Acute Respiratory Infections (Update September 2009): Previous page | 1,2,3,4,5,6,7

The A/2009 H1N1 influenza virus pandemic

ARI Introduction Influenza Respiratory syncytial virus and parainfluenza viruses Streptococcus pneumoniae Tuberculosis The A/2009 H1N1 influenza virus pandemic References

Introduction

Since the global H1N1 influenza virus pandemic of 1918, influenza virus gene reassortment has been well documented and observed to occur frequently between human virus subtypes, between human and avian and among avian influenza viruses. Such reassortments led to the global pandemics of 1957 (H2N2) and 1968 (H3N2) [407] [408] . Although A/H1N1 viruses continued to circulate among humans, seasonal epidemics of influenza A virus from 1968 to 2009 were dominated by A/H3N2 virus variants generated by antigenic drift [409] [410] , until, In March and early April 2009, a new influenza A (H1N1) virus brutally emerged among humans in California and in Mexico, quickly spreading worldwide through human-to-human transmission, generating the first influenza pandemic of the twenty-first century. The virus was found to be antigenically unrelated to human seasonal influenza viruses but genetically related to viruses known to circulate in pigs. In view of its likely swine origin, it is often referred to as 'swine-origin influenza virus' (S-OIV) A/H1N1, or 2009 A/H1N1 influenza virus.

Swine H1N1 influenza viruses had been circulating in pig populations for at least 80 years but too often lacked surveillance and molecular characterization. In 1998, a new triple-reassortant H3N2 virus emerged in the North American pig population, comprising genes from classical swine H1N1, North American avian and human H3N2 influenza viruses. Co-circulation and mixing of this North American triple-reassortant with viruses of swine lineage generated further H1N1 and H1N2 reassortant swine viruses. In Europe, an avian H1N1 virus ('avian-like' swine H1N1) was first isolated from pigs in Belgium in 1979 [411] , and gradually replaced classical swine H1N1 viruses [412] . The 'avian-like' virus lineage spread all over Europe and Asia while also reassorting with other influenza virus strains. In Asian pig populations, the classical swine H1N1 virus lineage still circulated together with the 'avian-like' swine H1N1, H1N2 reassortants and the North American H3N2 triple-reassortant [413] .

Molecular studies of the new A/H1N1 pandemic virus genome showed that it was derived from several viruses which had been circulating in pigs for a long time, namely the North American H3N2 triple-reassortant, the classical swine H1N1 lineage, and the Eurasian 'avian-like' swine H1N1 virus (see details under Virology). Initial transmission to humans is believed to have taken place at least several months before recognition of the first outbreak and phylogenetic data even suggest that the reassortment of swine lineages may have occurred years before emergence in humans [415] [416] [417] . Surprizingly however, there has been no evidence so far that swine are playing any role in the epidemiology or in the worldwide spread of the virus in human populations [418] .

The World Health Organization declared a pandemic alert on 11 June 2009, whose level was quickly raised to level 6, in view of the number of regions which officially reported A/H1N1 influenza cases in their communities. In view of the rapid spread of the pandemic H1N1 virus strain, its propensity to primarily affect children and young adults, as well as those with an underlying lung or cardiac disease condition [419] , and the risk of a possible increase in pathogenicity through further reassortment with avian or human virus strains, the development of a specific vaccine was promptly engaged in collaboration between the World Health Organization, Health Ministers and National Health Agencies and the vaccine industry. Numerous unknowns still exist at this time regarding the safety, immunogenicity, efficacy and availability of the candidate vaccines under development but it is hoped that the picture will become clearer as soon as results from clinical studies become available.

Disease Burden and Epidemiology

Epidemiology

Since the initial detection of the first two cases of human infection with pandemic A (H1N1) 2009 S-OIV in April 2009, the number of laboratory confirmed A/H1N1 cases in humans that were reported to WHO soared to 8780 cases, including 72 deaths, on May 17, 2009, then 94 512 cases including 429 deaths on July 6, and finally reached 174 913 cases, including 1411 deaths in 166 countries on August 6, 2009. These numbers however do not take into account the fact that many countries are no longer attempting to identify all human cases of pandemic flu [420] .

[421] It was recently estimated from mathematical modeling that >1 million people had been infected in the USA as of 10 July 2009, the time when official reports were mentioning only 37 246 official cases. In many countries, the capacity for laboratory diagnosis has been so severely stressed that virological surveillance had to be restricted to patients attending hospitals [421] . The actual number of people who have been infected by the H1N1 virus since the beginning of 2009 is most likely, therefore, a few orders of magnitude greater than that of the laboratory-confirmed cases.

