Clinical importance and intra-host diversity of Torque teno sus virus (TTSuV) in swine (2018) Master thesis by Julia Lienhard

Torque teno viruses (TTV) are circular, single-stranded DNA viruses, which belong to the family Anelloviridae. The rather newly discovered virus can be found in a lot of different species, including humans, non-human primates, various farm animals and pets. The Torque teno sus virus (TTSuV) has a high prevalence in swine herds all over the world. It was first thought to be non-pathogenic, however, recent studies suggest TTSuV to be involved in the post-weaning multisystemic wasting syndrome (PMWS) and in respiratory diseases. Torque teno viruses have a high genetic diversity. In swine, the two genera Iotatorquevirus (TTSuV1) and Kappatorquevirus (TTSuVk2) can be found and some studies suggest up to 4 different species per genus.
After TTSuV1 was found in the brain of a pig with neurological signs, the brains of 100 pigs were tested by real-time PCR for TTSuV1 in a previous master thesis. Though no association of the virus with neurological signs was found in that thesis, an association with pathologic changes in the respiratory tract was found. Therefore, in this master thesis, the lungs of the same animals were screened for TTSuV1, in order to gain more information about that association. Furthermore, the spleen was also screened for TTSuV1. Due to the high genetic diversity of Torque teno viruses, it was also of interest, whether an animal could be infected with more than one strain. Therefore, samples with CT-values below 30 in all three organs were sequenced by using Sanger sequencing. The sequences within one animal were then compared to search for coinfections and mutations within the host. In 4 animals, next generation sequencing (NGS) was carried out as well and the received sequences were compared to the corresponding Sanger sequences.
In total, 100 brains, 96 lungs and 97 spleens were tested. The total viral prevalence was 57%, but it differed in the different organs. In the lung, it was highest (52%), followed by the spleen (46%) and the brain (42%). Pigs with changes in the respiratory tract had a higher prevalence (81%) and lower CT-values in the lung than pigs with a normal respiratory tract (prevalence 41%). Those results suggest an affinity of TTSuV1 to the respiratory tract and an association of the virus with respiratory diseases, though the virus is probably rather a co-factor than the primary cause. The CT-values were lowest in the spleen. This can be explained by the high number of T-lymphocytes in the spleen and T-lymphocytes being the major target cells of TTV. Furthermore, the prevalence and the viral load increased with the age of the animals. In older pigs, it was also more likely, that all three organs were infected.
The results from the phylogenetic analysis showed, that coinfections with different strains are possible. Additionally, it seems that mutations within a host can occur and quasispecies might exist. The TTSuV1 sequences obtained from NGS supported the findings from the Sanger sequencing. Furthermore, other viruses were found, which might have been involved in some of the clinical signs of the pigs. Those viruses include the porcine astrovirus, the porcine bocavirus, the porcine parvovirus, the porcine cytomegalovirus, the porcine kobuvirus, the porcine sapelovirus, the porcine teschovirus, the porcine torovirus and the porcine hemagglutinating encephalomyelitis virus.