Wild boar is the main sylvatic reservoir of the genotype 3 of hepatitis E virus (HEV). The occurrence of HEV-3 human cases has been linked to the consumption of raw or undercooked pig and wild boar meat and liver. The zoonotic transmission of HEV-3 has been confirmed by sequencing identical or strictly related viral strains in humans, wild boar, and derived food. The HEV sequences classified within the HEV-3 genotype are highly variable, and although only one serotype has been identified so far, the observed differences allow for the further classification of the HEV-3 genotype into subtypes, named in alphabetical order. Compared to human and pig strains, an even higher heterogeneity is observed among strains infecting wild boar. In the present study, the genetic variability of eight HEV-3 strains detected in wild boars living in a small geographical area in central Italy (Lazio and Umbria regions) was investigated by full genome sequencing and phylogenetic analysis. The strains were classified within the HEV-3a, HEV-3c, HEV-3f subtypes and within two new recently proposed subtypes. Results demonstrate – despite the relatively small geographic area of origin – an unexpected divergence within HEV-3 strains hosted by the investigated wild boar population and highlights the need for extensive sequencing of HEV in reservoirs to fully understand diversity, geographical distribution and evolution of this group of viruses.
Hyalomma ticks are important vectors of Crimean-Congo Haemorrhagic Fever Virus (CCHFV) and other pathogens. They are frequently carried as immatures from Africa, the Middle East and Mediterranean areas to temperate Europe via migratory birds and emergence of its adults has been reported in many countries where it has so far been non-endemic. Our aim was to implement the first steps of the DAMA (Document, Assess, Monitor, Act) protocol by monitoring the potential arrival of adult Hyalomma ticks in Hungary applying citizen-science methods. Ticks were collected from April-December 2021 by asking volunteer participants through a self-made website to look for unusual hard ticks on themselves, their pets and livestock. Owing to the intensive media campaign, the project website had over 31 thousand visitors within seven months and 137 specimens and several hundreds of photos of hard ticks were submitted by citizen scientists from all over the country. Beside Ixodes ricinus, Dermacentor reticulatus, Dermacentor marginatus and Haemaphysalis inermis, a specimen from a dog was morphologically identified as a male Hyalomma marginatum and another removed from a cattle as a male Hyalomma rufipes. The dog and the cattle had never been abroad, they were approximately 280 km apart, thus the two Hyalomma observations can be considered as separate introductions. Amplification of the partial mitochondrial cytochrome C oxidase subunit I gene was successful for both specimens. Sequencing verified the previous morphological identification for both ticks. Based on the phylogenetic analyses the Hy. marginatum individual most likely belongs to the Eurasian population and the Hy. rufipes to a clade of mixed sequences from Europe and Africa. We summarize the scattered historical reports about the occurrence of Hyalomma ticks and CCHFV in Hungary. Our data highlight the effectiveness of citizens science programmes in the monitoring and risk assessment of CCHFV emergence and preparedness in our region.
Viruses of veterinary significance such as African swine fever virus, are known to survive for extended periods in plant-based feed ingredients imported into North America. To reduce the likelihood of virus introduction, high-risk ingredients, such as oil seed meals, are stored in designated facilities for extended periods under controlled environmental conditions to minimize viral infectivity prior to use in diets. While 30 days has become a standard storage period, the required ambient temperature to inactivate viruses during this time is not known. To address the question, 1-metric ton totes of conventional soybean meal were inoculated with PRRSV 144 lineage 1C variant and SVA prior to storage for 30 days at 23.9º C, 15.5º C, or 10º C, and feeding to pigs. Virus infectivity was evaluated through detection of viral RNA in oral fluid samples, along with clinical signs. Results indicated that inactivation of both viruses occurred in soy stored at 23.9º C. In contrast, SVA infectivity was observed in soy stored at both 15.5º C and 10º C, while PRRSV 144 L1C variant infectivity was only observed in soy stored at 10º C. These results suggest that a storage period of 30-days and a temperature of 23.9º C are required to reduce the risk of virus contaminated plant-based feed ingredients, such as soybean meal.
Summary: The unusual genetic diversity of the Omicron strain has led to speculation about its origin. The mathematical modeling platform developed for the Stockholm Paradigm (SP) indicates strongly that it has retro-colonized humans from an unidentified animal reservoir originally infected by humans. The relationship between Omicron and all other SARS-CoV-2 variants indicates oscillations among hosts, a core part of the SP. Such oscillations result from the emergence of novel variants following colonization of new hosts, replenishing and expanding the risk space for disease emergence. The SP predicts that pathogens colonize new hosts using pre-existing capacities. Those events are thus predictable to a certain extent. Novel variants emerge after a colonization and are not predictable. This makes it imperative to take proactive measures for anticipating emerging infectious diseases (EID) and mitigating their impact. The SP suggests a policy protocol to accomplish this goal. This is the DAMA Protocol: comprising DOCUMENT to detect pathogens before they emerge in new places or colonize new hosts; ASSESS to determine risk; MONITOR to detect changes in pathogen populations that increase the risk of outbreaks; and ACT to prevent outbreaks when possible and minimize their impact when they occur.
