (HA) genes and other segments. The severity of influenza was represented as the case fatality ratio (CFR) in the hospitalized cases. The CFRs in waves 1 and 2, the interwave period and wave 3 were 6.4%, 5.1%, 15.2% and 9.8%, respectively. The results highlight the association of virus evolution and variable influenza severity. Further analysis revealed that the major affected groups were shifted in the waves to older individuals, who had higher age-specific CFRs. The successive pandemic waves create challenges for the strategic preparedness of health authorities and make the pandemic uncertain and variable. Our findings indicate that the emergence of new variants and age shift to high fatality groups might contribute potentially to the occurrence of successive severe pandemic waves and offer insights into the adjustment of national responses to mitigate influenza pandemics.
Since an influenza outbreak caused by swine-origin influenza A (H1N1) viruses was detected initially in Mexico and USA during March and April 2009 , the viruses spread rapidly to an increasing number of countries. During the early stage of the 2009 pandemic, data from genetic analyses suggested that the influenza A (H1N1) 2009 viruses (termed “2009 H1N1 viruses” for convenience) had begun to evolve and diversified from April 1 to July 9, 2009 into at least 7 clades (clades 1–7) with spatial and geographic patterns , and the viruses in the early stage did not possess genomic signatures associated with high pathogenicity in the PB2, PB1-F2, HA and NS1 proteins . Among the circulating viruses, the clade 7 viruses with a signature S220T substitution in the HA protein have spread more widely and become a globally major strain, and this dominated early in New York from April to July 2009 . Some new variants derived from clade 7 were detected later in Australia, New Zealand, Singapore, Hong Kong and the United Kingdom , , , which raised the concern that the evolving viruses might be responsible for increased disease severity. The severity during the early 2009 pandemic was estimated to be less than that seen in the 1918 influenza pandemic and comparable to that seen in the 1957 pandemic . The severity of the following autumn-winter pandemic wave in 2009–2010 remained mild and did not change, with mortality rates in the range from lower to slightly higher than that associated with seasonal influenza , , . In the successive waves, increased severity was reported in Wales, UK and Wisconsin, USA , , , but data from New Zealand revealed that the overall impact of the second wave of the 2009 pandemic in 2010 was between one half and two thirds that of the first wave in 2009 . The severity of the 2009 pandemic in the following years remains uncertain.
Past influenza pandemics, such as those caused by influenza A (H1N1) from 1918 to 1919, influenza A (H2N2) from 1957 to 1963 and influenza A (H3N2) from 1968 to 1970, have been characterized by several distinct features, including changes in the virus subtype, shifts of the highest death rates to younger populations, multiple waves, higher transmissibility than seasonal influenza, and varying impacts in different geographic regions . These factors, especially information on virus evolution and disease severity during the continuous pandemic waves, were all crucial for evaluating the impact of the disease and for consideration of influenza response plans. For the 2009 pandemic, until now, the features of multiple waves remained unclear. The estimated severity indicated by the CFRs in hospitalized cases was 7% during April to June 2009 in the USA  and 4.1–8% in the USA, Norway and Austria in the following fall and winter , , . In the Southern Hemisphere, the CFRs in hospitalized patients in 2009 (the first wave) varied between 2.4% and 7.6% in various studies . In Taiwan, the CFR of the hospitalized cases calculated from July 2009 to January 2010 in this study was 5.7% (53/931), while those of the influenza A (H3N2) and influenza B viruses were 8.6% (71/820) and 4.9% (7/142), respectively. The data revealed that severity of 2009 H1N1 illness in the early stage was milder than that of seasonal influenza A (H3N2) viruses. However, in the successive wave from December 2010, the new genetic variants of clades 9, 10 and 11 viruses emerged with an increase in CFRs from 6.4% and 5.1% to 9.8% (p<0.05), indicating that successive severe waves of the 2009 pandemic occurred in Taiwan. Although the reasons for increased severity in successive waves were unclear, they were likely to include virus changes, seasonality, medical measures and the overall immunity of the population . In this study, these factors also were considered. First, the increase in fatality between the waves of a pandemic was likely to be attributable to the generation and emergence of mutated viruses, with increased pathogenicity and greater adaptation to the human host, while we had observed that various variants of 2009 H1N1 viruses were dominant during different periods of the pandemic and associated with varying fatality in hospitalized patients. Genetic mutations and reassortments have been reported potentially to enhance the virulence of 2009 H1N1 viruses , , . In Taiwan, the genome signatures of the evolving 2009 H1N1 viruses in successive waves were identified in this study, including T257A in PB1, E391K in HA and M93I in the NS1 protein of clade 8 viruses in wave 2; A652V in PB1, N142D in HA, K400R-K452R in NP, and M15I-N189S in NA of clade 8-1 in the interwave period; V225I-V511I-V584I-V667I in PB2, R211K-I435V in PB1, D479E in PA, A151T-S200P-E391G-R526M in HA, I389V-V394I in NA, and E55Q in NS1 of clade 9; A221S in PB2, V113A-K386R in PB1, V14I in PA, T14I-R222K-I233V/G-V266L-K300E in HA, S299A-I374V in NA, and P162L in NS1 of clade 10; V344M-V354L in PB2, N321K in PA, S202T-S468N in HA, V241I-N369K in NA and V80I in M1 of clade 11 (additional N456S in PB2, I330V in PA, and D114N in HA of clade 11-1, as well as I397M in PB1, A343T in PA, A214T in HA, N44S in NA and L90I in NS1 of clade 