Approximately 150 Nucleotides from the 5′ End of an Influenza A Segment 1 Defective Virion RNA Are Needed for Genome Stability during Passage of Defective Virus in Infected Cells

AbstractDefective influenza A virus RNAs analyzed in two studies so far possess at least 80–90 nucleotides from the 5′ end of the virion RNA segment and more typically around 200 nucleotides, whereas the 3′ sequence could be as short as 25 nucleotides (P. A. Jennings et al., Cell 34, 619–627; 1983; S. D. Duhaut and N. J. Dimmock, Virology 247, 241–253, 1998). To determine the biological significance of the highly conserved 5′ sequence, we constructed plasmids that expressed a naturally occurring defective segment 1 RNA from A/equine/Newmarket/7339/79 (EQV, H3N8) or modified RNAs with lesser amounts of the 5′ end. These had terminal 5′ sequences of 220 nucleotides (POLI-220), 150 nucleotides (POLI-150), 80 nucleotides (POLI-80), and 30 nucleotides (POLI-30). Their remaining sequence came from the 3′ end of virion RNA, and all were exactly 445 nucleotides in length. After transfection with one of the RNA-expressing POLI plasmids and plasmids encoding PB1, PB2, PA, and NP proteins, Vero cells were infected with a helper influenza virus of one of three different subtypes (the parental H3N8, an H2N2, or an H1N1 virus). Progeny infectious and presumptive progeny defective virus in the resulting tissue culture fluids were then passaged serially to new cultures up to 10 times. We found that POLI-220 and POLI-150 RNAs proved stable on passage and POLI-80 RNA was detected intermittently, while POLI-30 was not detected beyond passage three. Data were essentially reproducible with the three helper viruses and in two cell lines. It thus appears that the terminal 5′ 150 nucleotides are necessary for influenza virion RNA molecules to be replicated and packaged consistently in cell culture. The possible functional significance of the 5′ sequence is discussed