Table of contents :

Epidemiology : first described by Hippocrates in 412 b.C.. Different strains also infect Aves spp. (chickens, turkeys, ostriches (various AI virus strains have been isolated in recent years from clinically affected ostriches, in several countries. All but one were not poultry-pathogenic : the only reported clinical outbreak in ostriches caused by a poultry-pathogenic strain (HPAI) was recorded in Italy (H₇N₁)^ref), quail, and peacocks; aquatic species : ducks, geese), Sus scrofa, Equus caballus, Phocidae, mustelids and Bos taurus^ref. Although viruses of relatively few subtype combinations have been isolated from mammalian species, all subtypes, in most combinations, have been isolated from birds.

• the sudden emergence of antigenically different strains in humans, termed antigenic shift (every 20-40 years) results in a pandemic : historically, flu pandemics have come in two or three waves, lasting a total of 13-23 months. Estimates of R₀ for pandemic influenza strains range from 1.8 to 3 for the 1918 Spanish flu^{ref1, ref2} and are around 1.9 for the H₃N₂ pandemic^ref
• the first documented one occurred in 1580
• 1889-1891 (H₂N_?) : Siberia => Europe
• it has occurred on 4 occasions in the 20^th Century, in .. :
• 1902 (H₃N_?)
• 1918-1919 (H₁N₁) : killed an estimated 40 to 50 million people; 3 peaks of mortality; the second and highest peak occurred 6 months after the initial outbreak
• 1932-1933 (H₁N₁) (A₀)
• 1947-1948 (H₁N₁) (A')
• 1957-1958 (H₂N₂) (Asian) : killed an estimated 2 million people, 70,000 in the USAs alone. The rate of infection with symptomatic flu that year exceeded 50% in urban populations
• 1968 (H₃N₂) (Hong Kong) : killed an estimated 1 million people, 34,000 in the USA
• 1976 (H₁N₁) (swine). In January and February 1976 200 soldiers were infected and 1-2 died at Fort Dix, New Jersey, because of swine flu virus (H₁N₁) (as detected by conversion of serial sera from negative to positive for swine flu hemagglutinins), thought to be a direct descendant of the virus that caused the pandemic of 1918. This conclusion was based on antibodies to H₁N₁ antigens found in survivors of the 1918 pandemic, and the belief that the 1918 virus was eventually transmitted to pigs in the Midwest, where it persisted and caused sporadic human cases. The Public Health Service decided to prepare an influenza vaccine with the Fort Dix strain and immunized 25% of the US population, or 45 million persons, within October, although the predicted pandemic never occurred. On the basis of available historical data, the R₀ of the strain was 1.1–1.2. This number suggests that swine flu would not have become a major epidemic (Neustadt RE, Fineberg HV. The swine flu affair: decision-making on a slippery disease. Washington: US Department of Health, Education and Welfare; 1978; Shilts R. And the band played on: politics, people, and the AIDS epidemic. New York: St. Martin's Press; 1987). Any narrative on the swine flu episode would be incomplete without mentioning the work of Richard Shope on the possible relationship between the putative influenza virus of 1918 and its eventful residence in pigs in Iowa, where it caused an influenzalike syndrome and where it remained as a reservoir (Shope RE. The influenzas of swine and man. In: The Harvey lectures, 1935–1936. New York: The Harvey Society; 1937. p. 183–213). Whatever the merits of this argument about the cause of swine flu virus infection in adults in the 1930s, of interest here is Francis's suggestion that the swine flu antibody in humans was the result of repeated exposure to human strains, and perhaps not due to prior infection with the 1918 virus. Surely his thoughts about this matter were the genesis of the concepts expressed in On the Doctrine of Original Antigenic Sin, published in 1960 (Francis T Jr. On the doctrine of original antigenic sin. Proc Am Philos Soc. 1960;104:572). Francis wrote, "The antibody of childhood is largely a response to dominant antigen of the virus causing the first type A influenza infection of the lifetime. The antibody-forming mechanisms are highly conditioned by the first stimulus, so that later infections with strains of the same type successfully enhance the original antibody to maintain it at the highest level at all times in that age group. The imprint established by the original virus infection governs the antibody response thereafter. This we have called the Doctrine of the Original Antigenic Sin." Francis died in 1969 and did not live to know the full explanations for antigenic shift through reassortment of gene segments from 2 parent viruses or antigenic drift through mutation. He surely would have been in awe, as we all are, of the molecular explanation of influenza virus variation with succeeding epidemics. And yet, even with the brilliant work of Taubenberger delineating the 1918 virus^ref, we can still ask Francis's question: Which strain will cause the next pandemic?
