AbstractsAstronomy & Space Science

A highly conserved RNA-motif, called stem-loop-2-motif (s2m), has been identified in the 3' end of the genomes of viruses belonging to different RNA virus families which infect a broad range of animal species. Currently, s2m has been found in 4 different virus families: Astroviridae, Picornaviridae, Coronaviridae and Caliciviridae. These viruses are all positive-sense single-stranded RNA viruses with a poly(A) tail in the 3' end of their genome. Because RNA viruses generally have a very high mutation rate, the extreme conservation of the primary, the secondary and the tertiary structure in this motif indicate that s2m has a very important function in the virus harbouring it. S2m is probably an element that can be transferred between different genomes of RNA viruses by recombination. Many of the viruses belonging to the four virus families infect the intestinal tract, and astroviruses are shown to often coinfect with other enteric viruses. A relatively high frequency of recombination is observed within these virus families as well. It is therefore likely that these viruses could infect the same cell in the intestinal tract at the same time, giving s2m an opportunity to recombine. Since s2m is such an extremely conserved motif, it is an ideal target for identification of the viruses harbouring it. An RT-PCR analysis has been developed which will detect all viruses with a polyadenylated, positive-sense single-stranded RNA genome that contains s2m. The main aim of this thesis was to detect and characterize novel viruses harbouring s2m in wild birds by using this s2m-specific amplification. To further characterize novel viruses, a 5' RACE and primer walking strategy was used. 84 % and 67 % of the samples from feral pigeons and wood pigeons, respectively, were found to contain a virus harbouring s2m. Four novel viruses were identified and characterized. Two of the new viruses belong to the genus Avastrovirus in the Astroviridae family. We propose two new species to be included in this genus, Feral pigeon astrovirus and Wood pigeon astrovirus. Two other novel viruses, Pigeon picornavirus A and Pigeon picornavirus B, belong to the Picornaviridae family, presumably to the genus Sapelovirus. Both the novel picornaviruses harbour two adjacent s2m, called s4m, suggesting a possible increased functional effect of s2m when present in two copies. Picornavirus was found in 29 % of the pigeons tested, while astrovirus was found in as much as 80 %. We could not detect any correlation between any of the novel viruses and illness in the pigeons. Furthermore, the recombinational potential of the s2m motif was studied, by coinfecting Caco-2 cells with a virus that contain s2m and a virus that do not contain s2m. One possible recombinant was detected, but we were not able to verify it.