The last known official number of deaths from H1N1 infection worldwide was 1964 on August 14, 2009, a little more than 50% of which had occurred in the southern hemisphere: 885 deaths were reported from South America, 122 from Australia-New Zealand, and 73 from Malaysia and Singapour. In comparison, 706 deaths were reported from North America, 97 from Thailand and 60 from Europe. Very few data exist regarding the African continent.

In the temperate areas of the southern hemisphere, where the virus has been spreading fast, the pandemic seemed to slow down around July 2009, at least in those areas affected early, such as Argentina, Chile and parts of Australia. However, the most recently affected areas in Australia, such as Queensland and Western Australia, as well as South Africa, which was affected late, were experiencing an upsurge of pandemic-related influenza cases at the beginning of August. The same situation also prevailed in New Caledonia and French Polynesia. Most countries in the southern hemisphere reported more pandemic H1N1 this year than any of the seasonal subtypes.

In the temperate areas of the northern hemisphere, the spread of the pandemic has been more gradual, with many countries reporting increasing rates of H1N1 respiratory illness in localized areas. The virus spread widely in the USA, Great Britain and Germany. The fear is that the situation will get much worse in the fall and winter and involve many more areas and countries. In the tropics, rates appeared to be quickly increasing in countries in both Central and South America and Asia, especially in Thailand.

It is not possible at this time to guess what will the future look like. The most pessimistic estimates are calling for 1 billion to 3 billion people (15% to 45% of the world's population) getting infected.


Age distribution

A characteristic feature of the H1N1 pandemic is that it mostly involves so far children and young adults. One of the early American studies showed that, although the age of H1N1 patients in the study ranged from 3 months to 81 years, 60% of patients were 18 years of age or younger [422] . In most countries, the majority of H1N1 cases have been occurring in young people, with the median age estimated to be 12 to 17 years in Canada, the USA, Chile, Japan and the UK. This age distribution speaks in favor of at least partial immunity to the virus in the older population.

Indeed, 33% of humans over 60 years of age were found to have cross-reacting antibodies to S-OIV A(H1N1) by haemagglutination inhibition test and neutralization tests, but antibody titers to A/H1N1 did not substantially increase after vaccination with a seasonal vaccine [415] [423] . In another study, no neutralizing antibodies against the pandemic A/H1N1 (2009) virus could be found in sera from people born after 1920 [424] . Nevertheless, a strong conservation of more than 50% of T cell epitopes (whether T-helper or CTL epitopes) was described between the 2009 A(H1N1) S-OIV and the seasonal influenza virus strains used to prepare the 2007 and 2008 influenza vaccines, which would provide a certain level of cross-reactive cellular immunity to the pandemic virus in the vaccinated human population [425] .


Clinical presentation and severity of the disease

H1N1 is a rather mild, self-limiting upper respiratory tract illness with (or at times without) fever, cough and sore throat. Up to 50% of patients present with gastrointestinal symptoms including diarrhea and vomiting. The spectrum of clinical presentation varies from asymptomatic cases to primary viral pneumonia resulting in respiratory failure, acute respiratory distress, multi-organ failure and death. Thus, 2% to 5% of confirmed cases in the USA and Canada and 6% of cases in Mexico had to be hospitalized, a fifth of them requiring management in intensive care unit. The rate of hospitalization could actually be as high as 10% in some cities. Most, but not all of the hospitalized patients had underlying conditions such as cardiovascular disease, respiratory disease including asthma, auto-immune disorders, obesity, diabetes or cancer. Pregnant women, especially in their second and third trimester, also are at a high risk for more severe disease [419] .

The overall H1N1 case fatality rate in Mexico was estimated to be around 0.4% [426] . The average case fatality rate that can be deduced from the laboratory-confirmed cases officially reported to WHO as of 06 August 2009 is much lower (0.08%). H1N1 deaths have occurred in middle-aged adults (median age around 40 years), contrary to seasonal Influenza where fatal disease occurs most often in the elderly (>65 years old).


Transmission

The modes of transmission of the pandemic A/H1N1 (2009) virus are not known but are thought to involve the dissemination of large droplets and possibly small-particle droplets expelled when an infected person coughs. There is most likely also transmission through contact with fomites that are contaminated with respiratory or possibly gastrointestinal fluids [427] . Many S-OIV-infected patients experienced diarrhea, making the potential for fecal-oral transmission a risk to take seriously into account [422].

The incubation period for S-OIV infection appears to range from 2 to 7 days, but it should be noted that most patients probably shed virus from day 1 before the onset of symptoms through 5 to 7 days after.