• 1977 (H₁N₁) (Russian); it did not replace the H₃N₂ subtype and both subtypes continued to cocirculate
• next (H₅N₁) (avian) ???
Pandemic influenza may originate through at least 2 mechanisms:
• reassortment between an animal influenza virus and a human influenza virus that yields a new virus :  a key event would probably be a change in the binding specificity of the virus from a receptor in the lower respiratory tract to one in the upper respiratory tract. This may result in a decrease in at least the initial pathogenicity, as the infection would be more likely to start with a tracheal bronchitis rather than pneumonia (see below). In addition, if human adaptation resulted from reassortment with a human virus, pathogenicity factors on gene segments not in the resulting reassortment would be lost, and there may be a degree of prior immunity in the population to the human virus–derived gene segments, both further reducing pathogenicity in humans


• direct spread and adaptation of a virus from animals to humans : pandemic strains of influenza A virus arise by genetic reassortment between avian and human viruses : pigs could serve as "mixing vessels" for such reassortment events since they express both a2-3-linked and a2-6 linked sialic acids on epithelial cells of the lungs and upper respiratory tract (see below)^ref. After the outbreaks of group A subtype H₅N₁ (A/H₅N₁) avian influenza viruses in Hong Kong in 1997, in which 6 people died, the hypothesis was put forward that not only pigs but also humans themselves might serve as mixing vessels for the next pandemic influenza virus^ref. It should be kept in mind also that the "mixing vessel" hypothesis is no more than a hypothesis, and the role of pigs as "mixing vessels" has not been established unequivocally. Genetic reassortment between avian and human influenza A viruses in Italian Sus scrofa occurred at some time between 1983 and 1985 : human-like H₃N₂ strains isolated from 1985 to 1989 contained the internal protein genes of avian-like H₁N₁ viruses, whereas those isolated in 1977 and 1983 did not^ref. Multiple genetic reassortment of avian and human influenza A viruses in European Sus scrofa, resulting in the emergence of an H₁N₂ virus of novel genotype^ref. Predictions for future human influenza pandemics^ref. The evolution of human influenza viruses^ref. Avian-to-human transmission of the PB1 gene of influenza A viruses in the 1957 and 1968 pandemics^ref. Emergence of influenza A viruses^ref.
The 1918 virus did not originate through a reassortment event involving a human influenza virus: all 8 genes of the H₁N₁ virus are more closely related to avian influenza viruses than to influenza from any other species, indicating that an avian virus must have infected humans and adapted to them in order to spread from person to person^{ref1, ref2}. In both 1957 and 1968, a new influenza virus emerged because of reassortment events involving 2 influenza viruses. The segmented genome allows each influenza A virus to exchange genetic material with other influenza A viruses. In 1957, dual infection of an individual animal — probably a human, but possibly another species, such as a pig — with an avian H₂N₂ influenza and a human H₁N₁ influenza resulted in the emergence of a new influenza virus containing the hemagglutinin, the neuraminidase, and the gene for one of the polymerase proteins (PB1) from the avian virus, along with the remaining 5 genetic segments from the human H₁N₁ influenza virus. The new reassortant virus circulated in humans until 1968, when it was replaced by another reassortant virus, the H₃N₂ Hong Kong virus — created by the replacement of the hemagglutinin (H₂) and polymerase (PB1) genes of the H₂N₂ virus with 2 new avian genes, H₃ and a new PB1. Today, the descendants of this virus continue to cause the majority of influenza infections in humans. 5 of the genes of today's H₃N₂ influenza virus have their origin in the 1918 pandemic.

