There is growing evidence that climatic factors could influence the evolution of the current COVID-19 pandemic. Here, we build on this evidence base, focusing on the southern hemisphere summer and autumn period. The relationship between climatic factors and COVID-19 cases in New South Wales, Australia was investigated during both the exponential and declining phases of the epidemic in 2020, and in different regions. Increased relative humidity was associated with decreased cases in both epidemic phases, and a consistent negative relationship was found between relative humidity and cases. Overall, a decrease in relative humidity of 1% was associated with an increase in cases of 7-8%. Overall, we found no relationship with between cases and temperature, rainfall or wind speed. Information generated in this study confirms humidity as a driver of SARS-CoV-2 transmission.
Animal health information systems or risk analysis tools are indispensable not only for animal health surveillance, but also to observe the evolution and risk of disease incursion into a disease-free area. Given their essential function in animal disease prevention, different international and national organizations have created their own aforementioned systems/tools. Moreover, with the increase of technology and data storage, they have become more accessible and widely used by professionals in animal and human health sciences. This study aimed to establish their preferences, needs and constraints in respect of these tools. An online survey was conducted and answered by 213 respondents from 132 countries. The respondents were animal or public health professionals in different employment sectors (mostly in government, research and university institutions) and various fields of competency (highest for animal and public health). The majority of respondents used the animal health information systems frequently and on a weekly basis, with prevention measures of diseases being regarded as the most useful information. Descriptive epidemiology is more used/needed than analytical epidemiology. Risk analysis was performed by the majority of the respondents (70%), using a qualitative approach more than a quantitative or semi-qualitative. The primary objectives was to produce risk assessment and preparedness in areas involving origin and spread of animal diseases. The features most sought after in risk assessment tools were pathways of introduction and spread assessment. The level of satisfaction was higher for the platform which is most used by the respondents. Thus, the platform choice is most likely influenced by its efficiency and functionality. Overall, these results could be taken into consideration when improving an already available platform, or when creating a new efficient tool.
Using a model developed previously by the authors, a risk assessment was conducted to predict the change in the risk of ASF entering Japan as a result of the coronavirus pandemic in humans. The annual probability of ASF entering Japan was calculated to be 23% (90% prediction interval: 0-91%), 4.7% (0-24%) in February, 0.4% (0-2.1%) in March and 0.004% (0-0.01%) in April 2020 indicating a significant decline in the risk of ASF entry into Japan from China. The decline was attributed to a decline in the number of air travelers from China and amount of restaurant food.
Following the increase in wild boar population recorded in urban and peri-urban areas through Europe, the present survey aimed to assess the occurrence of zoonotic tick-borne bacteria in animals and their ticks collected from southern Italy, in order to evaluate the potential risk of infection for animals and humans. From October to December 2019, a total of 176 ticks collected from 93 wild boars and their spleen samples were molecularly screened for Borrelia burgdorferi sensu lato complex, Coxiella burnetii and spotted fever group (SFG) Rickettsia species. Overall, all the wild boars were infested by ticks (mean intensity, 1.9) with Dermacentor marginatus and Ixodes ricinus being identified in 99.4% and 0.6%, respectively. Out of 93 wild boars, 17 (18.3%) were infested by ticks positive to spotted fever group (SFG) Rickettsia species. Rickettsia slovaca and Rickettsia raoultii were identified in 16 (9%) and 1 (0.6%) D. marginatus, respectively, whereas a single I. ricinus (0.6%) was infected by R. slovaca. A single wild boar (1.1%) scored positive to R. slovaca. All ticks and wild boars scored negative to C. burnetii and B. burgdorferi s.l. complex. Data herein obtained suggest wild boars are involved in the dissemination of D. marginatus, especially in peri-urban settlements of the study area. An integrated management approach is advocated for wild boar population control and preventing the potential risk of tick-borne bacteria in animals and humans.
Emerging and reemerging viral diseases can lead to devastating effects on human lives and at times also lead to economic crises. The ongoing COVID-19 pandemic due to the novel coronavirus (nCoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, China, has caused a global public health emergency. Still, the molecular mechanism of transmission of SARS-CoV-2, its clinical manifestations and pathogenesis is not completely understood. The global scientific community has intensified their efforts to understand the biology of SARS-CoV-2 to develop vaccines and therapeutic interventions to prevent the rapid spread of the virus and to control mortality and morbidity associated with COVID-19. To understand the pathophysiology of SARS-CoV-2, appropriate animal models that mimic the biology of human SARS-COV-2 infection is urgently needed. In this review, we outline animal models that have been used to study previous human coronaviruses (HCoVs), that includes severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Importantly, we discuss which model is appropriate for SARS-CoV-2 as well as the advantages and disadvantages of each.
