MicrobiologyBytes

The Great Flu is a free online game designed to introduce players to the nature of virus epidemics and means of controlling them. The game offers players the choice of five levels of flu severity (game difficulty), a €2 billion budget and a range of actions of varying effectiveness, such as sending researchers to afflicted areas, distribution of facemasks, stockpiling vaccines and antivirals, and closing schools, airports and public markets.  Taking various actions triggers various pieces of supporting material such as mocked-up news coverage and messages from governments or regional authorities, and also provides information on the nature and spread of earlier flu pandemics.

This summer on MicrobiologyBytes we’ll be revisiting a few old favourites – some of the most popular posts on this site. Today’s post is:

The results of a new study have provided fresh insights into influenza pandemics by raising the possibility that all three pandemic influenza strains of the 20th century may have been generated through a series of multiple reassortment events and emerged over a period of years before pandemic recognition. The results indicate that each of these strains was produced by reassortment between the previously circulating human virus and at least one virus of animal origin. The novel gene segments for the H2N2/1957 and H3N2/1968 pandemics seem to have originated from avian hosts, but the zoonotic sources of the introduced viral gene segments for the 1918 pandemic remain ambiguous. However, evidence suggests that, over a number of years, avian gene virus segments have entered mammalian populations where the viruses may have undergone reassortment with the prevailing human virus. Given the frequent interspecies transmission of influenza viruses between swine and humans, it is most likely that such reassortment events occurred in pigs before pandemic emergence.

This work suggests that in the 1918 and 1957 pandemics, novel NA and internal genes may have been introduced into the prevailing human virus strains before the acquisition of the novel pandemic HA. Frequent detection of seasonal human influenza strains in pigs indicates that pandemic precursor viruses probably have circulated in either swine or human populations. The precursors to the H2N2 and H3N2 pandemics have not been detected, probably because they originated in Asia where little or no surveillance was conducted at that time.

If future pandemics arise in this manner, this interval may provide the best opportunity for health authorities to intervene to mitigate the effects of a pandemic or even to abort its emergence. However, the findings argue the need for highthroughput characterization of all 8 gene segments of human virus isolates, even those that have unremarkable HA antigens, particularly of human viruses isolated in hotspots for zoonotic infections with avian influenza viruses. At present, global influenza surveillance in humans focuses attention primarily on hemagglutinin. Although this focus will continue to be required for strain selection for seasonal influenza vaccines, our findings argue that this surveillance will not suffice for early warning of an incipient pandemic.

Dating the emergence of pandemic influenza viruses. PNAS USA July 13, 2009. doi: 10.1073/pnas.0904991106
Pandemic influenza viruses cause significant mortality in humans. In the 20th century, 3 influenza viruses caused major pandemics: the 1918 H1N1 virus, the 1957 H2N2 virus, and the 1968 H3N2 virus. These pandemics were initiated by the introduction and successful adaptation of a novel hemagglutinin subtype to humans from an animal source, resulting in antigenic shift. Despite global concern regarding a new pandemic influenza, the emergence pathway of pandemic strains remains unknown. Here we estimated the evolutionary history and inferred date of introduction to humans of each of the genes for all 20th century pandemic influenza strains. Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts, i.e., swine and humans, as early as 1911 and was not likely to be a recently introduced avian virus. Phylogenetic relationships suggest that the A/Brevig Mission/1/1918 virus (BM/1918) was generated by reassortment between mammalian viruses and a previously circulating human strain, either in swine or, possibly, in humans. Furthermore, seasonal and classic swine H1N1 viruses were not derived directly from BM/1918, but their precursors co-circulated during the pandemic. Mean estimates of the time of most recent common ancestor also suggest that the H2N2 and H3N2 pandemic strains may have been generated through reassortment events in unknown mammalian hosts and involved multiple avian viruses preceding pandemic recognition. The possible generation of pandemic strains through a series of reassortment events in mammals over a period of years before pandemic recognition suggests that appropriate surveillance strategies for detection of precursor viruses may abort future pandemics.