To investigate how often antigenic shift happens, researchers looked at the published genome sequences of 156 flu strains that circulated in New York state between 1999 and 2004. They constructed family trees that show how these viruses slowly evolved over time. And they discovered at least 4 instances where a virus had picked up a gene from another virus through reassortment^ref. In one of these instances the gene swap resulted in a particularly nasty strain that struck New York in the winter of 2003-04. This 'Fujian' strain was produced when a virus that was common the previous year picked up a gene from a relatively harmless strain, which had been around for some years but infected very few people. The gene was for a protein that the virus uses to bind to cells it is going to infect. The version the dominant strain picked up was very different to the one it had before, catching people's immune systems, and vaccines, unawares. The researchers found a wider variety of strains circulating at any one time than expected, and more instances of gene swapping. Multiple lineages coexist at the same time and place, and the key thing is that they are reassorting and doing so quite frequently. Flu researchers already had a good idea of how reassortment happens, from studies that tracked specific genes for surface proteins, but Holmes's research goes beyond this by using whole genome sequences, giving a clearer picture of how often this happens. These analyses will help us understand in detail the evolution of the influenza virus, taking into account more than just these genes. Further studies investigating the genome sequences of bird-flu viruses could help us understand whether recombination is as just common in those. Some researchers are now trying to create recombinant strains in the lab, using bird and human viruses, to see what a pandemic virus might look like and how easily it might form. The longest inter-pandemic interval recorded with certainty is 39 years. It is not possible to know whether the current H₅N₁ is capable of adapting to humans so that it can spread with high efficiency through low-titer aerosol transmission to initiate an influenza pandemic. However, Taubenberger et al. provide some guidance on the genetic changes that might be required for such an event. The role of PB1 must be critical, since in both 1957 and 1968, this polymerase gene was transferred along with the hemagglutinin during reassortment. By comparing the consensus sequence of the 3 avian influenza polymerase genes PA, PB1, and PB2 with the 1918 sequence, as well as with more contemporary influenza viruses, Taubenberger et al. have identified 4 amino acids of PA, one of PB1, and 5 of PB2 that are found in human influenza viruses (including the 1918 virus) but generally not in avian influenza viruses. In 2 instances, these amino acids are found in nuclear localization signaling (NLS) regions, suggesting that some or all of these amino acid differences are critical for the virus to adapt to humans. The genetic sequences of the 1997 Hong Kong H₅N₁ virus and the 2004 Vietnam H₅N₁ virus reveal that several human isolates of these viruses contain 1 of the 5 amino acid changes in PB2 that have been identified as important to the ability of the 1918 virus to infect humans. This finding suggests that several additional genetic changes must occur before these viruses will begin to spread efficiently from person to person. The genetic sequences of avian viruses may provide a window through which to monitor these sporadic transmissions for the potential of the viruses to adapt to humans. The occurrence of additional genetic changes in the avian H₅N₁ virus circulating in birds that match the consensus sequence for PA, PB1, or PB2 in human influenza would be cause for heightened concern. On the basis of the rates of replacement of amino acids, Taubenberger et al. estimated that avian influenza polymerase genes had been circulating in humans as early as 1900. If this estimate is correct, then monitoring of the sequences of viruses isolated in instances of bird-to-human transmission for genetic changes in key regions may enable us to track viruses years before they develop the capacity to replicate with high efficiency in humans. Knowledge of the genetic sequences of influenza viruses that predate the 1918 pandemic would be extremely helpful in determining the events that may lead to the adaptation of avian viruses to humans before the occurrence of pandemic influenza. We could then conduct worldwide surveillance for similar events involving contemporary avian viruses^ref. Deaths occurred predominantly in infants and the elderly during the 1889 and 1947 pandemics, while young adults were most severely affected in 1918. Pandemic stages, as defined by the WHO in May 2005 :
• interpandemic period :
• phase 1 : no new influenza virus subtypes have been detected in humans. An influenza virus subtype that has caused human infection may be present in animals. If present in animals, the subnational levels. risk a of human infection or disease is considered to be low.
• phase 2 : no new influenza virus subtypes have been detected. However, a circulating animal influenza virus subtype poses a substantial risk a of human disease.
• pandemic alert period :
• phase 3 : human infection(s) with a new subtype, but no human-to-human spread, or at most rare instances of spread subtype and early detection, notification to a close contact.