African swine fever (ASF), considered as the most dreadful swine disease due to its very high mortality, emerged in India in 2020. The complete genome analysis of ASF viruses isolated during the first outbreaks in India showed a few unique non-synonymous mutations in MGF 369-11L, MGF 505-4R, K205R and B263R genes. Frame shiftsin the protein coding sequences were observed in DP60R, ASFV-G_ACD 00190, MGF 110-10-L- MGF110-14L fusion, MGF 360-14L and I267L genes of Indian ASFVs as compared to ASFV/Georgia/2007. Complete genome based phylogenetic analysis of p72-genotype-II viruses showed the clustering of Indian isolates with ASFV/Wuhan/2019 in a separate clade. Phylogenetic analysis of concatenated sequences of 14 open reading frames (ORF) having single nucleotide polymorphisms (SNP) showed distinct grouping of Indian ASFVs with other Asian ASFVs.Thisis the first complete genome characterization of ASF viruses isolated from domestic pigs in India. The resultsindicate that number of Tandem Repeat Sequence in the intergenic region between I73R and I329L genes, and the 14 ORFs with SNP reported in this study could be the genetic determinants to differentiate the closely related p72-genotype II viruses circulating in Asia.
Livestock trading through live animal markets are potential pathways for the introduction and spread of economically important pathogens like the African swine fever virus (ASFV) to new areas in several countries. Due to the high demand for live pigs in Nigeria both for restocking and slaughter, live pigs are sold at designated live pig markets (LPM) in the country. This involves movement of pigs over long distances. Despite, reports of ASF outbreaks following restocking of pigs bought from LPMs, there is paucity of information on the role of LPMs in the epidemiology of ASF. In this study, data and pig samples (whole blood, sera, tissue) were collected from 4 selected LPMs in Nigeria (Dawaki, Katsit, Numan & Pandam) between 2019 and 2020. Samples were analysed by polymerase chain reaction (PCR) and Enzyme-linked Immunosorbent Assay (ELISA). Four genes of ASFV positive samples were characterized to identify the circulating genotypes. Results revealed trade activities involving transportation of pigs from these selected markets to 42 major cities and towns in thirteen (13) States of Nigeria. PCR results revealed an overall ASF prevalence of 10.77% (66/613). ASFV was confirmed by PCR in all the selected LPMs with a prevalence rate of 3.13%-23.81%. The phylogeny revealed genotype I and serogroup 4 based on the p72 protein that encodes the B646L gene and the EP402R gene encoding the CD2V. While sequence analysis of CVR of B602L gene revealed 8 tetrameric repeats variants, six of which have never been reported in Nigeria. Analysis of sera samples recorded a seroprevalence of 6.9% (16/217) within the study period. Findings from this study show that LPM are hotspots and channels for transmission and continuous spread of ASFV in Nigeria. Therefore, for ASF to be controlled in Nigeria, disease surveillance and regulation at LPMs are critical.
The emergence of Zika virus (ZIKV) infection, which is unexpectedly associated with congenital defects, has prompted the development of safe and effective vaccines. The gram-positive enhancer matrix-protein anchor (GEM-PA) display system has emerged as a versatile and highly effective platform for delivering target proteins for vaccines. In this article, we developed a bacterium-like particle vaccine ZI-△-PA-GEM based on the GEM-PA system. The fusion protein ZI-△-PA, which contains the prM-E-△ protein of ZIKV (with a stem-transmembrane region deletion) and the protein anchor PA3, was expressed. The fusion protein was successfully displayed on the GEM surface, forming ZI-△-PA-GEM. Moreover, when BALB/c mice were immunized intramuscularly with ZI-△-PA-GEM combined with 201 VG and poly(I:C) adjuvants, durable ZIKV-specific IgG and protective neutralizing antibody responses were induced. Potent B cell/DC activation was also be stimulated early after immunization. Remarkably, splenocyte proliferation, the secretion of multiple cytokines, T/B cell activation and central memory T cell responses were elicited. These data indicate that ZI-△-PA-GEM is a promising bacterium-like particle vaccine candidate for ZIKV.
African swine fever (ASF) and classical swine fever (CSF) are two major transboundary animal diseases of swine with important socioeconomic consequences at farm, subnational and national level. The objective of this study was to evaluate the direct cost of outbreaks and their control at country/regional level in four countries: namely CSF in Colombia in 2015-2016, the retrospective cost of ASF in the Philippines in 2019 and in a province of Vietnam in 2020, and a hypothetical ASF scenario in one region in North Macedonia, using the newly developed Outbreak Costing Tool (OutCosT). The tool calculates the costs of 106 different items, broken down by up to four types of farms, and by who assumes the cost (whether veterinary services, farmers or other stakeholders). The total cost of CSF in Colombia was US$ 3.8 million of which 88% represented the cost of the vaccination campaign. For ASF, there were wide differences between countries: US$ 826,911 in Lao Cai (Vietnam), US$ 3,319,666 in North Macedonia and over US$ 58 million in the Philippines. While in the Philippines and Vietnam, 96-98% of the cost occurred in the affected farms, the highest expenditure in North Macedonia scenario was the movement control of the neighbouring and at-risk farms (77%). These important differences between countries depend on the spread of the disease, but also on the production systems affected and the measures applied. Apart from the financial cost, these diseases have other negative impacts, especially in the livelihoods of smallholder farms. The OutCosT tool also allows users to evaluate qualitatively other important aspects related to the epidemics, such as the impact on human health, the environment, animal welfare, socio-economic vulnerability, trading and political response. The main purpose of the OutCosT, which will become a FAO corporate tool, is to support country authorities to rapidly respond to ASF outbreaks by estimating the associated costs, and for advocacy purposes to mobilize resources at national or international levels.
