Genome-scale molecular and phylogenetic characterization of Middle Point orbiviruses from Australia.

Middle Point orbivirus (MPOV) is an Australian arbovirus, belongs to the Yunnan orbivirus species found in China. First detected and reported from Beatrice Hill, Northern Territory (NT), MPOV has to date, only been exclusively reported from the NT, Australia. Whilst genetic characterization of MPOV has been previously described, only restricted to sequence information for segments 2 and 3 coding core protein VP2 and outer capsid protein VP3, respectively. This study presents for the first time nearly full-length genome sequences of MPOV, which represent 24 isolates collected over a span of more than 20 years from 1997 to 2018. Whilst the majority of isolates were sampled at Beatrice Hill, NT where MPOV is most frequently isolated, this report also describes the first two isolations of MPOV from Queensland (QLD), Australia. One of which is the first non-bovine isolate obtained from the mosquito vector Aedes vittiger. We further compared these MPOV sequences with known sequences of the Yunnan orbivirus and other known orbivirus sequences of mosquito origin found in Australia. The phylogenetic analyses indicate the Australian MPOV sequences are more closely related to each other than other known sequences of Yunnan orbivirus. Furthermore, MPOV sequences are closely related to sequences from the Indonesian isolate JKT-8650. The clustering of Australian sequences in the phylogenetic tree suggests the monophyletic lineage of MPOV circulating in Australia. Further, ongoing surveillance is required to assess the existence and prevalence of this or other yet undetected lineages of MPOV and other orbiviruses in Australia.

Pigeon adenovirus and pigeon torque teno virus associated with acute multifocal hepatic necrosis in pigeons in Queensland, Australia.

In 2018, an outbreak resulting in deaths of 28 breeding pigeons was reported north of Brisbane, Australia. The affected birds had runny nasal discharge and poor body condition. Two birds were submitted to Biosecurity Sciences Laboratory, Brisbane, for investigation. A range of diagnostic tests excluded a number of known pathogens, and no virus was isolated in cell culture. Histopathological examination revealed severe acute multifocal necrosis in the liver with eosinophilic intranuclear inclusions in hepatocytes and Kupffer cells. High-throughput sequencing (HTS) revealed full-length sequences for pigeon adenovirus 1 (PiAd-A) and pigeon torque teno virus (PTTV). This report indicates concomitant PiAd-1and PTTV infections in Australian pigeons.

The genome of the fire ant Solenopsis invicta.

Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant Solenopsis invicta, are also major pests. Here, we present a draft genome of S. invicta, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothers. We used comparative genomic methods to obtain insight into the unique features of the S. invicta genome. For example, we found that this genome harbors four adjacent copies of vitellogenin. A phylogenetic analysis revealed that an ancestral vitellogenin gene first underwent a duplication that was followed by possibly independent duplications of each of the daughter vitellogenins. The vitellogenin genes have undergone subfunctionalization with queen- and worker-specific expression, possibly reflecting differential selection acting on the queen and worker castes. Additionally, we identified more than 400 putative olfactory receptors of which at least 297 are intact. This represents the largest repertoire reported so far in insects. S. invicta also harbors an expansion of a specific family of lipid-processing genes, two putative orthologs to the transformer/feminizer sex differentiation gene, a functional DNA methylation system, and a single putative telomerase ortholog. EST data indicate that this S. invicta telomerase ortholog has at least four spliceforms that differ in their use of two sets of mutually exclusive exons. Some of these and other unique aspects of the fire ant genome are likely linked to the complex social behavior of this species.

Identification of a canine coronavirus in Australian racing Greyhounds.

Coronavirus infection can cause a range of syndromes, which in dogs can include mild-to-severe enteritis that generally resolves rapidly. Fatalities can occur from coinfection with other pathogens, including canine parvovirus. Between late December 2019 and April 2020, canine coronavirus (CCoV) was detected in Australian racing Greyhounds that displayed signs of gastrointestinal disease. The CCoV was genotyped using high-throughput sequencing, recovering 98.3% of a type IIb CCoV, generally thought to cause a mild but highly contagious enteric disease. The Australian CCoV was almost identical (99.9%, whole-genome sequence) to another CCoV associated with an outbreak of severe vomiting in dogs in the United Kingdom at the same time (December 2019-March 2020).

A cohort study of duplicate faecal immunochemical testing in patients at risk of colorectal cancer from North-West England.