• phase 4 : small cluster(s) with limited human-to-human transmission but spread is highly localized, suggesting that the virus is not well adapted to humans.
• phase 5 : larger cluster(s) but human-to-human spread still localized, suggesting that the virus is becoming increasingly better adapted to humans, but may not yet be fully transmissible (substantial pandemic risk).
• pandemic period :
• phase 6 : pandemic: increased and sustained transmission in general population
• frequent epidemics have occurred between the pandemics as a result of gradual antigenic change in the distal region of HA of the prevalent virus, termed antigenic drift (every 2-3 years). Antigenic differences among viral isolates are measured by the hemagglutination inhibition (HI) assay, but these data are sometimes difficult to interpret. Antigenic cartography resolves many of these difficulties, increases the resolution at which antigenic data can be interpreted, makes the interpretation more quantitative, and provides a visualization of antigenic differences among strains^ref. These methods are now integrated into the biannual WHO seasonal vaccine strain-selection process. They are also being used to map the antigenic evolution of H₅ viruses and will be used to evaluate the breadth of immunity offered by pandemic vaccines. Currently, epidemics occur throughout the world in the human population due to infection with influenza A viruses of subtypes H₁N₁ and H₃N₂ or with influenza B virus : each year an ordinary flu epidemic causes approximately 250,000-1,000,000 deaths worldwide (36,000 deaths and 114,000 hospitalizations in USA and 4,000 deaths in UK) : > 90% of deaths occur among people aged > 65. The circulating viral subtype is associated with varying severity of influenza epidemics^ref : in the last 2 decades in the USA, estimated excess death rates were on average 2.8-fold higher in A/H₃N₂-dominated seasons than in A/H₁N₁ and B seasons^ref. Within a given subtype, however, the strain-specific determinants of epidemic severity are still poorly understood. For instance in the USA in the same period, excess death rates varied nearly 4-fold among A/H₃N₂ seasons, even after adjustments for population aging^ref. During 1990 to 1999, about 92 influenza-related deaths occurred annually among children aged <5 years in the USA^ref. > 18,000 (>90%) of these deaths and approximately 48,000 of the pneumonia and influenza hospitalizations per year occur among persons who are at highest risk for influenza-related complications. Children aged < 5 and women in the third trimester of pregnancy are also at higher risk for serious complications. Annual influenza epidemics have resulted in an average of >18,000 excess deaths (i.e., the number of influenza-related deaths above a projected baseline of expected deaths) and 48,000 pneumonia and influenza hospitalizations among older persons in the USA. Influenza season typically peaks in the USA between December and March. An analysis of data collected by the European Influenza Surveillance Scheme (EISS) during the past 5 winters (1999 to 2004) reveals a possible west-east spread of influenza across Europe^ref. In 3 of the 5 winters (2003/2004, 2002/2003, 2001/2002), the analysis suggests that there was west-east spread and during one of these seasons (2001/2002) there was also a south-north spread. clinical activity (usually cases of influenza-like illness (ILI), but occasionally cases of acute respiratory infection) reported by sentinel physicians and collected by EISS is a valid indicator of influenza activity and that, for Europe as a whole, increased influenza activity lasts for 10 to 22 weeks (2 to 5 months) each season^ref. West-east spread is counter to the prevailing notion that flu outbreaks spread East-west to Europe from Asia. Anecdotal accounts exist in the literature of historical influenza epidemics associated with unusual numbers of deaths, such as occurred in the 1951 epidemic in England in the midst of the first era of A/H₁N₁ viruses (1918–1957) (Burnet M. The influenza virus. Scientific American. 