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About viruses and viral disease

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Wuhan spiny eel influenza virus

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Influenza B viruses, unlike influenza A viruses, do not cause pandemics. There are many non-human animal reservoirs of influenza A viruses which provide gene segments that go towards making reassortant viruses that can infect humans. Influenza B viruses do not appear to have an animal reservoir other than humans – they have been isolated from seals but these appear to be human viruses. Influenza viruses discovered in fish and amphibians, however, are clearly not human viruses.

A sampling of viruses in amphibians, fish, and reptiles revealed influenza B virus sequences in the spiny eel, hagfish, and Asiatic toad. An important question to answer is whether these putative viruses have to potential to donate RNA segments to viruses that infect humans. To answer this question, functions of the HA and HA proteins of Wuhan spiny eel influenza virus (WSEIV) were studied. These two glycoproteins, found in the viral membrane, are important determinants of host range.

The HA protein of influenza A and B viruses binds the cell receptor, sialic acid, and catalyzes membrane fusion. These viruses can also hemagglutinate red blood cells. The HA protein of WSEIV does not hemagglutinate red blood cells. Influenza virus HA binds alpha2,3 and alpha2,6 linked silica acids, but the WSEIV HA binds alpha2,3 sialic acids only when they are present in a ganglioside – a sialic acid-containing lipid. HA cleavage by cell proteases is required for fusion, but none of the human airway proteases that cleave influenza A or B virus HA cleave WSEIV HA. Furthermore, the HA of WSEIV cannot catalyze fusion of cells in culture. It is therefore functionally divergent from other influenza virus HA proteins.

In contrast, the NA protein of WSEIV does have neuraminidase activity – the ability to cleave sialic acid from glycoproteins – as do other influenza virus NA proteins. Furthermore, the NA of WSEIV has similar biochemical properties as the NA of other influenza viruses, and its activity can be inhibited by the antiviral drug Tamiflu.

Both the HA and NA proteins of WSEIV are antigenically diverged from other influenza viruses – they do not react with a panel of monoclonal antibodies directed against influenza B viruses. Furthermore, human sera do not appear to contain antibodies that bind the WSEIV HA or NA, indicating that humans have not been infected with this virus.

These data show that WSEIV is a bona fide influenza virus; the HA is functionally diverged from that of other influenza viruses while the NA has similar properties. Based on these observations it seems unlikely that the WSEIV HA RNA segment could be part of a virus that infects humans. However, the similarity of the WSEIV NA with those of other influenza viruses suggest that it might be compatible with reproduction in humans. The fact that there is little antigenic conservation of the WSEIV glycoproteins with those of other influenza viruses means that an influenza virus carrying them would encounter an immunologically naive human population. Sound familiar?

An important lesson of this work is that we have woefully undersampled wildlife for viruses. Consequently, conclusions about what viruses are found in which hosts are likely to be wrong.

TWiV 571: Piwi koalas

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The League of Extraordinary Virologists celebrate the eradication of wild poliovirus type 3, and consider the effectiveness of an influenza vaccine produced in insect cells, and how small RNAs are protecting the Koala germline from retroviral invasion.

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Show notes at microbe.tv/twiv

How a toupee compromised influenza vaccine

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The influenza virus vaccine is frequently updated to ensure that it protects against infection with circulating virus strains. In some years the vaccine matches the circulating strains, but in others, there is a mismatch. The result is that the vaccine is less effective at protecting from infection. During the 2014-15 influenza season there was a mismatch due to growing the vaccine in embryonated chicken eggs.

[Read more…] about How a toupee compromised influenza vaccine

Unusual mortality pattern of 1918 influenza A virus

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1918 influenza mortalityThe 1918 influenza pandemic was particularly lethal, not only for the very young and the very old (as observed for typical influenza), but unexpectedly also for young adults, 20 to 40 years of age (pictured). It has been suggested that the increased lethality in young adults occurred because they lacked protective immunity that would be conferred by previous infection with a related virus. Reconstruction of the origins of the 1918 influenza virus provides support for this hypothesis.

