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    Mask or no mask? This simple ethical approach can help with your pandemic etiquette
    (The Conversation Media Group Ltd, 2020-08-18) Tilley E
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    Transmission models indicate Ebola virus persistence in non-human primate populations is unlikely
    (The Royal Society, 2022-02-02) Hayman DTS; Sam John R; Rohani P
    Infectious diseases that kill their hosts may persist locally only if transmission is appropriately balanced by susceptible recruitment. Great apes die of Ebola virus disease (EVD) and have transmitted ebolaviruses to people. However, understanding the role that apes and other non-human primates play in maintaining ebolaviruses in Nature is hampered by a lack of data. Recent serological findings suggest that few non-human primates have antibodies to EVD-causing viruses throughout tropical Africa, suggesting low transmission rates and/or high EVD mortality (Ayouba A et al. 2019 J. Infect. Dis.220, 1599-1608 (doi:10.1093/infdis/jiz006); Mombo IM et al. 2020 Viruses12, 1347 (doi:10.3390/v12121347)). Here, stochastic transmission models of EVD in non-human primates assuming high case-fatality probabilities and experimentally observed or field-observed parameters did not allow viral persistence, suggesting that non-human primate populations are highly unlikely to sustain EVD-causing infection for prolonged periods. Repeated introductions led to declining population sizes, similar to field observations of apes, but not viral persistence.
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    Present and future distribution of bat hosts of sarbecoviruses: implications for conservation and public health
    (The Royal Society, 2022-05-25) Muylaert RL; Kingston T; Luo J; Vancine MH; Galli N; Carlson CJ; John RS; Rulli MC; Hayman DTS
    Global changes in response to human encroachment into natural habitats and carbon emissions are driving the biodiversity extinction crisis and increasing disease emergence risk. Host distributions are one critical component to identify areas at risk of viral spillover, and bats act as reservoirs of diverse viruses. We developed a reproducible ecological niche modelling pipeline for bat hosts of SARS-like viruses (subgenus Sarbecovirus), given that several closely related viruses have been discovered and sarbecovirus-host interactions have gained attention since SARS-CoV-2 emergence. We assessed sampling biases and modelled current distributions of bats based on climate and landscape relationships and project future scenarios for host hotspots. The most important predictors of species distributions were temperature seasonality and cave availability. We identified concentrated host hotspots in Myanmar and projected range contractions for most species by 2100. Our projections indicate hotspots will shift east in Southeast Asia in locations greater than 2°C hotter in a fossil-fuelled development future. Hotspot shifts have implications for conservation and public health, as loss of population connectivity can lead to local extinctions, and remaining hotspots may concentrate near human populations.
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    The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations
    (American Society for Microbiology, 2022-04-26) Carlson CJ; Gibb RJ; Albery GF; Brierley L; Connor RP; Dallas TA; Eskew EA; Fagre AC; Farrell MJ; Frank HK; Muylaert RL; Poisot T; Rasmussen AL; Ryan SJ; Seifert SN; Pickett BE; Jurado K
    Data that catalogue viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open sharing, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically maintained database of vertebrate-virus associations, called The Global Virome in One Network (VIRION). The VIRION database has been assembled through both reconciliation of static data sets and integration of dynamically updated databases. These data sources are all harmonized against one taxonomic backbone, including metadata on host and virus taxonomic validity and higher classification; additional metadata on sampling methodology and evidence strength are also available in a harmonized format. In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus "species" (of which 1,661 are ICTV ratified), 3,692 resolved vertebrate host species, and 23,147 unique interactions between taxonomically valid organisms. Together, these data cover roughly a quarter of mammal diversity, a 10th of bird diversity, and ∼6% of the estimated total diversity of vertebrates, and a much larger proportion of their virome than any previous database. We show how these data can be used to test hypotheses about microbiology, ecology, and evolution and make suggestions for best practices that address the unique mix of evidence that coexists in these data. IMPORTANCE Animals and their viruses are connected by a sprawling, tangled network of species interactions. Data on the host-virus network are available from several sources, which use different naming conventions and often report metadata in different levels of detail. VIRION is a new database that combines several of these existing data sources, reconciles taxonomy to a single consistent backbone, and reports metadata in a format designed by and for virologists. Researchers can use VIRION to easily answer questions like "Can any fish viruses infect humans?" or "Which bats host coronaviruses?" or to build more advanced predictive models, making it an unprecedented step toward a full inventory of the global virome.