1953;188:28–31). In Liverpool, where the epidemic was said to originate, it was "the cause of the highest weekly death toll, apart from aerial bombardment, in the city's vital statistics records, since the great cholera epidemic of 1849"^ref. This weekly death toll even surpassed that of the 1918 influenza pandemic : the 1951 influenza epidemic had greater death rate than all subsequent influenza epidemics or pandemics in England and Canada. But what sets the 1951 epidemic apart from pandemics is that the older population was also severely affected, with twice the deaths as occurred in the 1957 pandemic. By contrast, the 1951 epidemic had minor impact in the USA, except possibly in New England. Laboratory surveillance data from the World Health Organization (WHO) indicate that influenza A viruses circulating at the time were characterized as H₁N₁^ref, a subtype circulating since the 1918 pandemic^ref. Although an unusually large drift event in the hemagglutinin of A/H₁N₁ viruses was reported in 1947^ref, subsequent changes in this protein remained minor until after 1951^ref. Hence, no virologic evidence of a shift or unusual drift in the hemagglutinin antigen exists for 1951 viruses. In support of the virologic evidence, we have shown that no epidemiologic pandemic signature occurred in 1951, as indicated by an age shift of deaths towards younger age groups^ref. The 1951 epidemic exhibited geographic disparities in influenza-related deaths, as illustrated by the contrast between England and Canada (countries with high death rate) and the United States (low death rate). These disparities are in part explained by laboratory surveillance reports by WHO^{ref1, ref2}, indicating that 2 antigenically distinct influenza A/H₁N₁ strains cocirculated in the Northern Hemisphere during the 1951 epidemic^{ref1, ref2}. The so-called Scandinavian strain was isolated in northern Europe and associated with mild illnesses. By contrast, the "Liverpool strain" was associated with severe illnesses and high deaths in Great Britain, Canada, southern Europe, and Mediterranean countries^ref. As both strains cocirculated in some countries^ref, intrasubtypic cross-immunity might have existed, with these 2 strains competing for susceptible hosts. The precise reasons for the unusually high death rate associated with the Liverpool strain remain elusive. The genetic markers of influenza virulence are still unclear today, but a multibasic cleavage site in the hemagglutinin, as well as minor changes in internal genes, are believed to enhance viral pathogenicity^ref (Nicholson K, Hay A. Textbook of influenza. Oxford: Blackwell; 1998). Only hemagglutinin inhibition tests could be performed in 1951, and to our knowledge, no influenza virus isolate or genetic sequence from 1951 is available in the public domain. Further molecular analysis of 1951 influenza specimens could help explain the extreme local pathogenicity in that season. We have described an influenza season that was unexpectedly severe in some countries and mild in others. This geographic disparity in influenza-related deaths is not common; influenza mortality is generally correlated between the USA and Europe and within the USA^{ref1, ref2}. Occasional disparities have been reported, however. For instance, the impact of the 2 waves of the 1968 pandemic differed markedly between North American and Eurasian countries, perhaps because of differences in preexisting immunity and evolving viruses^ref. In this context, the 1951 epidemic appears as another striking example of geographic disparities in influenza impact, perhaps explained in this case by cocirculation of 2 influenza A/H₁N₁ strains. Other competing hypotheses include differences in preexisting population immunity or socioeconomic factors, but these are less parsimonious explanations^ref

• interhuman : 7 (H) subtypes (H₁, H₂, H₃, H₅, H₇, H_{9, and H}) and 3 (N) subtypes (N₁, N₂ and N₇) have been isolated in the past from humans
• both influenza A and B viruses survive for 24-48 hr on hard, nonporous surfaces such as stainless steel and plastic but survive for < 8-12 hr on cloth, paper, and tissues. Measurable quantities of influenza A virus are transferred from stainless steel surfaces to hands for 24 hr and from tissues to hands for up to 15'. Virus survives on hands for up to 5' after transfer from the environmental surfaces. These observations suggest that the transmission of virus from donors who are shedding large amounts could occur for 2-8 hr via stainless steel surfaces and for a few minutes via paper tissues. Thus, under conditions of heavy environmental contamination, the transmission of influenza virus via fomites may be possible^ref.
• cross-species :
• some strains can be passed from humans to Mustela putorius furo.
• birds : 16 haemagglutinin (H) and 9 neuraminidase (N) subtypes of Influenza A viruses have been isolated from birds;
• avian influenza (AI) has been detected in Sus scrofa :
• WU Rui, et al. Isolation and identification of swine influenza virus. Virologica Sinica 2003; 18(6): 553-6.