11-2) in wave 3 (Table S1). Among these HA mutations, N142D was located in the known antigenic Sa site, and R222K was located in the antigenic Ca site . The mutations, S200P, A214T and I233V, near receptor binding sites may affect the interaction of HA with its receptor , . Although only few of these residues had been reported , , their undetermined effects on virus pathogenicity may be significant. Another important amino acid substitution, D239G, was analyzed and compared in different waves; this is known to cause a shift to a dual α2–3/α2–6-sialic acid linkage specificity, allowing the mutant protein to bind to both human and avian receptors  and has reportedly been associated with severe cases . In our study, the respective percentages of this D239G substitution in 2009 H1N1 viruses from hospitalized cases during waves 1 and 2, the interwave period and wave 3 were 1.9% (4/210), 1.5% (4/276), 7.9% (3/38) and 1.4% (6/438), while those in community cases were 0.3% (4/1597), 0% (0/977), 0.5% (1/190) and 0.1% (1/977), respectively. The percentages of viruses harboring 239G were in the ratio of 6.3–15 between those from hospitalized and community cases during the three major waves (1.9% vs. 0.3%; 1.5% vs. 0%; 1.4% vs. 0.1%, respectively). Of note, a dramatic percentage increase (7.9% of hospitalized vs. 0.5% of community cases, p<0.05) in the interwave period, accompanied by the highest CFR in hospitalized cases, also was observed. The occurrence of this substitution was not clade-specific, but these data could highlight the important impact of virus changes on influenza severity in future waves and it was therefore essential for continuous surveillance of the trends of virus evolution. The second factor, seasonality of various waves, was analysed. In Taiwan, wave 1 and the interwave period were outside the regular influenza season. Waves 2 and 3 were in the winter influenza season, although wave 2 was two months earlier than the usual timing. As cold temperature and low humidity have been reported to enhance influenza transmission in an animal model , the effect of seasonality on the severity of various waves of influenza was not observed in this study. The other factors, medical measures and overall immunity of the population, such as antiviral medication and vaccine administration, were discussed. During the two-year period, only few sporadic 2009 H1N1 viruses from cases after drug-treatment were found to carry the substitution H275Y in the NA protein, conferring resistance to oseltamivir . The policy of use of government-funded antiviral agents, which aimed to decrease the spread of viruses and to minimize the occurrence of severe cases, is consistent and antiviral agents were prescribed for cases from cluster outbreaks and of reported severity, and extended to the patients who presented danger signs of developing severe disease during the peak of influenza activity. Therefore, the consistent policy of antiviral agents in Taiwan did not seem to involve in the variety of influenza severity in various waves. Finally, for overall immunity of the population, which was attributed to pre-exposure to infection and vaccination, was considered. Serologic data from previous studies at the early stage of the 2009 pandemic suggested that a higher proportion of persons aged above 60 years may have pre-existing immunity to the 2009 H1N1 viruses due to past infection . It was also shown that the major population of hospitalized and fatal cases in the 2009 pandemic was younger than those commonly seen with seasonal influenza . In our study, the attack rates of 2009 H1N1 viruses showed that school children aged 5-17 years were also the major affected targets of this virus in waves 1 and 2, which differed from those of influenza A (H3N2) viruses (Table 1 and 2; p<0.05). During the interwave period and wave 3, the predominant infected cases shifted to young adults and the percentages of school children in community and hospitalized cases decreased from 68.1% (2110/3100) and 39.2% (365/931) to 35.7% (476/1335) and 8.6% (93/1084), respectively. Of note, the cumulative percentage of hospitalized individuals aged >50 years increased from 18.9% (176/931) to 46.9% (508/1084), accompanied by an increasing number of fatal cases (p<0.05). These data suggested that the age shifts may result from the possible protection of infection-acquired immunity in the younger population after the early waves, following a higher attack rate at the beginning of the 2009 pandemic. Another possible effect may be attributed to influenza vaccination. In Taiwan, the vaccine coverage rates of populations, who had received at least one dose of H1N1 vaccine from November 2009 to March 2010, reached 22%, including 29%, 72%, and 11% of persons aged 6 months to 6 years, 7–18 years, and above 19 years, respectively , while the cumulative percentage of those who had received at least one dose of H1N1 vaccine from October 2010 to May 2011, reached 12.6%, including 25.8%, 64.4% and 37.3% of persons aged 6 months to 6 years, 7–12 years,and older than 65 years, respectively (data not shown). Individuals aged 13–64 years were not included in the government-funded vaccination program in 2010–2011 influenza season. This showed that the school children had the highest vaccination rate and adults aged 18–64 were the shortfall in influenza vaccination and the age-specific vaccine coverage seemed to contribute to the shift of age to older groups. In this study, we found that people aged above 50 years were the population with the highest age-specific CFR during the 2009 pandemic in Taiwan. This was similar to the scenario of the past influenza illness and data from the early 2009 pandemic, which showed that persons aged above 50 years had the highest rates of mortality once hospitalized , , , , . The shift to older groups, who had relatively higher age-specific CFRs, may have contributed to the increased influenza severity in the successive waves of the 2009 pandemic in Taiwan. Source: http://doi.org/10.1371/journal.pone.0028288