Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the ...evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.
Climate variability and anomalies are known drivers of the emergence and outbreaks of infectious diseases. In this study, we investigated the potential association between climate factors and ...anomalies, including El Niño Southern Oscillation (ENSO) and land surface temperature anomalies, as well as the emergence and spillover events of bat-borne viral diseases in humans and livestock in the Asia-Pacific region and the Arabian Peninsula. Our findings from time series analyses, logistic regression models, and structural equation modelling revealed that the spillover patterns of the Nipah virus in Bangladesh and the Hendra virus in Australia were differently impacted by climate variability and with different time lags. We also used event coincidence analysis to show that the emergence events of most bat-borne viral diseases in the Asia-Pacific region and the Arabian Peninsula were statistically associated with ENSO climate anomalies. Spillover patterns of the Nipah virus in Bangladesh and the Hendra virus in Australia were also significantly associated with these events, although the pattern and co-influence of other climate factors differed. Our results suggest that climate factors and anomalies may create opportunities for virus spillover from bats to livestock and humans. Ongoing climate change and the future intensification of El Niño events will therefore potentially increase the emergence and spillover of bat-borne viral diseases in the Asia-Pacific region and the Arabian Peninsula.
The dietary preferences of most rodents, especially in tropical countries, are poorly known. In the tropics, rodent diversity can be high and several species can coexist in the same habitats. In ...order to better document the dietary habits of Southeast Asian murid and diatomyid rodents, we examined microwear patterns in 21 species, with a particular focus on those living in karst habitats. Five variables of microwear scars (scratches and pits) were counted and measured on the dental facet of the first molar hypocone. We observed large variation and overlap in microwear patterns between and within genera, suggesting that feeding ecology is diverse (mostly generalist omnivorous species) within species and genus. For species living in agro-ecosystems, few differences were observed when we compared sympatric species within a genus, suggesting that niche partitioning is not achieved by feeding, neither in terms of diet composition nor in the way food is processed, or that food items are more homogeneous in terms of physical properties that affect microwear patterns. Differences between sympatric species were more pronounced in forest or karst contexts, suggesting that specialisation and niche differentiation have persisted in more preserved environments. Finally, differences were also observed in urban ecosystems suggesting that the communities of rodents evolved niche partitioning in these human-modified habitats. Our results also revealed differences in microwear patterns between karst and non-karst rodents, with all karst species showing a trend towards increasing numbers of small scratches and small pits. This suggested that the karst environment may influence the dietary habits of rodents, either in terms of the composition of the diet or by altering the general characteristics of the food.
As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of ...the core virome of diverse rodents should therefore assist in efforts to reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens.
This study aimed to describe the viral range that could be detected in the lungs of rodents from Mainland Southeast Asia. Lung samples were collected from 3284 rodents and insectivores of the orders Rodentia, Scandentia, and Eulipotyphla in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006-2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of the mammalian viruses within these lungs and the ecological and genetic imprints of the novel viruses. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genomic and evolutionary characteristics, host species, and locations.
These results expand our understanding of the core viromes of rodents and insectivores from Mainland Southeast Asia and suggest that a high diversity of viruses remains to be found in rodent species of this area. These findings, combined with our previous virome data from China, increase our knowledge of the viral community in wildlife and arthropod vectors in emerging disease hotspots of East and Southeast Asia. Video abstract.
Interactions between humans and animals are the key elements of zoonotic spillover leading to zoonotic disease emergence. Research to understand the high-risk behaviors associated with disease ...transmission at the human-animal interface is limited, and few consider regional and local contexts.
This study employed an integrated behavioral-biological surveillance approach for the early detection of novel and known zoonotic viruses in potentially high-risk populations, in an effort to identify risk factors for spillover and to determine potential foci for risk-mitigation measures.
Participants were enrolled at two community-based sites (n = 472) in eastern and western Thailand and two hospital (clinical) sites (n = 206) in northeastern and central Thailand. A behavioral questionnaire was administered to understand participants' demographics, living conditions, health history, and animal-contact behaviors and attitudes. Biological specimens were tested for coronaviruses, filoviruses, flaviviruses, influenza viruses, and paramyxoviruses using pan (consensus) RNA Virus assays.