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    The future of zoonotic risk prediction
    (The Royal Society, 2021-11-08) Carlson CJ; Farrell MJ; Grange Z; Han BA; Mollentze N; Phelan AL; Rasmussen AL; Albery GF; Bett B; Brett-Major DM; Cohen LE; Dallas T; Eskew EA; Fagre AC; Forbes KM; Gibb R; Halabi S; Hammer CC; Katz R; Kindrachuk J; Muylaert RL; Nutter FB; Ogola J; Olival KJ; Rourke M; Ryan SJ; Ross N; Seifert SN; Sironen T; Standley CJ; Taylor K; Venter M; Webala PW
    In the light of the urgency raised by the COVID-19 pandemic, global investment in wildlife virology is likely to increase, and new surveillance programmes will identify hundreds of novel viruses that might someday pose a threat to humans. To support the extensive task of laboratory characterization, scientists may increasingly rely on data-driven rubrics or machine learning models that learn from known zoonoses to identify which animal pathogens could someday pose a threat to global health. We synthesize the findings of an interdisciplinary workshop on zoonotic risk technologies to answer the following questions. What are the prerequisites, in terms of open data, equity and interdisciplinary collaboration, to the development and application of those tools? What effect could the technology have on global health? Who would control that technology, who would have access to it and who would benefit from it? Would it improve pandemic prevention? Could it create new challenges?
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    Isolation and charaterisation of adenoviruses and reoviruses of domestic hens in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University, New Zealand
    (Massey University, 1974) Green, Allan Fraser
    This investigation was undertaken to determine whether or not adenoviruses or reoviruses could be recovered from domestic hens in New Zealand. Using cultures derived from neonatal chicken kidney tissue 30 cytopathic agents were recovered from domestic hens. Electron microscope examination following staining by sodium phosphotungstate showed that 25 of these agents had the morphology of adenoviruses and the remaining 5 agents were morphologically indistinguishable from reoviruses. Some selected strains of adenoviruses and reoviruses were subjected to physico-chemical tests and it was found that both groups of agents were unaffected by chloroform and the replication of adenovirus strains, but not the reovirus, was inhibited by IDU. These results provide confirmatory evidence for the identification of these agents as avian adenoviruses and reoviruses. The avian adenoviruses like the analogous mammalian agents were found to have diminished thermostability in the presence of 1.OM Ca++. Cross-neutralisation tests showed that four serologically distinct adenovirus strains were recovered and 16 of the remaining adenovirus isolates were assigned to one or other of the four serotypes. All 5 reoviruses were assigned to one serological type on the basis of neutralisation tests. A preliminary serum survey for neutralising antibody to the 4 adenovirus serotypes showed that antibody to one or more of these viruses was present in a high proportion of flocks of domestic fowl in the Manawatu district of New Zealand and antibody to two of the serotypes was particularly common. This work represents the first report of the recovery of avian adenovirus and reovirus from domestic hens in New Zealand. However their clinical and pathological significance remain to bo investigated.