Related:

• How influenza pandemics get started
• The Pathogenicity of Pandemic Influenza Viruses

The best ways of managing patients with influenza H5N1 infection are debated by experts in this week’s PLoS Medicine (What Is the Optimal Therapy for Patients with H5N1 Influenza? PLoS Med 6(6): e1000091 doi:10.1371/journal.pmed.1000091). In 2007 the World Health Organization described a new process for rapidly developing clinical management guidelines in emergency situations. This guideline recommends giving the antiviral drug oseltamivir (Tamiflu) at a dose of 75 mg twice daily for five days. Doses higher than this recommended amount should be used to fight H5N1 influenza, argues Nicholas White.  In contrast to the current WHO guidelines, he argues that higher doses should be given for H5N1 infection to avoid any possibility of under-dosing those patients with unusual pharmacokinetics and more resistant organisms. This will come at the expense of increased toxicity, he says, but is necessary given the mortality burden of H5N1 infection and the fact that H5N1 replicates more rapidly than seasonal influenza viruses, reaches much greater viral burdens than do other human influenza viruses, and resistance develops swiftly.

Robert Webster and Elena Govorkova disagree. They argue that we must instead consider a multidrug approach to managing patients with H5N1, an approach that is supported by animal data and “can guard against the emergence of resistant strains.”  Tim Uyeki from the Centers for Disease Control and Prevention in Atlanta, USA, emphasizes theneed for more data to help inform clinical management of patients with H5N1 infections. In the absence of these data, he argues, we need a multipronged strategy: pharmacological strategies including combination antiviral treatment, anti-inflammatory agents, and immunotherapy, and non-pharmacological strategies such as the standardization of optimal ventilator and fluid management, especially for acute respiratory distress syndrome, and management of other complications.

Related:

• MicrobiologyBytes: H5N1 | Influenza | Oseltamivir

Acute respiratory viruses cause substantial morbidity and mortality worldwide. Lower respiratory-tract infections are the leading cause of communicable disease death and among the top five contributors to disability-adjusted life years. Viruses are the primary cause of lower respiratory-tract infections in children and a substantial cause of such infections in all age-groups. The incubation period of an infectious disease is the time between infection and symptom onset. This period is widely reported because it is useful in infectious disease surveillance and control, in which the time of symptom onset may be the only indication of the time of infection. The incubation period plays an essential part in surveillance for healthcare-associated infections, and may aid in diagnosis if laboratory facilities are unavailable. The incubation period is clinically relevant in the administration of antiviral medications, many of which are most effective when given before or immediately after symptom onset. Epidemiological studies depend on the incubation period to identify potential sources of infection. Predictive models designed to inform policy decisions use the incubation period to evaluate the potential of surveillance programmes and interventions to confront emerging epidemics.

The length of the incubation period by comparison with the latent period (the time between infection and becoming infectious) determines the potential effectiveness of control measures that target symptomatic individuals. “4–5 days” may refer to the most common range, the highest and lowest incubation periods in a study, or some other interval. Without knowing which summary measure is being stated, it is hard to use this information to make clinical or infection control decisions. Estimates given without attribution or based on few observations do not meet the standards of evidence we demand for modern medical information. A recent paper reviews the literature on nine respiratory viruses selected for their clinical or public-health importance: adenovirus, human coronavirus, SARS-associated coronavirus, influenza, measles, human metapneumovirus, parainfluenza, respiratory syncytial virus (RSV), and rhinovirus. By systematic review and analysis of published estimates and data, the authors aimed to capture the consensus in the medical literature on these incubation periods, characterise the evidence underlying this consensus, and provide improved estimates of incubation periods for these infections.

Incubation periods of acute respiratory viral infections: a systematic review. Lancet Infect Dis 2009;
9: 291–300
Knowledge of the incubation period is essential in the investigation and control of infectious disease, but statements of incubation period are often poorly referenced, inconsistent, or based on limited data. In a systematic review of the literature on nine respiratory viral infections of public-health importance, we identified 436 articles with statements of incubation period and 38 with data for pooled analysis. We fitted a log-normal distribution to pooled data and found the median incubation period to be 5·6 days (95% CI 4·8–6·3) for adenovirus, 3·2 days (95% CI 2·8–3·7) for human coronavirus, 4·0 days (95% CI 3·6–4·4) for severe acute respiratory syndrome coronavirus, 1·4 days (95% CI 1·3–1·5) for influenza A, 0·6 days (95% CI 0·5–0·6) for influenza B, 12·5 days (95% CI 11·8–13·3) for measles, 2·6 days (95% CI 2·1–3·1) for parainfluenza, 4·4 days (95% CI 3·9–4·9) for respiratory syncytial virus, and 1·9 days (95% CI 1·4–2·4) for rhinovirus. When using the incubation period, it is important to consider its full distribution: the right tail for quarantine policy, the central regions for likely times and sources of infection, and the full distribution for models used in pandemic planning. Our estimates combine published data to give the detail necessary for these and other applications.