The objective of the study was to define and then evaluate an early decision indicator (EDI) trigger that operated within the first 5 weeks of a response that would indicate a large outbreak of FMD was developing, in order to be able to inform control options within an adaptive management framework. To define the trigger, a previous dataset of 10,000 simulated FMD outbreaks in New Zealand, controlled by the standard stamping-out approach, was re-analysed at various time points between days 11–35 of each response. The two predictive metrics adopted comprised the mean third quartiles of cumulative numbers of infected premises (IPs) at weekly time points, and estimated dissemination rate (EDR) values indicating sustained spread, specifically > 2.0 between days 11-14 or > 1.5 at any time point between days 15–35 of the response. To evaluate the trigger, the trigger was parameterized within the InterSpread Plus modelling framework, and a new series of simulation generated. The trigger was treated like a series of diagnostic tests that were applied during days 11–35 of each simulated outbreak, and its results recorded and then compared to the final size of each outbreak. The performance of the test was then evaluated across the population of outbreaks, and the sensitivity (Se), specificity (Sp), positive predictive value (PPV) and negative predictive value (NPV) calculated. The Se, Sp, PPV and NPV for predicting large outbreaks were 0.997, 0.513, 0.404 and 0.998 respectively. The study showed that the complex EDI incorporating both the cumulative number of IPs and EDR was very sensitive to detecting large outbreaks, although not all outbreaks predicted to be large were so, whereas outbreaks predicted to be small invariably were small. Therefore, it shows promise as a tool that could support an adaptive management approach to FMD control.
Landscape anthropization has been identified as one of the main drivers of pathogen emergence worldwide, facilitating pathogen spillover between domestic species and wildlife. The present study investigated Carnivore protoparvovirus-1 (CPPV) infection using molecular methods in 98 free-ranging wild guignas (Leopardus guigna) and 262 co-occurring owned, free-roaming rural domestic cats. We also assessed landscape anthropization variables as potential drivers of infection. CPPV DNA was detected in guignas across their entire distribution range, with observed prevalence of 13.3% (real-time PCR) and 9% (conventional PCR) in guignas, and 6.1% (conventional PCR) in cats. Prevalence in guigna did not vary depending on age, sex, study area or landscape variables. Prevalence was higher in juvenile cats (16.7%) than in adults (4.4%). Molecular characterization of the virus by amplification and sequencing of almost the entire vp2 gene (1746 bp) from one guigna and five domestic cats was achieved, showing genetic similarities to canine parvovirus 2c (CPV-2c) (one guigna and one cat), feline panleukopenia virus (FPV) (one cat), CPV-2 (no subtype identified) (two cats), CPV-2a (one cat). The CVP-2c-like sequence found in a guigna clustered together with domestic cat and dog CPV-2c sequences from South America, suggesting possible spillover from a domestic to a wild species as the origin of infection in guigna. No clinical signs of disease were found in PCR-positive animals except for the CPV-2c-infected guigna, which had hemorrhagic diarrhea and died a few days after arrival at a wildlife rescue center. Our findings reveal widespread presence of Carnivore protoparvovirus-1 across the guigna distribution in Chile and suggest that virus transmission potentially occurs from domestic to wild carnivores, causing severe disease and death in susceptible wild guignas.
Coronavirus (CoV) pandemics have become a huge threat to the public health worldwide in the recent decades. Typically, severe acute respiratory syndrome CoV (SARS-CoV) caused SARS pandemic in 2003 and SARS-CoV-2 caused the ongoing COVID-19 pandemic. Both viruses have been reported to originate from bats. Thus, direct or indirect interspecies transmission from bats to humans is required for the viruses to cause pandemics. Receptor utilization is a key factor determining the host range of viruses which is critical to the interspecies transmission. Angiotensin converting enzyme 2 (ACE2) is the receptor of both SARS-CoV and SARS-CoV-2, but only ACE2s of certain animals can be utilized by the viruses. Here, we employed pseudovirus cell-entry assay to evaluate the receptor-utilizing capability of ACE2s of 20 animals by the two viruses and found that SARS-CoV-2 utilized less ACE2s than SARS-CoV, indicating a narrower host range of SARS-CoV-2. Especially, SARS-CoV-2 tended not to use murine or non-mammal ACE2s. Meanwhile, pangolin CoV, another SARS-related coronavirus highly homologous to SARS-CoV-2 in its genome, yet showed similar ACE2 utilization profile with SARS-CoV rather than SARS-CoV-2. To clarify the mechanism underlying the receptor utilization, we compared the amino acid sequences of the 20 ACE2s and found 5 amino acid residues potentially critical for ACE2 utilization, including the N-terminal 20th and 42nd amino acids that may determine the different receptor utilization of SARS-CoV, SARS-CoV-2 and pangolin CoV. Our studies promote the understanding of receptor utilization of pandemic coronaviruses, potentially contributing to the virus tracing, intermediate host screening and epidemic prevention for pathogenic coronaviruses.
