T’is the season to be queasy

As the flu season continues to wreak havoc – with so-called ‘Aussie flu’ on the rampage ­– we get to the science behind the headlines

Influenza is a complicated and therefore fascinating virus. Its genome is single stranded, negative sense RNA and it is in the order Mononegavirales. This makes it related to some interesting pathogens including the viruses which cause mumps, measles , rubella, rabies and ebola.

Four types of influenza have been recognised - A, B, C and D. Influenza D is found in cattle but it is not associated with human infection. Although influenza C has been isolated from symptomatic humans and pigs, it is not thought to be clinically important in either. Both humans and seals can be infected with (different) strains of Influenza B virus. In contrast, Influenza A is a significant pathogen in birds, pigs and horses as well as humans and interspecies transmission can occur. Influenza A and B are associated with ‘seasonal influenza’ while pandemics are caused by sub-types of Influenza A.

The process of virus assembly is a remarkable feat of stereochemistry and thermodynamics

Virus replication is an amazing process. The virus uses glycoproteins in its surface to bind to specific receptors on particular host cell types. Inside the cell, the particle opens up (‘uncoats’) releasing the genomic DNA or RNA so that it can be copied and have proteins translated from it. The process of virus assembly is a remarkable feat of stereochemistry and thermodynamics¹. The result is a mixture of infectious viruses and many non-viable particles.

Influenza viruses enter host respiratory epithelial cells and uncoat allowing the genomic RNA to migrate to the host cell nucleus for replication. Their genomes are segmented (Influenzas A and B have 8 segments), which leads to extra complexity at the reassembly stage. In the seemingly unlikely, but apparently not uncommon, event that an individual animal is infected with more than one sub-type of Influenza A, then re-assortment of the eight segments can occur, leading to a new sub-type. Again, most of the outcomes of such an event will not be capable of infecting other cells (due to insufficient or incorrect configuration of segments), but occasionally a new pathogen can emerge.

A shuffle of the pack This is because the sub-types of Influenza A are categorised by their surface glycoproteins haemagglutinin (H) and neuraminidase (N) and the genes for these proteins are on different segments (4 and 6 respectively). So, a newly formed and viable particle which has segment 4 from one sub-type and segment 6 from another, is a novel subtype. This is called ‘antigenic shift’.

Since eukaryotic host cells do not have mechanisms to detect and correct mistakes in RNA transcription, errors can be introduced into the genome of RNA viruses. Most mutations lead to changes which are detrimental to the virus, but sometimes a slightly different, but fully functional strain will emerge. This gradual variation is regularly observed in both Influenza A and B and is known as ‘antigenic drift’. A further level of variability is introduced when a re-assortment event occurs between two different strains of the same sub-type of Influenza A. Detailed sequence analysis of the Influenza A H1N1 virus, which caused the pandemic of 2009/10, suggests that it appears to have arisen through multiple instances of mixing genome segments. It contained elements of an H3N2 strain known to have been circulating in pigs in North America, H1N1 ­– considered to be ‘classical’ swine influenza – and another variant of H1N1 which was also a pig virus, but which contained features of an avian influenza A².

Viral ID Our global, interconnected 24/7 world facilitates transmission of viruses via contaminated inanimate objects (fomites) and inside travelling hosts. This is illustrated by how rapidly the 2009/10 Swine ‘flu spread around the world. Since the ‘season’ for influenza is winter, the highest incidence of ‘flu between April and October is in the Southern hemisphere.

Laboratory scientists are constantly isolating and characterising influenza viruses. Diagnostic tests are important to determine whether a patient presenting with ‘flu-like’ symptoms is actually infected with influenza, another common respiratory virus or a tropical disease such as Dengue fever or malaria. Point of care tests are widely used in routine microbiology laboratories. These are often lateral flow immunochromatographic assays which are intended to identify antigens from the pathogen in a patient’s sample using an immunological detection system.

Bench top PCR systems are also becoming more widely used³. Some, but not all, of the commercially available point of care kits can distinguish between Influenza A and B in respiratory specimens. Diagnostic virology laboratories use a respiratory virus multiplex PCR panel, which would give a more precise identification. For epidemiological purposes, sequencing of influenza viruses is also important. Hospital laboratories can do this themselves or they can send specimens to the Public Health England Respiratory Viruses Unit in Colindale, North London. Here the data is collated and reported nationally for the United Kingdom.

This department is also the World Health Organisation (WHO) European Region coordinating centre for influenza so specimens and sequence results from across Europe are also processed and outcomes are reported for the WHO and the European Centre for Disease Prevention and Control (ECDC). Information about which influenza strains are circulating and how they are changing is important in controlling transmission. It takes 6 months to develop the seasonal influenza vaccine and so it is based in the types and strains of influenza which had been circulating during the previous winter.

Latest threat In Europe, the prevailing viruses in 2016/17 were strains of Influenza A H1N1, Influenza A H3N2 and Influenza B. The H1N1 isolates are all shown to be variants of the pdm09 virus, which was responsible for the pandemic. This shows that after emerging, a viable new subtype can become established in the host population. The Influenza B viruses which have been sequenced are predominantly in the Yamagata classification (named after the city in Japan); a small proportion are Influenza B/Victoria which indicates an Australian origin.

Most outcomes of re-assortment will not be capable of infecting other cells but occasionally a new pathogen can emerge

Antigens designed to elicit protection against each of these types of influenza have been included in the vaccine being offered for winter 2017/18. However, the circulating strains have all been modified in the intervening 6 months. The H3N2 in particular seems to have undergone antigenic drift and possibly within-subtype re-assortment during 2017. In Australia, there were around 94,000 laboratory confirmed cases of influenza infection in 2017, which includes 1,400 people admitted to hospital and 52 deaths.

All of these figures are more than double those recorded for 2016. The most commonly identified virus type was Influenza A H3N2 and this was also associated with the most serious clinical outcomes. European laboratory scientists, doctors and healthcare managers have therefore been expecting problems with H3N2 this winter. There have been more cases of influenza reported than last year, particularly in the UK , Spain and Portugal. People do seem to be more susceptible to serious disease if infected with H3N2, especially those who are elderly or immunocompromised.

However, it interesting to note that characterisation of isolates shows that the most prevalent type of influenza virus in Europe this winter is Influenza B⁴.

 

References

1. Perlmutter, J.D. and Hagan, M.F., 2015. Mechanisms of virus assembly. Annual review of physical chemistry, 66.
2. Girard, M.P., Tam, J.S., Assossou, O.M. and Kieny, M.P., 2010. The 2009 A (H1N1) influenza virus pandemic: A review. Vaccine, 28(31), pp.4895-4902.
3. Kozel, T.R. and Burnham-Marusich, A.R., 2017. Point of Care Testing for Infectious Diseases--Past, Present and Future. Journal of Clinical Microbiology, pp.JCM-00476.
4. https://ecdc.europa.eu/en/seasonal-influenza

 

Dr Sarah Pitt is a Health and Care Professions Council (HCPC) registrant Biomedical Scientist and Fellow of the Institute of Biomedical Science (IBMS). She lectures at the University of Brighton in microbiology, with a particular expertise in clinical virology and parasitology