66 research outputs found
Ecological dataset from: 'Rats and the city: implications of urbanization on zoonotic disease risk in Southeast Asia'
No full textThis dataset includes the ecological and environmental data, a description of the analysis steps, and the related R code associated with the manuscript: "Rats and the city: implications of urbanization on zoonotic disease risk in Southeast Asia" by Kim R. Blasdell, Serge Morand, Susan G.W. Laurance, Stephen L Doggett, Amy Hahs, David Perera, and Cadhla Firth, available at: https://www.pnas.org/doi/abs/10.1073/pnas.2112341119
This dataset also relates to the preprint: "Rats in the city: implications for zoonotic disease risk in an urbanizing world" available at: https://www.biorxiv.org/content/10.1101/2021.03.18.436089v1
A detailed description of the files can be found in README.txtThis study was funded by the Australian Research Council (Award #: DE150101259
The Genomics of Emerging Pathogens
No full textGlobalization and industrialization have dramatically altered the vulnerability of human and animal populations to emerging and reemerging infectious diseases while shifting both the scale and pace of disease outbreaks. Fortunately, the advent of high-throughput DNA sequencing platforms has also increased the speed with which such pathogens can be detected and characterized as part of an outbreak response effort. It is now possible to sequence the genome of a pathogen rapidly, inexpensively, and with high sensitivity, transforming the fields of diagnostics, surveillance, forensic analysis, and pathogenesis. Here, we review advances in methods for microbial discovery and characterization, as well as strategies for testing the clinical and public health significance of microbe-disease associations. Finally, we discuss how genetic data can inform our understanding of the general process of pathogen emergence
Viral surveillance and discovery
No full textThe field of virus discovery has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that include wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for viral surveillance and discovery, strategies and pitfalls in linking discoveries to disease, and identify opportunities for improvements in sequencing instrumentation and analysis, the use of social media and medical informatics that will further advance clinical medicine and public health
Phylogenetic Analysis Reveals Rapid Evolutionary Dynamics in the Plant RNA Virus Genus Tobamovirus
No full textEarly studies on the evolutionary dynamics of plant RNA viruses suggested that they may evolve more slowly than their animal counterparts, sometimes dramatically so. However, these estimates were often based on an assumption of virus–host codivergence over time-scales of many millions of years that is difficult to verify. An important example are viruses of the genus Tobamovirus, where the assumption of host–virus codivergence over 100 million years has led to rate estimates in the range of ~1 × 10−8 nucleotide substitutions per site, per year. Such a low evolutionary rate is in apparent contradiction with the ability of some tobamoviruses to quickly overcome inbred genetic resistance. To resolve how rapidly molecular evolution proceeds in the tobomaviruses, we estimated rates of nucleotide substitution, times to common ancestry, and the extent of congruence between virus and host phylogenies. Using Bayesian coalescent methods applied to time-stamped sequences, we estimated mean evolutionary rates at the nucleotide and amino acid levels of between 1 × 10−5 and 1.3 × 10−3 substitutions per site, per year, and hence similar to those seen in a broad range of animal and plant RNA viruses. Under these rates, a conservative estimate for the time of origin of the sampled tobamoviruses is within the last 100,000 years, and hence a far more recently than proposed assuming codivergence. This is supported by our cophylogeny analysis which revealed significantly discordant evolutionary histories between the tobamoviruses and the plant families they infect
Occupancy of urban roosts by spectacled flying-foxes (Pteropus conspicillatus) is not affected by diurnal microclimate
No full textOne of the most significant changes to Earth's climate in recent decades has been an increase in the frequency, intensity and duration of heatwaves. During heatwaves, animal's thermal window can be exceeded, and in extreme cases, mass mortality events have been observed. In 2018, a heatwave in north-eastern Australia resulted in the death of approximately one-third of the spectacled flying-fox (Pteropus conspicillatus) population at urban roosts in Cairns. The species has now been listed as endangered with future heatwaves considered the greatest threat to its survival. In this study, we investigated long-term climatic trends for Cairns, paying particular attention to the frequency of extreme heat events from 1943 to 2022. We then characterized