Viruses and human disease

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Such methods have shown how H7N9 AIV spread from eastern to southern China, possibly as a result of poultry trading, from where it seeded many infections in the second epidemic wave [ 3 ]. Genomic epidemiology has been also used to evaluate the outcome of local interventions, such as the closure of live poultry markets, in controlling AIVs in a specific region [ 4 ].

When applied on a global scale, phylogeographic analyses revealed an association between long-distance bird migration and the spread to Europe and America in of the highly pathogenic Asian H5 subtype AIV [ 5 ], which cost the US poultry industry hundreds of millions of dollars.

In addition to supporting epidemiological studies, rapid virus genome sequencing can identify molecular markers that are associated with important influenza A virus phenotypes, and can thereby help to predict the pathogenicity, transmissibility, antigenicity, and drug sensitivity of newly emergent strains [ 6 , 7 ]. Sequence-based assessment is now a routine component of many influenza surveillance programs and can inform estimates of emergence risk and help to evaluate the effectiveness of vaccines.

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Evolutionary analysis of influenza virus genomes is already being used to predict the antigenic evolution of the virus and, in collaboration with the World Health Organisation WHO , is helping to inform influenza vaccine strain selection [ 8 ]. Furthermore, genomic surveillance showed that influenza viruses that were circulating during the —17 season carried an N-linked glycosylation site that was absent from egg-adapted vaccines, reducing the effectiveness of those vaccines in antibody-binding experiments [ 9 ].

In some instances, the association between genome sequence and phenotype may be relatively straightforward, such as the presence of a polybasic cleavage site in the hemagglutinin connecting peptides, which in most instances confers high pathogenicity to AIV strains. For example, genome analysis of recent H7N9 viruses revealed mutations conferring high pathogenicity to birds and humans, highlighting the threats posed by AIV to public health and food supply [ 10 ].

In other cases, influenza virus mutations on different genes may interact, in which case a complete genome sequence is needed to forecast the viral phenotype in question. Despite their obvious importance, our understanding of the phenotypic effects of most influenza virus mutations is still poor. Genomic surveillance is enabling the rapid investigation of the evolutionary and transmission dynamics of influenza viruses at local, regional, and international scales.

Viruses: What are they and what do they do?

In addition, viral genomes can be used to assist public health policies, such as live poultry market closures or the annual update of influenza vaccine strains. Future interdisciplinary work that aims to combine virus genomes with data on human demography, international travel, wild bird movements, poultry trade, and human genetics therefore has great potential to improve our ability to predict the risk of influenza infection in people and poultry.

Successful control of AIVs on a global scale will require increased genomic surveillance in poorly characterized regions, timely data sharing, and the development of new analytical methods to test hypotheses concerning influenza virus emergence and transmission. Genomic analysis of the emergence, evolution, and spread of human respiratory RNA viruses. Annu Rev Genomics Hum Genet. Direct RNA sequencing of the complete influenza A virus genome. Dissemination, divergence and establishment of H7N9 influenza viruses in China.

Effect of live poultry market interventions on influenza a H7N9 virus, Guangdong, China. Emerg Infect Dis. Role for migratory wild birds in the global spread of avian influenza H5N8. Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses.

Predictive modeling of influenza shows the promise of applied evolutionary biology.


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Trends Microbiol. Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies elicited by egg-adapted vaccine strains. After infecting the cell, the virus continues to reproduce, but it produces more viral protein and genetic material instead of the usual cellular products.

Other shapes are possible, including nonstandard shapes that combine both helical and icosahedral forms.

Viruses: What are they and what do they do?

Viruses do not leave fossil remains, so they are difficult to trace through time. Three competing theories try to explain the origin of viruses. A virus exists only to reproduce. When it reproduces, its offspring spread to new cells and new hosts. Viruses may transmit from person to person, and from mother to child during pregnancy or delivery.

Some viruses can live on an object for some time, so if a person touches an item with the virus on their hands, the next person can pick up that virus by touching the same object. The object is known as a fomite. As the virus replicates in the body, it starts to affect the host. After a period known as the incubation period, symptoms may start to show. When a virus spreads, it can pick up some of its host's DNA and take it to another cell or organism. If the virus enters the host's DNA, it can affect the wider genome by moving around a chromosome or to a new chromosome.

This can have long-term effects on a person.

Overview of Viruses

In humans, it may explain the development of hemophilia and muscular dystrophy. Some viruses only affect one type of being, say, birds. If a virus that normally affects birds does by chance enter a human, and if it picks up some human DNA, this can produce a new type of virus that may be more likely to affect humans in future. Some viruses, such as the human papilloma virus HPV , can lead to cancer. Just as there are friendly bacteria that exist in our intestines and help us digest food, humans may also carry friendly viruses that help protect against dangerous bacteria, including Escherichia coli E.