Virology

The novel S-OIV A/H1N1 2009 can be grown in canine kidney (MDCK) cell cultures or primary human airway epithelial cell cultures, or in embryonated hens eggs. Scanning electron microscopy revealed virions of remarkably filamentous shape [424] .

Sequence analyses showed the absence of markers associated with high pathogenicity in avian or mammalian species, such as a multibasic haemagglutinin cleavage site [428] or a lysine residue at position 627 in the PB2 protein [429] .


Molecular and antigenic characterization

Phylogenetic analyses of A (H1N1) virus isolates collected prior to August 2009 revealed a great homogeneity of genomic sequences, with the HA (H1), NP and NS gene segments coming from the classical swine H1N1 lineage. The H1 sequence could actually be traced back to the 1918 H1N1 pandemic virus (the "Spanish flu"), which has remained endemic in swine and continued to circulate among pigs in Asia, the America's and until the 1980s also in Europe [419] [430] [431] .

The NA (N1) and M genes of the 2009 H1N1 pandemic virus come from the 'avian-like' Eurasian swine H1N1 lineage, which emerged in Europe in 1979 after reassortment between a classical swine and an avian H1N1 virus, then spread through Europe and Asia [432] , displacing the classical swine H1N1 virus from Europe and also generating new reassortants in swine with different human origin influenza A viruses [433] .

Finally, the PA, PB1 and PB2 genes of the 2009 pandemic H1N1 virus are from the North American H3N2 'triple-reassortant' lineage, which was first isolated from American pigs in 1998 in which it showed unusual pathogenicity [434] 435] [436] . The name 'triple-reassortant' relates to the fact that the virus has HA, NA and PB1 genes of human influenza virus origin, NP, M and NS genes of classical swine influenza virus origin and PA and PB2 of North American avian virus origin.

The 2009 S-OIV H1N1 therefore has inherited virus gene segments of all three swine, human and avian origin: its HA, NP and NS gene segments have been inherited from swine classical virus, its NA and M segment from the avian-like Eurasian reassortant lineage, and its PA and PB2 segments from North American avian lineage. Indeed, all gene segments of the pandemic A (H1N1) S-OIV were already established in the North-American 'triple-reassortant' (H3N2) swine virus and in the 'avian-like' Eurasian (H1N1) swine virus but no data are available to help evaluate when, where, nor between which parent viruses did the initial reassortment actually occur.

Antigenically, all S-OIV isolates look similar to classical swine viruses and to triple reassortant H1N1 viruses that have been circulating among pigs in the USA over the last decade, showing no antigenic cross-reactivity with contemporary human seasonal H1N1 viruses.


Pathogenicity in animals

Experimental pathogenicity of the 2009 A/H1N1 S-OIV was tested in mice, ferrets and nonhuman primates [424]. S-OIV replicated more efficiently in the lungs of infected mice, generating earlier bronchitis and alveolitis, and eliciting more markedly increased production of interleukin-10 (IL-10), interferon gamma (IFN-Y), IL-4 and IL-5 than infection with a recent human H1N1 virus (A/Kawasaki/UTK-4). Similarly, it induced in nonhuman primates more elevated fever, more severe lung lesions with oedematous exudate and inflammatory infiltrates and higher antigenic loads in pneumocytes, similar to what was reported for highly pathogenic avian H5N1 influenza viruses [437] . It also was more pathogenic in ferrets, replicating to higher titers in trachea and lungs than human seasonal H1N1 virus and caused more severe bronchopneumonia with prominent viral antigen expression in the peribronchial glands and alveolar cells.

In contrast, it was devoid of overt pathogenicity for pathogen-free miniature pigs, although the virus did replicate efficiently in the respiratory tract of the animals.

The 2009 A(H1N1) S-OIV was also found to be more pathogenic than a seasonal 2007 A (H1N1) virus in ferrets and mice, with extensive virus replication occurring in the trachea, bronchi and bronchioles of the animals, while replication of the seasonal virus was limited to the upper respiratory tract [438] . The 2009 A(H1N1) influenza virus also replicated in the intestinal tract of inoculated ferrets, consistent with gastrointestinal involvement in many human A(H1N1) cases [439] .

Transmission of the virus via aerosol or respiratory droplets was also tested in ferrets, and found to be either as efficient as [438] or less efficient than [439], highly transmissible seasonal A(H1N1) virus. The latter observation seems to be in agreement with unpublished epidemiological data from the Centers for Disease Control which suggest that the virus is not easily transmissible among humans as only 10% of patients' household contacts become infected [440] .