the microclimate of urban flying-fox roosts during the Austral summers of 2021/2022 and 2022/2023 across Cairns to assess the long-term feasibility of urban spectacled flying-fox roosts. From the long-term climate records, we observed an overall increase in Cairns' average annual temperature of 1.3°C from 1943 to 2022 and an increase in the number of excessively hot days per decade, from 16 in the first decade (1943–1952) to 67 in the last (2013–2022). We regularly detected maximum roost temperatures of 30–35°C during our study, with excessively hot days (>35°C) recorded more frequently than expected compared to Cairns's maximum temperatures from the last decade (2013–2023). We detected only 1 day where roost temperatures exceeded 40°C and no period that replicated the 2018 heatwave conditions. Furthermore, we found a significant negative relationship between roost ambient temperature and humidity, where the hottest days also coincided with those with the lowest humidity. Importantly, we found no difference in microclimate between roosts that were occupied and unoccupied by flying-foxes during our study, suggesting that other environmental or behavioural factors are more influential for roost selection than the roosting microclimate. Ensuring the long-term conservation of spectacled flying-foxes under a changing climate will require the management of urban roosts to increase their thermal resistance to heatwaves, and more research is needed to identify the variables modulating this aspect
High Prevalence of Rodent-Borne Bartonella spp. in Urbanizing Environments in Sarawak, Malaysian Borneo
No full textRodents are the most prominent animal host of Bartonella spp., which are associated with an increasing number of human diseases worldwide. Many rodent species thrive in urban environments and live in close contact with people, which can lead to an increased human risk of infection from rodent-borne pathogens. In this study, we explored the prevalence and distribution of Bartonella spp. in rodents in urban, developing, and rural environments surrounding a growing city in Sarawak, Malaysian Borneo. We found that although Bartonella spp. infection was pervasive in most rodent species sampled, prevalence was highest in urban areas and infection was most commonly detected in the predominant indigenous rodent species sampled (Sundamys muelleri). Within the urban environment, parks and remnant green patches were significantly associated with the presence of both S. muelleri and Bartonella spp., indicating higher localized risk of infection for people using these environments for farming, foraging, or recreation
In Search of the Original Skewball
No full textThe well-known horseracing ballad ‘Skewball’ has been widely documented in oral tradition on both sides of the Atlantic, as well as on numerous English broadside printings. It recounts the tale of a mid-eighteenth-century horserace held at The Curragh of Kildare, in which a heavily-backed mare is comprehensively beaten by a relatively unknown skewbald gelding leaving the mare’s owner — along with much of the assembled onlookers — significantly out of pocket. The ballad became widely popularised in North America where it was first published in a song book in 1826 (Benton 1826:3-4). It was later subsumed into African-American song tradition, whereupon it was reconstructed in numerous versions as a ‘call-and-answer’ work anthem sung by slaves who gave it the new title of ‘Stewball’. Alan Lomax has also documented African-American chain-gang versions of the ballad in his various prison recordings (Lomax 1994:68-71; Scarborough 1925:61-4). Versions bearing distinctive similarities in style, form and content to the earliest collected versions of ‘Skewball’, were widely collected throughout North America as late as the 1930’s (Flanders 1939:172-4), while oral versions have been documented in Ireland throughout the eighteenth-, nineteenth- and twentieth-centuries, the latest being in March 1979 (Shields 2011:58-9). While always retaining a certain degree of continuity in terms of the general narrative recounted, the ballad has undergone numerous metamorphoses over time — particularly with reference to the dramatis personae involved — which has often resulted in the obfuscation of the original race detail. By closely examining contemporary records, as well as drawing relevant comparisons with a diverse range of collected versions of the ballad, the author has sought to establish the historical facts which lie behind the narrative recounted in ‘Skewball’. The earliest version of the ballad to which a date has been definitively assigned is that published in the songbook, The Vocal Library (Souter 1818:526). Due to the significant timeframe between this publication and the actual mid-eighteenth-century horserace recounted in ‘Skewball’, the author has also examined the preceding period with a view towards unearthing possible earlier sources for the ballad and will present a recently discovered MS version which provides further evidence of the historical origins of the ballad under review