African swine fever virus variants with different numbers of a 10-bp tandem repeat were isolated in South Korea soon after being identified in wild boar. The short emergence periods and sympatric distributions within a narrow geographical region suggest that the variants were sporadically generated in the pre-existing viral population.
In this study, we introduce the vulnerability index to measure the regional ASF epidemic and present the ASF severity ratings of 31 provincial regions of China. The index is defined based on the data from investigation, national statistical yearbook and reports. The data to be used includes pig breeding, financial resources, human resources, epidemic information of ASF and price fluctuation from the 31 regions. Then we use the data envelopment analysis (DEA) model to define the vulnerability index, the relative severity values for each region which quantitatively reflect the damage degree caused by the epidemic of ASF. The method allows us to provide a systematic classification for regional vulnerability level of ASF in China. Using the index, we find that the vulnerability of the whole country is at a high level, and there is no regional aggregation phenomenon. The vulnerability level of the 31 provinces are quite different and the provinces with high vulnerability level are dispersive geographically. For the five major prevention and control zones for ASF in China, the northern region has the highest vulnerability level, while the level of eastern zoon is the lowest.
Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen capable of causing severe gastrointestinal diseases in humans. Cattle and sheep are the natural reservoir hosts of STEC strains. Previously, we isolated 56 STEC strains from anal and carcass swab samples of cattle and sheep in farms and slaughterhouses. In this study, we performed whole-genome sequencing of these isolates and determined their serotypes, virulence profiles, sequence types (STs), and genetic relationships. Our results showed that the 56 isolates belong to 20 different STs, 29 O:H serotypes, and 8 stx subtype combinations. The highly prevalent serotypes were O8:H25 and O87:H16 for bovine and ovine isolates, respectively. Five serotypes of cattle or sheep isolates are novel. The majority (63%) of cattle isolates contain stx1+stx2, subtyped into stx1a, stx2a, and stx2c. In contrast, most of the sheep isolates contain stx1 only, primarily subtyped into stx1a and stx1c. None of the isolates tested eae-positive, but virulence factors such as ehxA and espP were present with variable prevalence rates. The prevalence of saa (19.6%) and espP (12.5%) in cattle isolates is much higher than that in sheep isolates, whereas that of subA (34%), katP (14.3%), and ireA (28.6%) in sheep isolates is considerably higher than that in cattle isolates. Core-genome SNP analysis revealed that the majority of isolates could be clustered based on their serotypes or STs, whereas some clustering is associated with more than one ST or serotype. Seven-gene Multilocus Sequence Typing (MLST) indicated that nine sheep isolates and four cattle isolates were related to a few E. coli isolates associated with human HUS, suggesting their potential in causing severe human infections. Collectively, we described the characteristics of cattle and sheep STEC isolates from Xinjiang, China, which may be utilized in comparative studies of other geographic regions and sources of isolation and for surveillance.
Infection with the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) induces the coronavirus infectious disease 19 (COVID-19). Its pandemic form in human population and its probable animal origin, along with recent case reports in pets, make drivers of emergence crucial in carnivore domestic pets, especially cats, dogs and ferrets. Few data are available in these species; we first listed forty-six possible drivers of emergence of COVID-19 in pets, regrouped in eight domains (i.e. pathogen/disease characteristics, spatial-temporal distance of outbreaks, ability to monitor, disease treatment and control, characteristics of pets, changes in climate conditions, wildlife interface, human activity, and economic and trade activities). Secondly, we developed a scoring system per driver, then elicited experts (N = 33) to: (i) allocate a score to each driver, (ii) weight the drivers scores within each domain and (iii) weight the different domains between them. Thirdly, an overall weighted score per driver was calculated; drivers were ranked in decreasing order. Fourthly, a regression tree analysis was used to group drivers with comparable likelihood to play a role in the emergence of COVID-19 in pets. Finally, the robustness of the expert elicitation was verified. Five drivers were ranked with the highest probability to play a key role in the emergence of COVID-19 in pets: availability and quality of diagnostic tools, human density close to pets, ability of preventive/control measures to avoid the disease introduction or spread in a country (except treatment, vaccination and reservoir(s) control), current species specificity of the disease causing agent and current knowledge on the pathogen. As scientific knowledge on the topic is scarce and still uncertain, expert elicitation of knowledge, in addition with clustering and sensitivity analyses, is of prime importance to prioritize future studies, starting from the top five drivers. The present methodology is applicable to other emerging pet diseases.