OBJECTIVES: We sought to investigate if duplicate faecal immunochemical testing (FIT) sampling improves the negative and positive predictive value of patients thought to be at risk of colorectal cancer (CRC). Specifically, we aimed to investigate whether the proportion of FIT-negative CRC missed by a single FIT test in symptomatic patients could be reduced by duplicate FIT testing. DESIGN: A retrospective service evaluation cohort study of the diagnostic accuracy of duplicate FIT testing. SETTING: Patients referred from primary care with suspected CRC to four secondary care trusts in North-West England. PARTICIPANTS: 28 622 patients over 18-years-old with lower gastrointestinal symptoms suggestive of CRC who completed two FIT samples. PRIMARY AND SECONDARY OUTCOME MEASURES: The performance of duplicate FIT for detecting CRC at a threshold of 10 µgHb/g. RESULTS: The sensitivity if either test was >10 µgHb/g was 0.978 (0.955-0.989), specificity was 0.662 (0.657-0.668), positive predictive value 0.031 (0.028-0.035) and negative predictive value 1.00 (0.999-1.00). Despite two-thirds of patients (18952) being negative following two tests, at this threshold only seven CRC were missed over a 26-month period. All seven patients had other high-risk features which should have prompted investigation. CONCLUSIONS: This study suggests that in routine NHS practice, a duplicate FIT sample strategy together with clinical evaluation for evidence of anaemia and weight loss is superior to a single FIT sample alone and would allow symptomatic patients to be managed in primary care without the need for urgent referral to secondary care for urgent colonic imaging.

Comparison of four high-throughput, automated immunoassays for the detection of SARS-CoV-2 antibodies.

BACKGROUND: A number of immunoassays have been developed to measure antibodies specific to SARS-CoV-2. More data is required on their comparability, particularly among those with milder infections and in the general practice population. The aim of this study was to compare four high-throughput automated anti-SARS-CoV-2 assays using samples collected from hospitalized patients and healthcare workers with confirmed SARS-CoV-2 infection. In addition, we collected general practice samples to compare antibody results and determine seroprevalence. METHODS: Samples were collected from 57 hospitalized patients and nine healthcare workers at 14 days and at 28 days following confirmed SARS-CoV-2 infection. Samples were also collected from 225 patients presenting to general practice. Four assays were used: Abbott Architect IgG, Beckman Coulter DxI 800 IgG, Roche Cobas e801 total antibody and Siemens Advia Centaur XPT total antibody. RESULTS: All four assays showed concordance at 14 days in 83.9% of hospitalized patients and in 66.7% of healthcare workers. All four assays showed concordance at 28 days in 88.4% of hospitalized patients and 77.8% of healthcare workers. The sensitivity to detect recent infection was higher for the IgG assays than the total assays. All four assays showed concordance of 95.1% in the general practice population. Seroprevalence ranged from 4.9 to 5.8% depending on the assay used. CONCLUSIONS: All four assays showed excellent comparability, but it may be possible to obtain a negative result for any of the anti-SARS-CoV-2 assays in patients with confirmed previous SARS-CoV-2 infection. An equivocal range would be useful for all anti-SARS-CoV-2 assays.

An unprecedented cluster of Australian bat lyssavirus in Pteropus conspicillatus indicates pre-flight flying fox pups are at risk of mass infection.

In November 2017, two groups of P. conspicillatus pups from separate locations in Far North Queensland presented with neurological signs consistent with Australian bat lyssavirus (ABLV) infection. These pups (n = 11) died over an 11-day period and were submitted to a government laboratory for testing where ABLV infection was confirmed. Over the next several weeks, additional ABLV cases in flying foxes in Queensland were also detected. Brain tissue from ABLV-infected flying foxes during this period, as well as archived brain tissue, was selected for next-generation sequencing. Phylogenetic analysis suggests that the two groups of pups were each infected from single sources. They were likely exposed while in crèche at night as their dams foraged. This study identifies crèche-age pups at a potentially heightened risk for mass ABLV infection.

Confirmation of Elsey virus infection in a Queensland horse with mild neurologic signs.

In 2011, a 2-year-old horse in northern Queensland, Australia, was reported to have developed mild neurologic signs, and a blood sample was submitted for laboratory investigation. Virus isolation was performed using the blood sample, and an orbivirus was isolated. This was confirmed to be a strain of Elsey virus (ELSV) after transmission electron microscopy and nucleotide sequencing. The nucleotide sequence was compared with those in GenBank, and had 100% identity with ELSV previously reported from the Northern Territory, Australia. ELSV is taxonomically closely related to Peruvian horse sickness virus.

