To determine the epidemiology of outbreaks of avian influenza A virus (subtypes H5N1, H9N2) in chickens in Bangladesh, we conducted surveys and examined virus isolates. The outbreak began in backyard chickens. Probable sources of infection included egg trays and vehicles from local live bird markets and larger live bird markets.

To evaluate risk factors for infection with highly pathogenic avian influenza A virus (H5N1) in backyard chickens in Bangladesh, we conducted a matched case–control study. We enrolled 25 case farms (cases March–November 2007) and 75 control farms (June–November 2007). We used a questionnaire to collect farm data, which were analyzed by matched-pair analysis and multivariate conditional logistic regression. Factors independently associated were offering slaughter remnants of purchased chickens to backyard chickens (odds ratio [OR] 13.29, 95% confidence interval [CI] 1.34–131.98, p = 0.027), having a nearby water body (OR 5.27, 95% CI 1.24–22.34, p = 0.024), and having contact with pigeons (OR 4.47, 95% CI 1.14–17.50, p = 0.032). Separating chickens and ducks at night was protective (OR 0.06, 95% CI 0.01–0.45, p = 0.006). Reducing these risks and taking protective measures might reduce the risk for influenza (H5N1) infection in backyard chickens.

Eucalyptus pauciflora (the snow gum) is a long-lived tree with high economic and ecological importance. Currently, little genomic information for E. pauciflora is available. Here, we sequentially assemble the genome of Eucalyptus pauciflora with different methods, and combine multiple existing and novel approaches to help to select the best genome assembly. We generated high coverage of long- (Nanopore, 174×) and short- (Illumina, 228×) read data from a single E. pauciflora individual and compared assemblies from 5 assemblers (Canu, SMARTdenovo, Flye, Marvel, and MaSuRCA) with different read lengths (1 and 35 kb minimum read length). A key component of our approach is to keep a randomly selected collection of ∼10% of both long and short reads separated from the assemblies to use as a validation set for assessing assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in 8 ways: contig N50, BUSCO scores, LAI (long terminal repeat assembly index) scores, assembly ploidy, base-level error rate, CGAL (computing genome assembly likelihoods) scores, structural variation, and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ∼0.006 errors per base. We report a draft genome of E. pauciflora, which will be a valuable resource for further genomic studies of eucalypts. The approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies from a single dataset.

Over the last few years, continuous development of high-throughput sequencing platforms and sequence analysis tools has facilitated reliable identification and characterization of genetic variants in many cattle breeds. Deep sequencing of entire genomes within a cattle breed that has not been thoroughly investigated would be imagined to discover functional variants that are underlying phenotypic differences. Here, we sequenced to a high coverage the Danish Holstein cattle breed to detect and characterize single nucleotide polymorphisms (SNPs), insertion/deletions (Indels), and loss-of-function (LoF) variants in protein-coding genes in order to provide a comprehensive resource for subsequent detection of causal variants for recessive traits. We sequenced four genetically unrelated Danish Holstein cows with a mean coverage of 27X using an Illumina Hiseq 2000. Multi-sample SNP calling identified 10,796,794 SNPs and 1,295,036 indels whereof 482,835 (4.5 %) SNPs and 231,359 (17.9 %) indels were novel. A comparison between sequencing-derived SNPs and genotyping from the BovineHD BeadChip revealed a concordance rate of 99.6–99.8 % for homozygous SNPs and 93.3–96.5 % for heterozygous SNPs. Annotation of the SNPs discovered 74,886 SNPs and 1937 indels affecting coding sequences with 2145 being LoF mutations. The frequency of LoF variants differed greatly across the genome, a hot spot with a strikingly high density was observed in a 6 Mb region on BTA18. LoF affected genes were enriched for functional categories related to olfactory reception and underrepresented for genes related to key cellular constituents and cellular and biological process regulation. Filtering using sequence derived genotype data for 288 Holstein animals from the 1000 bull genomes project removing variants containing homozygous individuals retained 345 of the LoF variants as putatively deleterious. A substantial number of the putative deleterious LoF variants had a minor allele frequency >0.05 in the 1000 bull genomes data set. Deep sequencing of Danish Holstein genomes enabled us to identify 12.1 million variants. An investigation into LoF variants discovered a set of variants predicted to disrupt protein-coding genes. This catalog of variants will be a resource for future studies to understand variation underlying important phenotypes, particularly recessively inherited lethal phenotypes.

A matched case‐control study was carried out to identify risk factors for highly pathogenic avian influenza A virus (subtype H5N1) infection in commercial chickens in Bangladesh. A total of 33 commercial farms diagnosed with H5N1 before September 9, 2007, were enrolled as cases, and 99 geographically matched unaffected farms were enrolled as control farms. Farm data were collected using a pretested questionnaire, and analysed by matched‐pair analysis and multivariate conditional logistic regression. Two factors independently and positively associated with H5N1 infection remained in the final model. They were ‘farm accessible to feral and wild animals’ (odds ratio [OR] 5.71, 95 per cent confidence interval [CI] 1.81 to 18.0, P=0.003) and ‘footbath at entry to farm/shed’ (OR 4.93, 95 per cent CI 1.61 to 15.1, P=0.005). The use of a designated vehicle for sending eggs to a vendor or market appeared to be a protective factor (OR 0.14, 95 per cent CI 0.02 to 0.88, P=0.036).

Siadenoviruses have been detected in wild and captive birds worldwide. Only nine siadenoviruses have been fully sequenced; however, partial sequences for 30 others, many of these from wild Australian birds, are also described. Some siadenoviruses, e.g., the turkey siadenovirus A, can cause disease; however, most cause subclinical infections. An example of a siadenovirus causing predominately subclinical infections is psittacine siadenovirus 2, proposed name psittacine siadenovirus F (PsSiAdV-F), which is enzootic in the captive breeding population of the critically endangered orange-bellied parrot (OBP, Neophema chrysogaster). Here, we have fully characterised PsSiAdV-F from an OBP. The PsSiAdV-F genome is 25,392 bp in length and contained 25 putative genes. The genome architecture of PsSiAdV-F exhibited characteristics similar to members within the genus Siadenovirus; however, the novel PsSiAdV-F genome was highly divergent, showing highest and lowest sequence similarity to skua siadenovirus A (57.1%) and psittacine siadenovirus D (31.1%), respectively. Subsequent phylogenetic analyses of the novel PsSiAdV-F genome positioned the virus into a phylogenetically distinct sub-clade with all other siadenoviruses and did not show any obvious close evolutionary relationship. Importantly, the resulted tress continually demonstrated that novel PsSiAdV-F evolved prior to all known members except the frog siadenovirus A in the evolution and possibly the ancestor of the avian siadenoviruses. To date, PsSiAdV-F has not been detected in wild parrots, so further studies screening PsSiAdV-F in wild Australian parrots and generating whole genome sequences of siadenoviruses of Australian native passerine species is recommended to fill the siadenovirus evolutionary gaps.