Sensitivity to antiviral drugs

Genetic and phenotypic analyses indicate that S-OIV is susceptible to neuraminidase inhibitors oseltamivir (TamifluTM) and zanamivir (RelenzaTM), but resistant to the adamantanes [441] . Treatment with oseltamivir is efficacious if initiated within the first 36 hrs after infection. The FDA recently issued an emergency use authorization approving the use of oseltamivir to treat influenza illness in infants under the age of 1 year and for chemoprophylaxis in infants older than 3 months of age.

A total of six A(H1N1) S-OIV isolates that are resistant to oseltamivir have been described so far, one each from Canada, China, and Denmark, and three from Japan. These cases have been sporadic and there was no evidence of further transmission of the resistance marker into the virus population.

Vaccines

Vaccines are considered to be one of the most effective tools, not only to prevent the spread of the influenza virus but also to mitigate the severity of illness and the impact of the disease [442] . Today, the development of a pandemic A(H1N1) influenza vaccine in the fastest time is a global priority. This stems both from the rapid spread of the pandemic worldwide, from the fear that the A(H1N1) virus might accidentally gain added virulence through mutations and/or reassortment with other human or avian influenza virus, and from the total lack of cross-immune reactivity observed between the pandemic and seasonal influenza virus strains, making the 2009 seasonal vaccine useless in the fight against the A(H1N1) pandemic. The development of a pandemic influenza vaccine however raises complex challenges, such as ensuring that sufficient seasonal influenza vaccine will still be available in the coming fall, estimating with accuracy short- and medium-term production capacity of the different producers, reserving part of the foreseen production capacity for poor countries with no or little access to the vaccine, etc [443] [444] .

As of June 2009, the total global annual capacity for trivalent seasonal influenza vaccine production stood at 876 million doses, with seven manufacturers responsible for 560 million doses (i.e. 64% of the capacity). In spite of the WHO global pandemic influenza action plan to increase the potential supply of pandemic influenza vaccine [445] , the supply of enough pandemic vaccine to immunize the world's population -should this be needed- would therefore take at least four years! Added to which, it still is not clear whether one or two doses of pandemic vaccine will be required to induce full protection, nor whether the use of water-in-oil adjuvants will have the same antigen dose-sparing effect as it had in the case of the H5N1 vaccines [446] [447] . Finally, the yields of virus production in eggs or cell cultures will be an important determinant of the amount of vaccine doses that can be manufactured.

At this time, a total of 24 vaccine manufacturers from America, Europe, Russia, Australia and Asia are in the process of developing A(H1N1) vaccines, whether whole-virus-based vaccines, split inactivated vaccines, subunit vaccines, live-attenuated vaccines or other formulations. Clinical trials have begun in 4 countries (The USA, UK, Australia and China) and are expected to take place soon in many others.

Preliminary reports indicate that a single 15-µg dose of an inactivated split influenza A (H1N1) 2009 vaccine induced a titer of 1:40 or more on hemagglutination-inhibition assay in 96.7% of 18-64 years-old subjects [448] . This result was not considered surprising in the cohort of volunteers who were 50 years of age or older, in view of their possible exposure to H1N1 virus strains that had been circulating before 1957 and shared antigenic determinants with the pandemic 2009 H1N1 strain (see [449] ). The robust immune response to the H1N1 vaccine observed in the 18-49 years-old volunteers cohort was however unanticipated. It could be that there is more similarity between the influenza A (H1N1) 2009 virus and recent seasonal virus strains than has been recognized so far. Indeed, cross-reactive antibodies to 2009 H1N1 have been detected in serum samples from trials of a seasonal trivalent inactivated vaccine predating the current pandemic [450] .

The NIAID Office of Communications also issued a preliminary report on their clinical trials, showing that among healthy volunteers who received a single 15-µg dose of either the Sanofi-Pasteur or the CSL Limited inactivated split A (H1N1) 2009 vaccines, a robust immune response was measured in 96% and 80%, respectively, of adults aged 18 to 64, and in 56% and 60%, respectively, of adults aged 65 and older [451] .

If these results are confirmed, the pandemic A (H1N1) S-OIV vaccine will contain 15 µg of HA antigen, the dose used in seasonal flu vaccines, and no adjuvant.

The use of adjuvanted vaccines would raise regulatory problems in the USA, which has never licensed an adjuvanted flu vaccine and has no fast-tracK system in place [452] . In any case complete safety and immunogenicity data on the pandemic flu vaccine in adults are unlikely to be available before the end of December 2009 and not until February 2010 for children.

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