Pyogranuloma caused by Mycobacterium asiaticum infection in a steer.

In 2003, a steer carcass was condemned at a Central Queensland abattoir because of metastatic tumors. In addition, a granulomatous lesion was found in the mediastinal lymph node. Histological examination showed this to be a pyogranuloma, typically associated with Rhodococcus or the Nocardia/Streptomyces group. However, in this case, the only etiological agent was an acid-fast bacillus, which would normally be associated with a more fibrous lesion. A number of nucleic acid-based techniques were used, and the isolate was identified as Mycobacterium asiaticum. This organism is a rarely encountered opportunistic pathogen of humans, associated with subtropical climates. This is the first report of this organism causing infection in cattle. The similarities between this case and cases of human disease are discussed.

Experimental bacteriophage-mediated virulence in strains of Vibrio harveyi.

Vibriosis is a major disease problem in prawn aquaculture. Until now there has been no clear explanation why some strains of Vibrio are pathogenic, while others are not. This study demonstrated that the presence of the bacteriophage V. harveyi myovirus like (VHML) may confer virulence to V. harveyi Strain 642. This was demonstrated by infecting naïve avirulent V. harveyi Strains 12, 20, 45 and 645 with the bacteriophage and converting them into virulent strains. The previously naïve strains of Vibrio infected with Bacteriophage VHML from V. harveyi Strain 642 demonstrated up-regulation of haemolysin, up-regulation of protein excretion, additional proteins which were recognised as toxic proteins from Strain 642 by monoclonal antibodies specific to the exotoxin sub-units, and a significant increase in mortality of larval Penaeus monodon. It was concluded that Bacteriophage VHML conferred virulence to V. harveyi Strains 12, 20, 45 and 645 and that Bacteriophage VHML either fully or partly confers virulence in V. harveyi Strain 642.

Variable-number tandem repeats genotyping used to aid and inform management strategies for a bovine Johne's disease incursion in tropical and subtropical Australia.

The application of variable-number tandem repeats (VNTR) genotyping of Mycobacterium avium subsp. paratuberculosis isolates to assist in investigating incidents of bovine Johne's disease in a low-prevalence region of Australia is described in the current study. Isolates from a response to detection of bovine Johne's disease in Queensland were compared with strains from national and international sources. The tandem application of mycobacterial interspersed repetitive unit (MIRU) and multilocus short sequence repeats (MLSSR) genotyping identified 2 strains, 1 that infected cattle on multiple properties with trace-forward histories from a common infected property, and 1 genotypically different strain recovered from a single property. The former strain showed an identical genotype to an isolate from India. Neither strain showed a genotypic link to regions of Australia with a higher prevalence of the disease. Genotyping has indicated incursions from 2 independent sources. This intelligence has informed investigations into potential routes of entry and the soundness of ongoing control measures, and supported strategy and policy decisions regarding management of Mycobacterium avium subsp. paratuberculosis incursions for Queensland.

Confirmed case of encephalitis caused by Murray Valley encephalitis virus infection in a horse.

A 5-year-old Australian stock horse in Monto, Queensland, Australia, developed neurological signs and was euthanized after a 6-day course of illness. Histological examination of the brain and spinal cord revealed moderate to severe subacute, nonsuppurative encephalomyelitis. Sections of spinal cord stained positively in immunohistochemistry with a flavivirus-specific monoclonal antibody. Reverse transcription polymerase chain reaction assay targeting the envelope gene of flavivirus yielded positive results from brain, spinal cord, cerebrospinal fluid, and facial nerve. A flavivirus was isolated from the cerebrum and spinal cord. Nucleotide sequences obtained from amplicons from both tissues and virus isolated in cell culture were compared with those in GenBank and had 96-98% identity with Murray Valley encephalitis virus. The partial envelope gene sequence of the viral isolate clustered into genotype 1 and was most closely related to a previous Queensland isolate.

Global invasion history of the fire ant Solenopsis invicta.

The fire ant Solenopsis invicta is a significant pest that was inadvertently introduced into the southern United States almost a century ago and more recently into California and other regions of the world. An assessment of genetic variation at a diverse set of molecular markers in 2144 fire ant colonies from 75 geographic sites worldwide revealed that at least nine separate introductions of S. invicta have occurred into newly invaded areas and that the main southern U.S. population is probably the source of all but one of these introductions. The sole exception involves a putative serial invasion from the southern United States to California to Taiwan. These results illustrate in stark fashion a severe negative consequence of an increasingly massive and interconnected global trade and travel system.