Overall 61/678 (9%) of participants tested positive for the viral families screened which included influenza viruses (75%), paramyxoviruses (15%), human coronaviruses (3%), flaviviruses (3%), and enteroviruses (3%). The most salient predictors of reporting unusual symptoms (i.e., any illness or sickness that is not known or recognized in the community or diagnosed by medical providers) in the past year were having other household members who had unusual symptoms and being scratched or bitten by animals in the same year. Many participants reported raising and handling poultry (10.3% and 24.2%), swine (2%, 14.6%), and cattle (4.9%, 7.8%) and several participants also reported eating raw or undercooked meat of these animals (2.2%, 5.5%, 10.3% respectively). Twenty four participants (3.5%) reported handling bats or having bats in the house roof. Gender, age, and livelihood activities were shown to be significantly associated with participants' interactions with animals. Participants' knowledge of risks influenced their health-seeking behavior.
The results suggest that there is a high level of interaction between humans, livestock, and wild animals in communities at sites we investigated in Thailand. This study highlights important differences among demographic and occupational risk factors as they relate to animal contact and zoonotic disease risk, which can be used by policymakers and local public health programs to build more effective surveillance strategies and behavior-focused interventions.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Introduction:
Influenza virus favours the respiratory tract as its primary site of host entry and replication, and it is transmitted mainly via respiratory secretions. Nasopharyngeal swab is the gold ...standard specimen type for influenza detection, but several studies have also suggested that the virus replicates in the human gastrointestinal tract.
Methods:
A retrospective study was conducted on all patients positive for influenza virus and initially recruited as part of the PREDICT project from 2017 to 2018. The objectives of the study were to investigate whether rectal swab could aid in improving influenza detection, and if there was any correlation between gastrointestinal disturbances and severity of infection, using length of hospital stay as an indicator of severity.
Results:
Of the 51 influenza-positive patients, 12 had detectable influenza virus in their rectal swab. Among these 12 rectal swab positive patients, influenza virus was not detected in the nasopharyngeal swab of three of them. Gastrointestinal symptoms were observed for 28.2% patients with a negative rectal swab negative and 25.0% patients with a positive rectal swab. Average length of hospital stay was 4.2 days for rectal swab positive group and 3.7 days for rectal swab negative group. This difference was not statistically significant (p = 0.288).
Conclusions:
There is no correlation between influenza virus detection in rectal swab and gastrointestinal disturbances or disease severity, and there is currently insufficient evidence to support replicative ability in the gastrointestinal tract.
We summarize the current knowledge on parasitism‐related invasion processes of the globally invasive Rattus lineages, originating from Asia, and how these invasions have impacted the local ...epidemiology of rodent‐borne diseases. Parasites play an important role in the invasion processes and successes of their hosts through multiple biological mechanisms such as “parasite release,” “immunocompetence advantage,” “biotic resistance” and “novel weapon.” Parasites may also greatly increase the impact of invasions by spillover of parasites and other pathogens, introduced with invasive hosts, into new hosts, potentially leading to novel emerging diseases. Another potential impact is the ability of the invader to amplify local parasites by spillback. In both cases, local fauna and humans may be exposed to new health risks, which may decrease biodiversity and potentially cause increases in human morbidity and mortality. Here we review the current knowledge on these processes and propose some research priorities.
The island of Sulawesi in Indonesia is an important site for the wildlife trade that is currently undergoing rapid exploitation of its local fauna to supply wild meat markets of North Sulawesi. In ...this study, we used field surveys, ethnographic interviews, and daily counts in markets to document species of terrestrial wildlife on sale in North Sulawesi markets, and to identify the hunting sites, practices, and key actors within the wildlife trade. We quantify the volume of wild meat traded and their prices, with a particular focus on the flying fox trade.