• Li Hai-yan, et al. Isolation and characterisation of H₅N₁ and H₉N₂ influenza viruses from pigs in China. Chinese Journal of Preventive Veterinary Medicine 2004; 26(1). During 2002-2003, 1936 sera samples were collected from the pig flocks of 14 provinces and cities for H₉ subtype influenza detection. 7.3, 6.8, 4.5 and 1.9% seropositivity rates against avian H₉ subtype virus were detected in serum samples collected in 2002 from Liaoning, Guangdong, Shandong provinces and Chongqing city, respectively. H₉ subtype was not detected from serum samples collected in 2003; but 4.7 and 8.2% of serum samples collected from Guangdong and Fujian provinces were H₅ subtype influenza positive. 6 H₉N₂ and 2 H₅N₁ subtype influenza viruses were isolated from the samples that were collected during 2001-2003. Sequence analysis confirmed that these viruses are closely related to the H₉N₂ or H₅N₁ subtype avian influenza viruses that have been isolated in China. Serological tests (apparently carried out in 2003?) showed that the % of the positive sample for H₅ was 35.0 (7/20), 23.8 (5/21), and 20.0 (3/15) for 3 swine farms tested, respectively. 2 isolates of the A H₅N₁ virus strain were obtained from pigs, the 1st one in 2001, named SIV SW/FJ/F1/2001. There is no mention of the kind of tested sample, which could be nasal swab, or tissue, or both. The 2nd isolate was obtained in 2003, named SIV SW/FJ/1/03, from a nasal swab. Obviously, both originated in the province of Fujian, though the exact location is not mentioned. However, 3 locations are mentioned in the acknowledgements: Nanping city, Fuqing city, and Putian city, all located in Fujian Province. It would be interesting to note the origin (nasal swab or infected tissue?) from which the recent isolate(s) was/were obtained. One H₅N₁ strain was isolated in 2002 from materials collected from pigs in the Fujian province in 2001. Subsequently, 1936 samples were collected in 2003 from pigs in 14 provinces including Fujian and again one H₅N₁ strain was isolated from that province. These 2 isolates have been subjected to detailed analysis and have been shown to be highly homologous to the duck-derived H₅N₁ virus isolated recently in birds in China. According to the Chinese authorities, no variation in the virus has been observed. More recently, as part of their ongoing epidemiological surveillance programme, 1.1 million samples including 4447 from pigs have been collected and analysed between April and August 2004 from 10 provinces including Fujian, and no infection from H₅N₁ has been detected in pigs. The above findings do not at this stage indicate any major evolution regarding H₅N₁ infection in pigs. However, the OIE wishes to insist on the necessity for Member Countries affected by avian influenza to increase their epidemiological surveillance to better understand the implications of the existence of H₅N₁ virus in pigs. This study confirms the H₉N₂ influenza infection in pig flocks in China, and also is the 1st report of the emergence of the H₅N₁ influenza virus in the pig species. Therefore, for both the veterinary and public health sectors, urgent attention should be paid to the pandemic preparation for these 2 influenza subtypes. The importance of the findings is difficult to assess since the samples were obtained during the period 2001-2003 and the information has only now been disclosed. The frequency of the H₅N₁ virus seems to be very low and occasional infection of pigs (not to mention humans) may occur infrequently without onward transmission of virus
• A/Swine/Shandong/1/2003(H₉N₂) probably originates from a reassortment of chicken influenza virus subtype H₉N₂, H₅N₁ and duck influenza virus subtype H₉N₂. Although A/Swine/Shandong/1/2003(H₉N₂) differs from human isolates A/Hongkong/1073/99(H₉N₂) and A/Hong Kong/1074/99(H₉N₂), we should still pay more attention to the prevalence of the H₉N₂ subtype^ref.
• neutralizing antibodies to H₁, H₃, H₄, and H₅ influenza viruses were detected in the serum samples collected in 1977­1982 and 1998, suggesting that pigs in China have been sporadically infected with avian H₄ and H₅ viruses in addition to swine and human H₁ and H₃ viruses^ref.
• preliminary virological and serological evidence of H₅N₁ virus infection of pigs in Fujian province have been obtained^ref.
• XU Chuan-tian, et al. Isolation and Identification of type A swine influenza virus from Shandong Province and sequence analysis of HA gene. Virologica Sinica 2004; 19(1): 27-31.