Tracing and isolation of close contacts is used to control outbreaks of coronavirus disease 2019 (COVID-19) in China. However, risk factors associated with occurrence of COVID-19 among close contacts have not been well described. 106 household contacts were included in this study, of whom 19 were developed into COVID-19 cases and the secondary attack rate was 17.9%. Multivariable analysis showed increasing risk of occurrence of COVID-19 among household contacts associated with female of index patients (Adjusted Hazard Ratio [aHR] = 5.61, 95%CI = 1.51-20.83), critical disease of index patients ([aHR] = 7.58, 95%CI = 1.66-34.66), effective contact duration with index patients >2 days ([aHR] = 4.21, 95%CI = 1.29-13.73), and effective contact duration >11 days ([aHR] = 17.88, 95%CI = 3.26-98.01).The sex and disease severity of index COVID-19 patients, and longer effective contact duration with COVID-19 confirmed cases could help epidemiologists to identify potential COVID-19 case among household contacts at an early stage.
The SARS-CoV-2 strain of the coronavirus is responsible for the current COVID-19 pandemic, with an ongoing toll of over 5 million infections and 333 thousand deaths worldwide within the first 5 months. Insight into the phylodynamics and mutation variants of this strain is vital to understanding the nature of its spread in different climate conditions. The incidence rate of COVID-19 is increasing at an alarming pace within subtropical Southeast Asian nations with high temperatures and humidity. To understand this spread, we analyzed 60 genome sequences of SARS-CoV-2 available in GISAID platform from 6 Southeast Asian countries. Multiple sequence alignments and maximum likelihood phylogenetic analyses were performed to analyze and characterize the non-synonymous mutant variants circulating in this region. Global mutation distribution analysis showed that the majority of the mutations found in this region are also prevalent in Europe and North America, and the concurrent presence of these mutations at a high frequency in Australia and Saudi Arabia indicate possible transmission routes. Unique spike protein and non-structural protein mutations were observed circulating within a localized area. We divided the circulating viral strains into 4 major groups and 2 sub-groups on the basis of the most frequent non-synonymous mutations. Strains with a unique set of 4 co-evolving mutations were found to be circulating at a high frequency within India, specifically, group 2 strains characterized by two co-evolving NS mutants which alter in RdRp (P323L) and spike protein (D614G) common in Europe and North America. These European and North American variants (Nextstrain clade A2) have rapidly emerged as dominant strains within Southeast Asia, increasing from a 0% presence in January to an 85% presence by May 2020. These variants may have an evolutionary advantage over their ancestral types and could present the largest threat to Southeast Asia for the coming winter.
Hirudo nipponia is not only an important economic pillar for farmers, but is also a precious raw material for medicinal materials. However, in recent years, H. nipponia suffered from diseases with symptoms including systemic edema and hyperemia. It has not yet been demonstrated which pathogen causes this disease and whether this could be transmitted to humans. In this study, Klebsiella pneumoniae was isolated and identified from diseased H. nipponia and the pathogenicity of the isolated strain was confirmed. Furthermore, by comparing the sequence of the pathogen isolated from leeches to the same pathogen infecting humans, we identified that the isolated strain is a threat to human health. This work emphasizes the importance of the first discovery of pathogenic bacteria from leeches similar to human pathogens, as well as the need for identifying comorbidities for both humans and aquatic animals.