Wildlife meat was routinely available for sale in 73% of the markets and supermarkets surveyed in North Sulawesi. The wildlife taxa most commonly found in these markets were flying foxes, wild pigs, rats and snakes. Wildlife hunting and trade networks extend to all provinces of the island through a well-organized, dynamic and easy to access network involving many actors. We identified 45 flying fox roosts in Sulawesi, 38 of which were under active hunting pressure. A third of the active hunting sites are located in Southeast Sulawesi, which acts as a hub for bat hunting and trade. We estimate that the number of flying foxes annually traded in Sulawesi ranges from 662,551 to more than one million individuals and conclude that current rates of flying fox harvest are unstainable. Stricter law enforcement, implementation of hunting quotas, and further research efforts are therefore urgently needed to improve the sustainability of the wildlife trade in Sulawesi.
A One Health cross-sectoral surveillance approach was implemented to screen biological samples from bats, pigs, and humans at high-risk interfaces for zoonotic viral spillover for five viral families ...with zoonotic potential in Viet Nam. Over 1600 animal and human samples from bat guano harvesting sites, natural bat roosts, and pig farming operations were tested for coronaviruses (CoVs), paramyxoviruses, influenza viruses, filoviruses and flaviviruses using consensus PCR assays. Human samples were also tested using immunoassays to detect antibodies against eight virus groups. Significant viral diversity, including CoVs closely related to ancestors of pig pathogens, was detected in bats roosting at the human-animal interfaces, illustrating the high risk for CoV spillover from bats to pigs in Viet Nam, where pig density is very high. Season and reproductive period were significantly associated with the detection of bat CoVs, with site-specific effects. Phylogeographic analysis indicated localized viral transmission among pig farms. Our limited human sampling did not detect any known zoonotic bat viruses in human communities living close to the bat cave and harvesting bat guano, but our serological assays showed possible previous exposure to Marburg virus-like (Filoviridae), Crimean-Congo hemorrhagic fever virus-like (Bunyaviridae) viruses and flaviviruses. Targeted and coordinated One Health surveillance helped uncover this viral pathogen emergence hotspot.
Despite the discovery of several closely related viruses in bats, the direct evolutionary progenitor of SARS-CoV-2 has not yet been identified. In this study, we investigated potential animal sources ...of SARS-related coronaviruses using archived specimens from Sunda pangolins (
) and Chinese pangolins (
) confiscated from the illegal wildlife trade, and from common palm civets (
) raised on wildlife farms in Viet Nam. A total of 696 pangolin and civet specimens were screened for the presence of viral RNA from five zoonotic viral families and from Sarbecoviruses using primers specifically designed for pangolin coronaviruses. We also performed a curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, to illustrate the global pangolin supply chain in the context of Viet Nam where the trade confiscated pangolins were sampled for this study. All specimens from pangolins and civets sampled along the wildlife supply chains between February 2017 and July 2018, in Viet Nam and tested with conventional PCR assays designed to detect flavivirus, paramyxovirus, filovirus, coronavirus, and orthomyxovirus RNA were negative. Civet samples were also negative for Sarbecoviruses, but 12 specimens from seven live pangolins confiscated in Hung Yen province, northern Viet Nam, in 2018 were positive for Sarbecoviruses. Our phylogenetic trees based on two fragments of the RdRp gene revealed that the Sarbecoviruses identified in these pangolins were closely related to pangolin coronaviruses detected in pangolins confiscated from the illegal wildlife trade in Yunnan and Guangxi provinces, China. Our curated data collection of media reports of wildlife confiscation events involving pangolins in Viet Nam between January 2016 and December 2020, reflected what is known about pangolin trafficking globally. Pangolins confiscated in Viet Nam were largely in transit, moving toward downstream consumers in China. Confiscations included pangolin scales sourced originally from Africa (and African species of pangolins), or pangolin carcasses and live pangolins native to Southeast Asia (predominately the Sunda pangolin) sourced from neighboring range countries and moving through Viet Nam toward provinces bordering China.
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