Related:

• One virus particle can be enough to cause infection
• Adenoviruses
• SARS Virus May Be Tough To Beat

Wild waterfowl and seabirds are major natural reservoirs of influenza A viruses. Genetic analysis has revealed that influenza A viruses found in all other host species, including humans, were ultimately derived from avian viruses. Geographical separation of host species has shaped the influenza gene pool into largely independently evolving Eurasian and American lineages, although some gene flow between these regions has been documented.

Reassortment between Eurasian and North American lineage viruses have also been documented in wild aquatic bird populations indicating that in these two geographically segregated lineages there is some mixing of viruses. However, the possible effects of virus gene flow between the Eurasian and American gene pools on influenza virus evolution and population structure had not been fully explored until recently. A new study shows that virus gene flow from Eurasia has led to the exclusion of some viruses from North America, most likely mediated by competition for susceptible hosts (Gene flow and competitive exclusion of avian influenza A virus in natural reservoir hosts. Virology, 5 June 2009 doi:10.1016/j.virol.2009.05.002).

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The researchers found that intercontinental gene flow is frequently mediated through seabirds, highlighting the need for increased surveillance of influenza viruses in a broader spectrum of potential host species. Such selection is only likely to occur in cases where the viruses in question are sufficiently antigenically similar to induce a cross-protective immune response.

Population genetics offers a number of concepts and principles to explain the evolutionary behavior of RNA viruses. For example, the competitive exclusion principle states that when two species compete for limited resources one species will eventually outcompete the other and become dominant. In the case of RNA viruses, a combination of high replication numbers and high nucleotide substitution rates makes the prolonged co-existence of two or more genetically distinct virus populations unlikely. In theory, the competitive pressure exerted by an invading influenza virus will select for viruses with increased reproduction and transmissibility. Therefore the adaptive advantage conferred through competition may contribute to influenza disease emergence.

Increased genome surveillance of influenza viruses in bird populations is critical for understanding the effects of gene flow between populations. The extent of virus competition in avian populations infected with influenza remains unknown. In Asia, the long-term endemicity of H5N1 influenza appears to have replaced, most probably through competitive selection, low pathogenic H5 subtype viruses that have been only rarely isolated from poultry in Asia since 2000 when compared to previous surveillance in the 1970′s. This new work provides a possible mechanism for disease emergence and transmission from natural reservoir hosts.

Related:

• The Biology of Influenza
• How influenza pandemics get started

Assessing the quality of information on the internet is all about filtering – whether it’s a blog post or a peer-reviewed journal. I don’t want to shock you, but not everything published in peer-reviewed journals is correct, you still need to use your judgement. And some blogs provide some of the best information out there. The best example of this I’ve come across recently is How do adamantane drugs block M2? by Michael Clarkson:

Vaccination plays such an important role in our seasonal influenza strategy in part because we don’t have many medicines that can be brought to bear on the disease. The neuraminidase inhibitors (specifically Tamiflu) are widely stockpiled, and continue to work for now, but the specter of resistance is already lurking. If these drugs are too widely or too improperly used, there is a good chance that resistance mutations will eventually render these drugs ineffective. Universal drug resistance may already be the fate of the drugs amantadine and rimantadine, built on an adamantane backbone. The adamantane drugs inhibit the M2 proton channel from influenza A, a tiny tetrameric protein that equalizes pH between the virus and the endosome of the cell that has swallowed it. This process releases the virus contents so that they can do their damage to the cell, so these medicines can significantly retard the infection process. Or rather, they could, if so many influenza strains didn’t harbor the S31N mutation that almost completely nullifies their effect. If we are to develop new drugs to attack the M2 channel, it would be helpful to know how this mutation causes drug resistance. Over the past few years a great deal of structural evidence has accumulated showing how adamantane drugs work on the older, non-resistant channels. The problem is that the evidence supports two different models of M2 inhibition, and so far it has proven difficult to determine which of them is probably correct…

read more…

Related:

• The Biology of Influenza
• Antiviral Drugs
• Viroporins

In the vast majority of systems, it is unknown how many individual pathogens are required to cause infection of a host organism. Estimates of this number are necessary to predict the likelihood that hosts are infected by multiple genotypes, and so predict the magnitude of genetic drift, the evolution of new pathogen genotypes and the interactions between pathogens and their hosts – all features which are highly relevant in the face of an influenza pandemic. These interactions include competition, complementation and recombination. There is experimental evidence that the number of virions causing an infection can be small, as shown by the data from two experimental approaches. First, genetic drift can be very strong when low virus doses are used, suggesting that only a small number of virions caused the infection. Second, results of dose–response experiments suggest that the number of virions causing infection is in some instances very small. Although the data suggest that the number may be small, there has been no absolute proof that one virus particle is enough be enough to cause infection of a host. Recent research with insect viruses has now shown that one virus particle is enough to cause infection and subsequent disease.

Virus populations are usually composed of collections of variants. In order to investigate whether virus particles (virions) can cause an infection independently from each other, and therefore individually, the researchers set up an experiment with two marked virus variants. The results showed that exposure to a low dose of virus particles resulted in a small number host infections, around 20%. The majority of these hosts turned out to be infected by a single virus genotype. In contrast, exposure to a high dose of virus resulted in virtually all the hosts becoming infected. Here most of the hosts were infected by both types of virus and only 14% were infected by only one of the variants.

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Based on the assumption that every virus particle operates independently from all other virus particles, the researchers set up a probability model to predict how many virus particles have caused an infection and how many different virus genotypes are present in infected hosts. The results of the infection experiments show that virus particles can indeed act independently, and that a single virus particle can be enough to cause an infection.

In infection caused by few virus particles (as may occur frequently in natural situations), the number of virus particles determines the degree of virus diversity that will be present within the host. This is an important finding because the interactions between virus variants, such as competition and exchanging genetic information, determine the progression of disease and the evolution of the virus. This is highly significant in the case of the new H1N1 influenza strain which has just entered the human population. Although each of the eight gene segments in the new virus has been seen in pigs in the past 10 years, this virus has only been in humans for a few months, and is quite unstable. Although less pathogenic than H5N1 influenza, which now seems to be endemic in countries like China, Indonesia, Vietnam and Egypt, recombination resulting in a virus which combines the high transmissibility of H1N1 with the killing power of the H5N1 becomes more likely as both viruses circulate in human populations.

Hold on tight, it might be a bumpy ride.

An experimental test of the independent action hypothesis in virus–insect pathosystems. 2009 Proc. R. Soc. B 276: 2233-2242
The independent action hypothesis (IAH) states that each pathogen individual has a non-zero probability of causing host death and that pathogen individuals act independently. IAH has not been rigorously tested. In this paper, we (i) develop a probabilistic framework for testing IAH and (ii) demonstrate that, in two out of the six virus–insect pathosystems tested, IAH is supported by the data. We first show that IAH inextricably links host survivorship to the number of infecting pathogen individuals, and develop a model to predict the frequency of single- and dual-genotype infections when a host is challenged with a mixture of two genotypes. Model predictions were tested using genetically marked, near-identical baculovirus genotypes, and insect larvae from three host species differing in susceptibility. Observations in early-instar larvae of two susceptible host species support IAH, but observations in late-instar larvae of susceptible host species and larvae of a less susceptible host species were not in agreement with IAH. Hence the model is experimentally supported only in pathosystems in which the host is highly susceptible. We provide, to our knowledge, the first qualitative experimental evidence that, in such pathosystems, the action of a single virion is sufficient to cause disease.

Related:

• How influenza pandemics get started
• Influenza Questions

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Related:

• 10 things you should know about H1N1 (swineflu)
• 10 more things you should know about H1N1 (swineflu)