Estimating population sensitivity and confidence of freedom from highly pathogenic avian influenza in the Victorian poultry industry using passive surveillance.

Highly pathogenic avian influenza (HPAI) is a serious disease affecting multiple organ systems and resulting in high levels of mortality in domestic poultry and may also be a serious zoonotic condition. In July-August 2020, HPAI was confirmed on 3 egg-laying chicken farms in Victoria, Australia, while a further two turkey farms and one emu farm were diagnosed with low pathogenicity viruses. All six farms were depopulated and decontaminated by 26 November 2020 and Australia declared regained freedom from HPAI on 26 February 2021. As part of the follow-up surveillance in support of claiming HPAI freedom, a scenario-tree model was developed to estimate the population sensitivity of passive surveillance for the detection of HPAI in the Victorian commercial poultry industry, and to also estimate the confidence of freedom from HPAI provided by passive surveillance, predicted over a 2-year period. Risk factors included in the model were industry sector (breeder, broiler, layer and other), flock size: small commercial (50 ≤ 5000 birds) or large commercial (> 5000 birds) and housing type (cage, barn or free-range). A detection cascade was also modelled, with probabilities allocated, to estimate the flock sensitivity for flocks in each risk stratum. System sensitivity and confidence of freedom were then estimated across all flocks in the industry. Design prevalence was set at 1, 2, 5 or 10 infected flocks and prior confidence of freedom at 0.5. Other model inputs were entered as probability distributions and the model was simulated for 10,000 iterations. Outputs were expressed as median and 95% probability intervals (PI), with the time period for analysis set at 1 month. Median system sensitivity was 0.58 (95% PI: 0.47-0.69) per time period for a single infected flock, increasing to 0.81, 0.985 and 0.9998 for 2, 5 and 10 infected flocks respectively. Median confidence of freedom was > 0.7 (95% PI: 0.65-0.76) after one time period and exceeded 0.95 and 0.99 after 4 and 7 months, respectively for one infected flock and 2 and 3 months respectively for 2 infected flocks. These results support the conclusion that passive surveillance is a highly effective tool for the detection of HPAI in commercial poultry and add further weight to evidence that HPAI has been successfully eradicated from the Victorian poultry industry and that the industry has regained HPAI free status.

Abo1, a conserved bromodomain AAA-ATPase, maintains global nucleosome occupancy and organisation.

Maintenance of the correct level and organisation of nucleosomes is crucial for genome function. Here, we uncover a role for a conserved bromodomain AAA-ATPase, Abo1, in the maintenance of nucleosome architecture in fission yeast. Cells lacking abo1(+) experience both a reduction and mis-positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re-establishment behind RNA polymerase II. Abo1 is recruited to gene sequences and associates with histone H3 and the histone chaperone FACT. Furthermore, the distribution of Abo1 on chromatin is disturbed by impaired FACT function. The role of Abo1 extends to some promoters and also to silent heterochromatin. Abo1 is recruited to pericentromeric heterochromatin independently of the HP1 ortholog, Swi6, where it enforces proper nucleosome occupancy. Consequently, loss of Abo1 alleviates silencing and causes elevated chromosome mis-segregation. We suggest that Abo1 provides a histone chaperone function that maintains nucleosome architecture genome-wide.

The impact of the HIRA histone chaperone upon global nucleosome architecture.

HIRA is an evolutionarily conserved histone chaperone that mediates replication-independent nucleosome assembly and is important for a variety of processes such as cell cycle progression, development, and senescence. Here we have used a chromatin sequencing approach to determine the genome-wide contribution of HIRA to nucleosome organization in Schizosaccharomyces pombe. Cells lacking HIRA experience a global reduction in nucleosome occupancy at gene sequences, consistent with the proposed role for HIRA in chromatin reassembly behind elongating RNA polymerase II. In addition, we find that at its target promoters, HIRA commonly maintains the full occupancy of the -1 nucleosome. HIRA does not affect global chromatin structure at replication origins or in rDNA repeats but is required for nucleosome occupancy in silent regions of the genome. Nucleosome organization associated with the heterochromatic (dg-dh) repeats located at the centromere is perturbed by loss of HIRA function and furthermore HIRA is required for normal nucleosome occupancy at Tf2 LTR retrotransposons. Overall, our data indicate that HIRA plays an important role in maintaining nucleosome architecture at both euchromatic and heterochromatic loci.

An alternative beads-on-a-string chromatin architecture in Thermococcus kodakarensis.

We have applied chromatin sequencing technology to the euryarchaeon Thermococcus kodakarensis, which is known to possess histone-like proteins. We detect positioned chromatin particles of variable sizes associated with lengths of DNA differing as multiples of 30 bp (ranging from 30 bp to >450 bp) consistent with formation from dynamic polymers of the archaeal histone dimer. T. kodakarensis chromatin particles have distinctive underlying DNA sequence suggesting a genomic particle-positioning code and are excluded from gene-regulatory DNA suggesting a functional organization. Beads-on-a-string chromatin is therefore conserved between eukaryotes and archaea but can derive from deployment of histone-fold proteins in a variety of multimeric forms.