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Study sheds light on a more effective way to study the influenza virus

Findings of a recent U.S. study provide insight into why the flu is so hard to beat, and a new way of looking at the influenza virus.

Influenza, also known as “the flu”, is a common respiratory illness that affects many people worldwide. Symptoms can be mild to severe, and can even result in death. There are an estimated 3 to 5 million severe cases of influenza worldwide each year, resulting in between 290,000 to 650,000 deaths.

Four types of influenzas viruses

The flu is caused by an influenza virus that infects the respiratory system. There are four primary types of influenza viruses: A, B, C, and D. Type A and B viruses infect the upper airway and are known to have the most widespread impacts on human health. Influenza viruses can also change over time, and vaccinations need to be updated each year to protect the immune system against new strains.

The virus is roughly spherical in shape and has a number of proteins inserted into its outer surface. In humans, the number and location of these proteins can vary from virus to virus. These changes mean that the flu in the human body is much different from what is cultivated in a petri dish for lab research; lab strains do not carry many of the structural changes seen in natural forms of the virus. Differences between lab and natural strains have made the flu and other viruses difficult to study and treat.

Fluorescent tags are difficult to attach to the flu virus

In molecular biology, fluorescent proteins are often attached to a molecule as a “tag” that helps researchers study an area of interest in a living organism. By following fluorescent tags, researchers can track where proteins and other molecules are located and how they change over time. However, attaching fluorescent proteins to the flu virus has been notoriously difficult. The surface of the influenza virus is crowded with proteins, providing less space for fluorescent proteins to attach. Fluorescent proteins are also relatively large, and adding them onto the surface of a virus can change how it works. New research into influenza A virus, the most common and harmful to humans, has overcome this obstacle by developing a novel way of studying the virus.

Researchers use different tagging technique for flu virus

In a recent U.S. study published in Cell, researchers used a technique called “site-specific labeling” to tag individual proteins of an influenza virus. Rather than inserting large fluorescent proteins, the authors embedded small sequences of 5- to 10-amino acids (the building blocks of proteins) into the proteins of a specific strain of influenza A virus. The amino acid tags—about 25 times smaller than large fluorescent proteins—lower the likelihood of disrupting protein activity.

After adding these tags, they introduced enzymes that could carry and attach fluorescent dyes to the now modified proteins in the virus. Once fluorescent dyes were attached to the proteins, researchers were able to better visualize individual proteins on the virus.

The study focused mainly on hemagglutinin (HA) and neuraminidase (NA), two proteins found on the surface of the influenza A virus. HA helps the virus bind to other cells in the human body which leads to infection. NA releases the virus from a cell so that it can continue binding to and infecting other cells. In the study, fluorescent dyes attached to HA and NA were used to detect the abundance and size of each protein on an individual virus.

Study provides new understanding of the flu virus

Site-specific labeling gave researchers a new view of the virus and helped them understand the reason behind the variation seen in individual viruses. Specifically, they wanted to know whether or not different amounts of HA and NA provided adaptive benefits to the virus—that is, allowed the virus to better survive and spread infection in its host. To do this, the authors looked at influenza A viruses that had been released from infected cells. Some of the cells were treated with antiviral drugs to prevent NA from functioning. By inhibiting NA, the drugs stop the virus from releasing the cell and infecting other cells.

The results showed that smaller viruses, or those with more NA proteins, were more immune to NA-blocking drugs, and fared better than larger proteins or those with fewer NA proteins. These viruses were better able to release from cells treated with NA blockers and could continue infecting other cells.

Because flu viruses replicate very rapidly in the human body, they need to be able to adapt to changing environments in order to survive. Adaptations such as changes to size, shape, and protein makeup can develop relatively quickly. As a result, later generations of the virus might be better able to survive and infect their host over longer periods of time.

More work needed to understand other strains and types of flu virus

Though the study focused on a single influenza virus strain, it provided insight into how protein makeup can benefit a virus under changing conditions. The authors note that more work is needed to understand the overall benefits of adaptations and how they apply to other strains and types of influenza viruses. These results might guide studies of other viral infections and can help develop vaccinations and antiviral drugs that limit survival adaptations in individual viruses.

Written by Braydon Black, BSc


  1. World Health Organization. Influenza (seasonal) [Internet]. Geneva: WHO. 2018 Nov 6 [cited 2018 Nov 24]. Available from:
  2. Centers for Disease Control and Prevention. Types of influenza viruses [Internet]. Atlanta, GA: U.S. Department of Health & Human Services. (unknown date) [updated 2017 Sep; cited 2018 Dec 15]. Available from:
  3. Vahey MD, Fletcher DA. Low-fidelity assembly of influenza A virus promotes escape from host cells. Cell. 2019 Jan;176:1-14. Epub 2018 Nov 29 [updated 2018 Dec 12; cited 2018 Dec 15]. Available from: doi: 10.1016/j.cell.2018.10.056
  4. Jefferson B. Flu’s clues: a new approach to studying influenza [press release]. (2018 Dec 3) [cited 2018 Dec 15]. Available from:
  5. World Health Organization. Virology of human influenza [Internet]. Geneva: WHO. (unknown date) [cited 2018 Dec 15]. Available from:


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