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    Epidemiology of porcine rotaviral infections : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Veterinary Virology at Massey University
    (Massey University, 1988) Fu, Zhen Fang
    The epidemiology of porcine group A rotavirus was studied in commercial herds of pigs in New Zealand. A commercial enzyme-linked immunosorbent assay (ELISA) kit (Dakopatts, Copenhagen) was found to be highly sensitive (100%) and specific (96.8%) for the detection of group A rotavirus in pig faeces when compared to electron microscopy (EM). A highly sensitive and specific ELISA test for the measurement of antibody against group A rotavirus in pigs was also developed. Of 521 faecal samples collected from Massey University Piggery in a cross-sectional survey, 47 (9%) were positive for group A rotavirus by the ELISA test. Only sucking (19.3%) and weaner (14.4%) pigs were shedding rotavirus. Rotavirus was not detected in the faeces of fattener pigs (over two months old) or adult pigs including sows and boars. Three cohort studies revealed that all pigs became infected with group A rotavirus before they were 40 days of age and shed the virus for an average of eight days. Some of the piglets shed rotavirus a second time approximately 10 days after the first period of shedding. All piglets ceased to shed the virus by two months of age. Rotaviral shedding was associated with the occurrence of milk scours in sucking piglets. Diarrhoea in weaner pigs (post-weaning diarrhoea, PWD) was more closely associated with the presence of haemolytic E.coli than with rotavirus in faeces. Infection with group A rotavirus was transmitted from piglet to piglet and from litter to litter. In one cohort of 50 piglets from five litters, shedding of rotavirus was first detected in one litter, then in the second litter two days later, and finally in other litters of piglets. Over a period of 16 days, all piglets in the five litters were infected. Group A rotavirus was also detected in dust, faeces and effluent collected from the farrowing and weaner houses, and from a weaner house which had not been used for three months. Rotavirus was not detected in any of the sows (11) during the period of investigation. Neither was rotavirus detected in fattener pigs (from two months of age to the time of slaughter), nor in the environments where old pigs (fattener and sow houses) were housed. It was not therefore possible to confirm that adult pigs, especially sows, act as carriers for rotaviral infection of young piglets as has been suggested by other workers. All the piglets acquired maternal antirotaviral antibody from their dams and the levels of antibody in piglets' sera were comparable to those in the colostrum of their dams. The maternally-derived antibody was also detected in piglets' faeces. Antibody in sera and in faeces declined rapidly after birth. Rotaviral shedding commenced in each of the cohorts when the geometric mean ELISA antibody titre fell below 1/1600 (equivalent to serum neutralizing antibody titre of 1/8 to 1/16). However, this correlation between antibody titres and protection was not observed in individual litters. In each of the cohorts studied, rotaviral shedding was usually detected initially in one or two piglets of a litter. The infection then spread to other piglets within the same litter and, finally, to piglets of other litters in the same group. Onset of rotaviral infection in particular litters was related to their location in the farrowing unit rather than to the levels of antibody. The shedding pattern of group A rotavirus was studied further in another five New Zealand piggeries and was found to be similar to that observed at the Massey University Piggery. Faecal samples from these piggeries were analyzed by polyacrylamide gel electrophoresis (PAGE) and no common electrophoretype of group A rotavirus was found in these piggeries. More than one electrophoretype of group A rotavirus was detected in three of these piggeries. Faecal samples collected from Massey University Piggery were also analyzed by PAGE and it was found that rotaviruses detected during the first two years of the present investigation had identical electrophoretypes, but one isolate detected in the third year had a distinctively different pattern. Non-group A rotaviruses were also detected for the first time in New Zealand. Nine samples had an electrophoretic pattern similar to that of group C rotavirus and one was similar to that of group B rotavirus. One of the samples containing group C rotavirus was from two litters of piglets with diarrhoea at two to four days of age. In one of these piggeries, five electrophoretypes of rotaviruses representing three groups were detected. These observations indicate that rotaviral infections are important causes of milk scours in piglets, and are probably significant in exacerbating PWD. The epidemiology of rotaviral infections is complicated by a number of factors. These include the continuous transmission of virus from pig to pig and from litter to litter, the survival of the virus in the piggery environment, the incomplete protection afforded by maternally-derived antibody, and the simultaneous circulation of different strains and different groups of rotavirus in one piggery.