Thesis (M. Phil.)--University of Hong Kong, 2010. / Includes bibliographical references (leaves 61-64). Also available in print.

Universiẗat, Diss., 2002--Würzburg.

Thesis (M. Phil.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

Thesis (M. Phil.)--University of Hong Kong, 2006. / Also available online.

Thesis (Ph. D.)--University of Hong Kong, 2010. / Includes bibliographical references (p. 212-238). Also available online.

Thesis (M. Med. Sc.)--University of Hong Kong, 2006.

Techn. Hochsch., Diss., 2002--Aachen.

Cap-snatching by the influenza A virus (IAV) RNA-dependant RNA polymerase (RdRp) is driven by the abundance of transcripts being actively transcribed by host RNA polymerase II (Pol II)[1]–[3]. Deviations from a direct correlation with abundance do arise, due to selective cleavage of transcripts with a compatible length (10 to 13 nucleotides) and nucleotide sequence (ending in 3’AG)[4]–[7]. Some cap-snatched primers are not directly used to transcribe mRNA, but instead undergo a prime-and-realign mechanism (PAR). As of yet it is unknown why this process occurs. My hypothesis is that the prime-and-realign process is related to the physical characteristics of the primers and their interactions with RdRp and the vRNA template. Here, I used four published deep sequencing datasets of the 5’ ends of IAV mRNA obtained from IAV infected A549 cells to examine PAR[1], [7]–[9]. Primers are biased towards PAR on the basis of length (<12 nucleotides) and RNA duplex stability (mediated by the base directed at 3’U1 and the pyrimidine-purine base pair at position four). PAR typically adds a GCA addition resulting in a primer three nucleotides longer ending in a compatible nucleotide sequence with 3’U1. Prime-and-realign converts poor primers on the basis of length and sequence compatibility with the 3’ end of the vRNA into one that can efficiently undergo transcription of the critical conserved sequence without errors, or failure. Prime-and-realign, therefore, affords tremendous flexibility to RdRp in cap snatched primer length and sequence compatibility.

No description available.

The genetic requirements for Influenza virus to infect and adapt to new species is largely unknown. To understand the evolutionary steps required by a virus to become virulent, a human virus (A/HK/1/68) (HK), avirulent in mice, was subjected to 20 and 21 serial lung-to-lung passages in mouse. Sequence analysis revealed the emergence of eleven mutations within the NS1 gene of the new virulent strains, many of which occurred in binding sites for transcriptional and translational cellular factors. In the present study we have rescued viruses containing each of the NS1 mouse adapted mutations onto A/PR/8/34 (PR8) backbone. We found 9 of 16 NS1 mutants were adaptive by inducing mortality, body weight loss in BALB/c mice and enhanced virus replication in MDCK cells with properties of host cell interferon transcription inhibition. Sequence comparisons with the highly pathogenic A/Hong Kong/156/1997 (H5N1) and the most severe pandemic A/Brevig Mission/1/1918 (H1N1) NS1 genes showed convergent evolution with some of the mouse adapted viruses for F103L plus M106I and V226I plus R227K mutations respectively. The F103L and M106I mutations in the HK NS1 gene were shown to be adaptive by assessment with respect to replication, early viral protein synthesis, interferon-β antagonism and tropism in the mouse lung. We extended the study and proved increased virulence associated with F103L+M106I mutations in their respective H5N1 NS1 gene on the PR8 and HK backbones, as well as the PR8 NS1 gene and the H9N2 (A/Ck/Bj/1/95) gene in the PR8 and A/WSN/33 backbones respectively. However the V226I and R227K mutations in their respective HK and 1918 NS1 genes slightly enhanced virulence and viral growth at later stages of infection. This study demonstrates that NS1 is a virulence factor; involved in multiple viral processes including interferon antagonism and viral protein synthesis. Furthermore, NS1 mutations acquired during mouse adaptation are proven to be adaptive in human, mouse and avian NS1 genes.