When the body's immune system detects a virus, it starts to respond , to enable cells to survive the attack. The immune system produces special antibodies that can bind to viruses, making them non-infectious. The body sends T cells to destroy the virus. Most viral infections trigger a protective response from the immune system, but viruses such as HIV and neurotropic viruses have ways of evading the immune system's defenses. Neurotropic viruses infect nerve cells. They are responsible for diseases such as polio, rabies, mumps, and measles.

They can affect the structure of the central nervous system CNS with delayed and progressive effects that can be severe. Bacterial infections can be treated with antibiotics , but viral infections require either vaccinations to prevent them in the first place or antiviral drugs to treat them. Antiviral drugs have been developed largely in response to the AIDS pandemic. These drugs do not destroy the pathogen, but they inhibit their development and slow down the progress of the disease.

Antivirals are also available to treat infection with the herpes simplex virus, hepatitis B , hepatitis C , influenza, shingles, and chicken pox. Vaccinations are generally the cheapest and most effective way to prevent viruses. Some vaccines have succeeded in eliminating diseases, such as smallpox. Live-attenuated vaccines carry the risk of causing the original disease in people with weak immune systems.

Currently, vaccinations exist for polio, measles, mumps, and rubella, among others. Widespread use of these vaccines has reduced their prevalence dramatically. The measles vaccine has achieved a percent reduction in the incidence of measles in the United States U. If there is an outbreak, it usually affects people who are not vaccinated. Some people choose not to vaccinate their children, and because most people around them do vaccinate, the risk of getting measles is low. However, if fewer than 92 to 95 percent of people receive the vaccine, a community can lose its "herd immunity," and an outbreak can occur.

The risk of disease increases dramatically. This can also affect vulnerable people who are unable to receive the vaccine for some reason, such as a compromised immune system. Viral infections usually resolve without treatment, but medication can relieve symptoms such as pain, fever, and cough.

Article last updated by Yvette Brazier on Tue 30 May All references are available in the References tab. CDC: With low vaccine rates, some areas risk losing herd immunity. DNA disruptor.

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Evolutionary analysis of influenza virus genomes is already being used to predict the antigenic evolution of the virus and, in collaboration with the World Health Organisation WHO , is helping to inform influenza vaccine strain selection [ 8 ]. Furthermore, genomic surveillance showed that influenza viruses that were circulating during the —17 season carried an N-linked glycosylation site that was absent from egg-adapted vaccines, reducing the effectiveness of those vaccines in antibody-binding experiments [ 9 ].

In some instances, the association between genome sequence and phenotype may be relatively straightforward, such as the presence of a polybasic cleavage site in the hemagglutinin connecting peptides, which in most instances confers high pathogenicity to AIV strains. For example, genome analysis of recent H7N9 viruses revealed mutations conferring high pathogenicity to birds and humans, highlighting the threats posed by AIV to public health and food supply [ 10 ].

In other cases, influenza virus mutations on different genes may interact, in which case a complete genome sequence is needed to forecast the viral phenotype in question. Despite their obvious importance, our understanding of the phenotypic effects of most influenza virus mutations is still poor.


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Genomic surveillance is enabling the rapid investigation of the evolutionary and transmission dynamics of influenza viruses at local, regional, and international scales. In addition, viral genomes can be used to assist public health policies, such as live poultry market closures or the annual update of influenza vaccine strains.

Future interdisciplinary work that aims to combine virus genomes with data on human demography, international travel, wild bird movements, poultry trade, and human genetics therefore has great potential to improve our ability to predict the risk of influenza infection in people and poultry. Successful control of AIVs on a global scale will require increased genomic surveillance in poorly characterized regions, timely data sharing, and the development of new analytical methods to test hypotheses concerning influenza virus emergence and transmission. Genomic analysis of the emergence, evolution, and spread of human respiratory RNA viruses.

Annu Rev Genomics Hum Genet. Direct RNA sequencing of the complete influenza A virus genome. Dissemination, divergence and establishment of H7N9 influenza viruses in China. Effect of live poultry market interventions on influenza a H7N9 virus, Guangdong, China.

Emerg Infect Dis. Role for migratory wild birds in the global spread of avian influenza H5N8. Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. Predictive modeling of influenza shows the promise of applied evolutionary biology. Trends Microbiol. Contemporary H3N2 influenza viruses have a glycosylation site that alters binding of antibodies elicited by egg-adapted vaccine strains. H7N9 virulent mutants detected in chickens in China pose an increased threat to humans. Cell Res. Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA.

PLoS Pathog. Download references.