Analysis of influenza virus genome sequences using a host-specific molecular clock together with seroarchaeology (analysis of stored sera for the presence of antibodies to influenza virus) indicates that the 1918 H1N1 virus arose ~1915 by reassortment of an avian influenza virus with an H1 virus that had previously emerged around 1907. The 1918 virus acquired the HA gene from the 1907 virus, and the NA gene and internal protein genes from an avian virus. This 1918 virus also infected pigs, in which descendants continue to circulate; however the human 1918 virus was displaced in 1922 by a reassortant with a distinct HA gene.

Seroarchaeology and mortality data indicate that an influenza pandemic in 1889-1893 was caused by an influenza H3N8 virus. This virus appears to have circulated until 1900, when it was replaced by a H1N8 virus (the N8 gene originating from the previously circulating H3N8 virus).

How do these events explain the unusual mortality pattern of the 1918 influenza A virus? High mortality among 20-40 year old adults might have been a consequence of their exposure to the H3N8 virus that circulated from 1889-1900. This infection provided no protection against the 1918 H1N1 virus. Protection of other age groups from lethal infection was likely a consequence of childhood exposure to N1 or H1 containing viruses (this may also have resulted in the lower than usual mortality in the elderly population). Influenza is typically highly lethal in very young children due to lack of immunologic memory.

These observations suggest that childhood exposure to influenza virus is a key predictor of virulence of a pandemic strain. Antibodies against the stalk of the HA protein protect against severe disease, but only within groups of HA subtypes (HA groups are determined by phylogenetic analysis). In 1918, antibodies against a group 2 HA subtype virus (H3) did not protect against severe disease caused by a group 1 HA subtype virus (H1). Childhood exposure might also determine mortality of seasonal influenza. For example, the high virulence of currently circulating H3N2 influenza viruses in those older than 65 years might be a consequence of infection with an H1N1 virus at a young age.

This logic can also explain mortality caused by influenza H5N1 and H7N9 viruses. Most fatalities caused by H5N1 viruses (the H5 is a group 1 HA) have been in individuals who were infected as children with an H3 virus (group 2 HA). Most fatalities caused by H7N9 viruses (group 2 HA) have occurred in individuals who were infected as children with H1N1 or H2N2 viruses (group 1 HA).

The practical consequence of this work are clearly stated by the authors:

Immunization strategies that mimic the apparently powerful lifetime protection afforded by initial childhood exposure might dramatically reduce mortality due to both seasonal and novel IAV strains.

Yet another avian influenza virus, H10N8, infects humans

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chicken market

To the collection of avian influenza viruses known to sporadically infect humans – H5N1, H7N9, H7N2, H7N3, H7N7, H9N2, and H10N7 – we can now add H10N8, recently found in two individuals in China.

Avian influenza virus H10N8 was first detected in tracheal aspirates from a 73 year old woman who was hospitalized in November 2013 for severe respiratory illness. The patient, who died, had previously visited a live poultry market. A second infection with this virus was detected in January 2014.

Virus isolated from tracheal aspirates on day 7 of illness was named A/Jiangxi-Donghu/346/2013(H10N8). Nucleotide sequence analysis of the viral genome reveals that it is a reassortant. The HA gene most closely resembles that of a virus isolated from a duck in Hunan in 2012, while the NA gene resembles that of a virus isolated from a mallard in Korea in 2010. All six other RNA segments resemble those from circulating H9N2 viruses in China. These viruses have also provided genes for H7N9 and H5N1 viruses.

Examination of the viral protein sequences provides some clues about virulence of the virus. The HA protein sequence reveals a single basic amino acid at the cleavage site, indicating that the virus is of low pathogenicity in poultry, like H7N9 virus. The sequence in the sialic acid binding pocket of the HA protein indicates a preference for alpha-2,3 linked sialic acids, typical  for avian influenza viruses (human influenza viruses prefer alpha-2,6 linked sialic acids). A lysine at amino acid 627 in the PB2 protein is known to enhance the ability of the virus to replicate at mammalian temperatures; the H10N8 virus has a mixture of lysine and glutamic acid, the residue associated with less efficient replication. The sequence of the M2 protein indicates that the virus is resistant to the antiviral adamantanes. In vitro testing indicated sensitivity to NA inhibitors Tamiflu and Relenza.

