Integrating patient and whole-genome sequencing data to provide insights into the epidemiology of seasonal influenza A(H3N2) viruses.

Genetic surveillance of seasonal influenza is largely focused on sequencing of the haemagglutinin gene. Consequently, our understanding of the contribution of the remaining seven gene segments to the evolution and epidemiological dynamics of seasonal influenza is relatively limited. The increased availability of next-generation sequencing technologies allows rapid and economic whole-genome sequencing (WGS) of influenza virus. Here, 150 influenza A(H3N2) positive clinical specimens with linked epidemiological data, from the 2014/15 season in Scotland, were sequenced directly using both Sanger sequencing of the HA1 region and WGS using the Illumina MiSeq platform. Sequences generated by the two methods were highly correlated, and WGS provided on average >90 % whole genome coverage. As reported in other European countries during 2014/15, all strains belonged to genetic group 3C, with subgroup 3C.2a predominating. Multiple inter-subgroup reassortants were identified, including three 3C.3 viruses descended from a single reassortment event, which had persisted in the population. Cases of severe acute respiratory illness were significantly clustered on phylogenies of multiple gene segments indicating potential genetic factors warranting further investigation. Severe cases were also more likely to be associated with reassortant viruses and to occur later in the season. These results suggest that WGS provides an opportunity to develop our understanding of the relationship between the influenza genome and disease severity and the epidemiological consequences of within-subtype reassortment. Therefore, increased levels of WGS, linked to clinical and epidemiological data, could improve influenza surveillance.

Prevalence of HCV NS3 pre-treatment resistance associated amino acid variants within a Scottish cohort.

BACKGROUND: Protease inhibitors (PI) including boceprevir, telaprevir and simeprevir have revolutionised HCV genotype 1 treatment since their introduction. A number of pre-treatment resistance associated amino acid variants (RAVs) and polymorphisms have been associated with reduced response to treatment. OBJECTIVES: We measured the prevalence of RAVs/polymorphisms in a PI treatment-naïve HCV genotype 1 Scottish cohort using Sanger sequencing. STUDY DESIGN: Chronically infected, treatment-naïve, HCV genotype 1 patients (n = 146) attending NHS Greater Glasgow and Clyde clinics were investigated for RAVs/polymorphisms to the PIs boceprevir, telaprevir and simeprevir. The NS3/4A region was amplified by nested polymerase chain reaction. The 1.4 kb amplified product was sequenced using an ABI 3710XL DNA sequencer. Sequence analysis was performed using web-based ReCall (beta 2.10). Amino acid positions 36, 41, 43, 54, 55, 80, 109, 122, 155, 156, 168 and 170 were analysed for RAVs/polymorphisms. RESULTS: Overall, 23.29% (34/146) of patients had an RAV or polymorphism detected. Overall, 13.69% (20/146) of patients had HCV virus that contained the Q8 K polymorphism. Other RAVs detected were: V36 M 0.70% (1/146), V36L 0.70% (1/146), T54S 6.85% (10/146), V55A 3.42% (5/146) and V/I170A 0.68% (1/146). Four patients had dual combinations of mutations (T54S+V36L; T54S+V55A and 2 patients with T54S+Q80K). CONCLUSIONS: Q80K was the most prevalent baseline polymorphism detected in the Scottish cohort. Simeprevir treatment is not recommended in patients infected with the Q80K genotype 1a variant. This highlights the need for baseline sequencing prior to administration of this drug in this population.

Neurovirulent factor ICP34.5 uniquely expressed in the herpes simplex virus type 1 Delta gamma 1 34.5 mutant 1716.

The herpes simplex virus type 1 (HSV-1) diploid gene gamma(1)34.5 encodes a neurovirulent factor, infected cell protein 34.5 (ICP34.5). The promoter to gamma(1)34.5 is located within the HSV-1 genome where there are repeated sequences. This region of the genome also contains important overlapping transcripts involved with the virus's ability to establish lytic and latent infections and reactivation. These transcripts include the latency-associated transcripts and regulator proteins ICP0 and ICP4. This study aimed to separate ICP34.5 from these overlapping transcripts and test if its expression from a single gene could restore wild-type HSV-1 strain 17+ virulence. To address these aims, different recombinant viruses were constructed using the Delta gamma(1)34.5 mutant 1716. Immunoblots probed with different ICP34.5 antisera demonstrated that one of the newly generated recombinant viruses, 1622, overexpresses ICP34.5 relative to a panel of wild-type viruses. Interestingly, the overexpression of ICP34.5 does not yield a more virulent virus. The onset of ICP34.5 expression from 1622-infected cells in vitro matched that of 17+, and its expression restored the function of maintaining protein synthesis in human neuroblastoma cells. Replication of 1622, however, was only partially restored to 17+ levels in vivo. Additionally, plaque morphology from 1622-infected cells indicates there is an additional defect. The authors report that the mutant virus 1622 can express ICP34.5 from a single gamma(1)34.5 gene and restore most (but not all) wild-type function. These findings are discussed with respect to the use of the gamma(1)34.5 deleted mutant, 1716, in oncolytic viral vector therapies and future studies for ICP34.5.