**1. Introduction**

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212 Current Issues in Molecular Virology - Viral Genetics and Biotechnological Applications

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The Age of Enlightenment is the period in time when the method of reasoning known as the Scientific Method was developed. This revolution in science began with the description of the sun as the center of our solar system rather than the earth. Natural phenomena previously explained by spiritualists were now described by science. Given our still evolving under‐ standing of influenza, it is perhaps no coincidence that we describe the combined effects of the influenza virus gene segments with the word 'constellation', which has astrological roots describing the position of the stars. Interestingly, the name influenza also has astrological roots: it was borrowed from the Italian word *influenza* in the mid-17th century which, in turn, was derived from the Medieval Latin word *influentia*, a 14th century term that refers to the influence of the stars. The scientific rational to describe the influence of the influenza gene constellation on virus phenotype is currently being resolved. Here we try to shine some light on the subject by providing the reader with background information, recent experimental results and provide a framework for questions that remain unanswered.

Influenza is a common infectious respiratory disease caused by influenza viruses. The host range of these viruses can include birds, humans and other mammals. Influenza viruses cause seasonal epidemics and are almost globally ubiquitous. They cause significant morbidity and mortality each year yet some infected persons remain asymptomatic. Influenza is typically transmitted by aerosols produced by coughing or sneezing. Although virus particles on contaminated surfaces can be easily inactivated, the virus is still able to spread easily and rapidly. Vaccination is the recommended approach to prevent disease because of the possible emergence of drug resistance.

Vaccines are produced each year to counter the currently circulating seasonal strains. The influenza vaccine seed viruses used to produce the immunogenic proteins are reassortant viruses. That is, they contain a mix of gene segments from different viruses. The genomes of

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the influenza A and B viruses are made up of eight negative-strand RNA segments. The haemagglutinin (HA) and neuraminidase (NA) proteins found on the surface of the virus are found on two different segments. Usually these two segments from a seasonal virus are combined with another six gene segments from a high yield strain to make a vaccine seed virus. HA is the major immunogenic protein recognized by the host immune system. Because of influenza's high rate of mutation, and the capacity of the genome to tolerate many mutations, there is a need to update the influenza vaccine seed virus strains each year. The influenza virus is able to avoid control by the host immune system via two major types of mutation. Antigenic drift is the process of gradual genetic mutation, especially in the HA gene, that results in newer viruses not being well recognized by antibodies that recognized the progenitor virus. Anti‐ genic shift is the replacement of one or more segments from one influenza virus with those of another. This unpredictable event can lead to a change in host range, transmission or patho‐ genicity. Likewise, genetic reassortment, the mixing of genomic segments from different strains, can generate undesirable characteristics in the influenza vaccine seed viruses. Here we explore possible reasons for this and describe approaches that might be beneficial to the development of influenza vaccine seed viruses.

that one of each segment is packaged into one virion. However, it also helps alleviate a problem faced by many RNA viruses, the high error rate inherent in RNA synthesis. The error rate for the influenza viruses has be calculated to be 2.0 x 10-6 and 0.6 x 10-6 mutations per site per infectious cycle for influenza A and B respectively [5]. Rates ranging from 3.72 to 6.77 x 10-4 substitutions per site per year have been calculated for the influenza C segments [6]. Influen‐ za viruses can exist as a quasispecies, that is, a group of diverse viruses that collectively contribute to the characteristics of the population (reviewed in [7]). This enables mutations to exist that, by themselves, may not increase the fitness of the virus and could even be detrimen‐ tal. A combination of these mutations, that together increase the fitness of the virus, may result in a virus with some selective advantage. Such a combination could occur by gene reassort‐ ment. The separation of different mutations on different virus segments facilitates this proc‐

PB2 (2348 nt)

C D

A B

PB1 (2319 nt)

PA (2269 nt)

HA (1833 nt)

NP (1806 nt)

M1 BM2 (1149 nt)

**Figure 1.** Genomes of influenza viruses. A) The ends of the negative strand influenza genomic RNA are complexed with the three polymerase proteins and the remaining sequence is encapsidated with nucleoprotein (vRNP (-)). The positive strand cRNP is similarly complexed. The mRNA is transcribed with a 5' cap structure and poly-A tail (see main text for details). Figure used with permission from Resa-Infante et al., 2011. B) Schematic of the influenza A virus ge‐ nome. The bold black lines represent the 3' and 5' untranslated regions. The blue and pink boxes represent the major protein coding regions. C) Schematic of the influenza B virus genome. The green and brown boxes represent the ma‐ jor protein coding regions. D) Schematic of the influenza C virus genome. The red and purple boxes represent the ma‐ jor protein coding regions. The protein coding regions are not to scale. Coding regions in a different reading frame are

shown above or below each other, coding regions in the same frame are show as contiguous blocks.

(1055 nt) NS1

(1513 nt) NB

NS2

NA

PB2 (2365 nt) PB1 (2363 nt) P3 (2183 nt)

(2363

(863 nt) NS1

PB2 (2280 nt)

(2274 nt) PB1 (& PB1-N40)

Gene Constellation of Influenza Vaccine Seed Viruses

http://dx.doi.org/10.5772/55289

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HA (1701 nt)

2152 nt) PA

NP (1497 nt) NA (1410 nt) (982 nt) M1 M2

(2365 (2280 (1701 (1497 (1410

NP (1802 nt) M1 CM2 (1180 nt)

(935 nt) NS1

NS2

NS2

PB1-F2

PA-X

HEF (2073 nt)