It is not known if this novel H10N8 virus will spread further in the human population. A novel influenza H7N9 virus was first detected in humans in early 2013 and has since caused 250 human infections with 70 deaths. Similar incursions of avian influenza viruses into humans have probably taken place for as long as humans have had contact with poultry. We are now adept at detecting viruses and therefore we are noticing these infections more frequently.

Live poultry markets are clearly a risk factor for humans to acquire infections with avian influenza viruses, as noted by Perez and Garcia-Sastre:

Live bird markets in Asia are undoubtedly the major contributor in the evolution of avian influenza viruses with zoonotic potential, a fact for which we seem to remain oblivious.

Given their role in transmitting new viruses from animals to humans, I wonder why live poultry markets are not permanently closed.

Update: George Gao agrees that the live poultry markets in China should be closed.

Changing influenza virus neuraminidase into a receptor binding protein

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neuraminidaseThe hemagglutinin (HA) and neuraminidase (NA) glycoproteins of the influenza virus particle serve distinct functions during infection. The HA binds sialic acid-containing cellular receptors and mediates fusion of the viral and cell membranes, while the NA removes sialic acids from glycoproteins. Apparently this division of labor is not absolute: influenza viruses have been identified with NA molecules that serve as receptor binding proteins.

An influenza virus was created that could not bind sialic acid by introducing multiple mutations into the HA gene. This mutant virus was not expected to be infectious, but nevertheless did propagate to moderate titers in cell culture. A single amino acid change was identified in the NA protein of this virus: G147R, which is just above the active site of the enzyme (illustrated; active site marked with green spheres). Passage of the virus in cell culture produced a virus that multiplied to higher titers; improved growth was caused by a K62E change in the HA stalk. The results of site-directed mutagenesis showed that the G147R change allowed the NA protein to serve the receptor binding function normally provided by HA. It is not clear how the HA change leads to improved growth of the G147 virus.

Although the G147R NA can serve as receptor binding protein, the HA is still required for fusion: abolishing this activity by mutation or by treatment with a fusion-blocking antibody did not allow virus growth.

The influenza NA protein is an enzyme (sialidase) that cleaves sialic acids from cellular and viral proteins. The G147R NA is active as a sialidase, and this activity can be blocked by the antiviral compound oseltamivir, which is an NA inhibitor. Treatment of G147R-containing virus with oseltamivir also blocked virus binding to cells. Virus-like particles that contain G147R NA but not HA can attach to sialic acid-containing red blood cells. This attachment can be reversed by oseltamivir. After binding to red blood cells, these virus-like particles slowly fall off, a consequence of NA cleaving sialic acid receptors. These observations indicate that the G147R NA binds to sialic acids at the active site of the enzyme, and cleaves the same receptor that it binds.

Treatment of cells with a bacterial sialidase that removes a broad range of sialic acids only partially inhibits G147R NA-mediated binding to cells. In contrast, growth of wild type influenza virus is completely blocked by this treatment. Therefore the receptor recognized by G147R NA is not the same as that bound by wild type virus.

Changing the influenza virus NA to a receptor binding protein is not simply a laboratory curiosity: the G147R NA change was found in 31 of 19,528 NA protein sequences in the Influenza Virus Resource. They occur in seasonal H1N1 viruses that circulated before 2009, in the 2009 swine-origin pandemic H1N1 virus, and in avian H5N1 viruses. The presence of this change in phylogenetic clusters of seasonal H1N1 and chicken H5N1 sequences suggests that they are also found in circulating viruses, and are not simply sequence errors or the product of passage in the laboratory.

These observations emphasize the remarkable flexibility of the influenza viral glycoproteins in their ability to switch receptor binding function from HA to NA. They might also have implications for vaccines, whose effectiveness are thought to depend largely on the induction of antibodies that block the function of HA protein. The work underscores the importance of serendipity in science: the HA receptor binding mutant virus was originally produced as a negative control for a different experiment.