First detection of a novel ‘unknown host’ flavivirus in a Malaysian rodent
No full textCurrent phylogenetic analysis of the flavivirus genus has identified a group of mosquito-borne viruses for which the vertebrate hosts are currently unknown. Here we report the identification of a novel member of this group from a peridomestic rodent species (Sundamys muelleri) collected in Sarawak, Malaysia in 2016. We propose to name this novel flavivirus Batu Kawa virus after the location in which it was identified, with the abbreviation BKWV. Characterization of the BKWV genome allowed identification of putative mature peptides, potential enzyme motifs and conserved structural elements. Phylogenetic analysis found BKWV to be most closely related to Nhumirim virus (from Brazil) and Barkedji virus (from Senegal and Israel). Both of these viruses have been identified in Culex mosquitoes and belong to a group of viruses with unknown vertebrate hosts. This is the first known report of a member of this group of viruses from a potential mammalian host
Association of rodent-borne Leptospira spp. with urban environments in Malaysian Borneo
No full textAlthough leptospirosis is traditionally considered a disease of rural, agricultural and flooded environments, Leptospira spp. are found in a range of habitats and infect numerous host species, with rodents among the most significant reservoirs and vectors. To explore the local ecology of Leptospira spp. in a city experiencing rapid urbanization, we assessed Leptospira prevalence in rodents from three locations in Malaysian Borneo with differing levels of anthropogenic influence: 1) high but stable influence (urban); 2) moderate yet increasing (developing); and 3) low (rural). A total of 116 urban, 122 developing and 78 rural rodents were sampled, with the majority of individuals assigned to either the Rattus rattus lineage R3 (n = 165) or Sundamys muelleri (n = 100). Leptospira spp. DNA was detected in 31.6% of all rodents, with more urban rodents positive (44.8%), than developing (32.0%) or rural rodents (28.1%), and these differences were statistically significant. The majority of positive samples were identified by sequence comparison to belong to known human pathogens L. interrogans (n = 57) and L. borgpetersenii (n = 38). Statistical analyses revealed that both Leptospira species occurred more commonly at sites with higher anthropogenic influence, particularly those with a combination of commercial and residential activity, while L. interrogans infection was also associated with low forest cover, and L. borgpetersenii was more likely to be identified at sites without natural bodies of water. This study suggests that some features associated with urbanization may promote the circulation of Leptospira spp., resulting in a potential public health risk in cities that may be substantially underestimated
Association of rodent-borne <i>Leptospira</i> spp. with urban environments in Malaysian Borneo
No full textAlthough leptospirosis is traditionally considered a disease of rural, agricultural and flooded environments, Leptospira spp. are found in a range of habitats and infect numerous host species, with rodents among the most significant reservoirs and vectors. To explore the local ecology of Leptospira spp. in a city experiencing rapid urbanization, we assessed Leptospira prevalence in rodents from three locations in Malaysian Borneo with differing levels of anthropogenic influence: 1) high but stable influence (urban); 2) moderate yet increasing (developing); and 3) low (rural). A total of 116 urban, 122 developing and 78 rural rodents were sampled, with the majority of individuals assigned to either the Rattus rattus lineage R3 (n = 165) or Sundamys muelleri (n = 100). Leptospira spp. DNA was detected in 31.6% of all rodents, with more urban rodents positive (44.8%), than developing (32.0%) or rural rodents (28.1%), and these differences were statistically significant. The majority of positive samples were identified by sequence comparison to belong to known human pathogens L. interrogans (n = 57) and L. borgpetersenii (n = 38). Statistical analyses revealed that both Leptospira species occurred more commonly at sites with higher anthropogenic influence, particularly those with a combination of commercial and residential activity, while L. interrogans infection was also associated with low forest cover, and L. borgpetersenii was more likely to be identified at sites without natural bodies of water. This study suggests that some features associated with urbanization may promote the circulation of Leptospira spp., resulting in a potential public health risk in cities that may be substantially underestimated.</div
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