As global trade of live animals expands, there is increasing need to assess the risks of invasive organisms, including pathogens, that can accompany these translocations. The movement and release of live baitfish by recreational anglers has been identified as a particularly high-risk pathway for the spread of aquatic diseases in the United States. To provide risk-based decision support for preventing and managing disease invasions from baitfish release, we developed a hazard identification and ranking tool to identify the pathogens that pose the highest risk to wild fish via this pathway. We created a screening protocol and semi-quantitative stochastic risk ranking framework, combining published data with expert elicitation (n=25) and applied the framework to identify high-priority pathogens for the bait supply in Minnesota, USA. Normalized scores were developed for seven risk criteria (likelihood of transfer, prevalence in bait supply, likelihood of colonization, current distribution, economic impact if established, ecological impact if established, and host species) to characterize a pathogen’s ability to persist in the bait supply and cause impacts to wild fish species of concern. The generalist macroparasite Schizocotyle acheilognathi was identified as presenting highest overall threat, followed by the microsporidian Ovipleistophora ovariae, and viral hemorrhagic septicemia virus. Our findings provide risk-based decision support for managers charged with maintaining both the recreational fishing industry and sustainable, healthy natural resources. The ranking process, implemented here for a single state case study, provides a standardized conceptual framework that could be applied across jurisdictions to inform risk-based management of the live baitfish pathway.
Mycobacterium bovis is the main causative agent of bovine tuberculosis (BTB) in cattle and it is also responsible for a proportion of human TB cases. The annual cost of BTB worldwide is estimated at US$3 billion. Zebu cattle are considered to be more resistant to some infectious diseases than Holstein-Friesian (HF) cattle, including BTB. However, epidemiological studies do not necessarily take into account usage differences of the two types of cattle. It could be argued that HF cattle suffer greater metabolic stress due to their mainly dairy use, whereas Zebu cattle are mainly used for beef production. However, in experiments comparing Zebu and European cattle, the number of animals has been too small to draw statistically robust conclusions on the differences in the level of resistance between these breeds of cattle. Here, we used a recently developed vaccination-and-BCG challenge model to compare the ability of naïve and vaccinated Zebu and HF cattle to control/kill mycobacteria. Young male cattle of both breeds with similar ages were housed in the same accommodation for the duration of the experiment; after correcting for multiple comparison, we found that there was a trend for vaccinated HF cattle to have lower cfu numbers than non-vaccinated HF cattle (ρ = 0.057). No such trend was observed between vaccinated and non-vaccinated Zebu cattle (ρ = 0.560); similarly, no difference was observed between naïve HF and Zebu (ρ = 0.862) cattle. In contrast, evaluation of antigen-specific IFNγ secretion indicated that Zebu and HF cattle differed in their response to mycobacteria. Thus, under the conditions used in this work, the data indicate that there are no differences between Zebu and HF cattle. Further experiments, using larger numbers of animals may be required to determine whether Zebu and HF cattle differ in their susceptibility to infection with M. bovis.
Bovine tuberculosis (bTB) prevalence substantially increased over the past two decades with relatively high impact on large dairy herds, raising the concern of regulatory authorities and industry stakeholders, and threatening animal and public health. Lack of resources, together with the economic and social consequences of whole-herd stamping-out, makes depopulation an impractical disease control alternative in these herds. The increase in bTB-prevalence was associated with demographic and management changes in the dairy industry in Uruguay, reducing the efficacy of the current control program (i.e. status quo) based on intradermal serial testing with caudal fold- and comparative cervical- tuberculin test-and slaughter of reactors (CFT-CCT). Here, we aimed to assess the epidemiological effectiveness of six alternative control scenarios based on test-and-slaughter of positive animals, using mathematical modeling to infer bTB-within-herd dynamics. We simulated six alternative control strategies consisting of testing adult cattle (>1 year) in the herd every three months using one test (in-vivo or in-vitro) or a combination in parallel of two tests (CFT, interferon-gamma release assay –IGRA- or Enzyme-linked immunosorbent assay). Results showed no significant differences overall in the time needed to reach bTB-eradication (median ranging between 61 to 82 months) or official bovine tuberculosis-free status (two consecutive negative herd-tests) between any of the alternative strategies and the status quo (median ranging between 50 and 59 months). However, we demonstrate how alternative strategies can significantly reduce bTB-prevalence when applied for restricted periods (6, 12, or 24 months), and in the case of IGRAc (IGRA using peptide-cocktail antigens), without incurring on higher unnecessary slaughter of animals (false-positives) than the status quo in the first 6 months of the program (P-value <0.05). Enhanced understanding bTB-within-herd dynamics with the application of different control strategies help to identify optimal strategies to ultimately improve bTB-control and -eradication from dairies in Uruguay and similar endemic settings.