NADC34-like PRRSV strains were first detected in China in 2017, with epidemic potential. In this study, the phylogenetic, epidemic, and recombinant properties of NADC34-like PRRSV in China were evaluated comprehensively. From 2020 to October 2021, 82 NADC34-like PRRSV isolates were obtained from 433 PRRSV-positive clinical samples. These strains accounted for 11.5% and 28.6% of positives in 2020 and 2021, respectively, and have spread to eight provinces. We selected 15 samples for whole-genome sequencing, revealing genome lengths of 15,009 to 15,113 nt. Phylogenetic analysis revealed that Chinese NADC34-like strains cluster with American sublineage 1.5 strains and do not form an independent branch. Recombination analysis revealed that six of fifteen complete genome sequences derived from recombination between NADC34-like and NADC30-like or HP-PRRSV; they all recombined with local strains in China, exhibiting a complex recombination pattern. Partial Nsp2 sequence alignment showed that nine of fifteen isolates have a continuous 100-aa deletion (similar to IA/2014/NADC34); other isolates have a 131-aa discontinuity deletion (similar to NADC30). Five of them also have additional amino acid deletions, all of which are reported for the first time here. In the last two years, NADC34-like PRRSV has become one of the main epidemic strains in some areas of China; it has changed significantly, its homology has decreased significantly, and it has undergone complex recombination with local Chinese strains. These results are of great significance for understanding the current epidemic situation of PRRSV in China.
Indirect costs of animal disease outbreaks often significantly exceed the direct costs. Despite their importance, indirect costs remain poorly characterised due to their complexity. In this study, we developed a framework to assess the indirect costs of a hypothetical African Swine Fever outbreak in Switzerland. We collected data through international and national stakeholder interviews, analysis of national disease control regulations and industry data. We developed a framework to capture the resulting qualitative and quantitative data, categorise the impacts of these regulations, and rank the impacts in order of importance. We then developed a spreadsheet model to calculate the indirect costs of one category of control measure for an individual group of stakeholders. We developed a decision tree model to guide the most economically favourable implementation plan for a given control measure category, under different outbreak scenarios. Our results suggest that the most important measure/impact categories were ‘Transport logistics’, ‘Consumer demand’, ‘Prevention of wild boar and domestic pig contact’ and ‘Slaughter logistics’. In our hypothetical scenario, the greatest costs associated with ‘Prevention of wild boar and domestic pig contact’ were due to assumed partial or total depopulation of pig farms in order to reduce herd size to comply with the simulated control regulations. The model also provides suggestions on the most economically favourable strategy to reduce contact between wild boar and domestic pigs in control areas depending on the duration of the outbreak. Our approach provides a new framework to integrate qualitative and quantitative data to guide disease control strategy. This method could be useful in other countries and for other diseases, including in data- and resource-poor settings, or areas with limited experience of animal disease outbreaks.
Against the backdrop of the second wave of COVID-19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole genome sequences of SARS CoV-2 circulating in India from 1 st January 2021 to 31 st August 2021. In the 43,102 SARS-CoV-2 genomic sequences analysed, we have identified 24, 260 mutations in the S protein, based on which 265 pango lineages could be categorised. The dominant lineage in most of the 28 states of India and its 8 union territories was B.1.617.2 (the delta variant). However, the states Madhya Pradesh, Jammu & Kashmir, and Punjab had B.1.1.7 (alpha variant) as the major lineage, while the Himachal Pradesh state reported B.1.36 as the dominating lineage. A detailed analysis of various domains of S protein was carried out for detecting mutations having a prevalence of >1%; 70, 18, 7, 3, 9, 4, and 1 (N=112) such mutations were observed in the N -terminal domain, receptor binding domain, C -terminal domain, fusion peptide region, heptapeptide repeat (HR)-1 domains, signal peptide domain, and transmembrane region, respectively. However, no mutations were recorded in the HR-2, and cytoplasmic domains of the S protein. Interestingly, 13.39% (N=15) of these mutations were reported to increase the infectivity and pathogenicity of the virus; 2%(N=3) were known to be vaccine breakthrough mutations; and 0.89%(N=1) were known to escape neutralising antibodies. Biological significance of 82% (N=92) of the reported mutations is yet unknown. As SARS-CoV-2 variants are emerging rapidly, it is critical to continuously monitor local viral mutations to understand national trends of virus circulation. This can tremendously help in designing better preventive regimens in the country, and avoid vaccine breakthrough infections.
Porcine Deltacoronavirus is a newly emergent enteric pathogen affecting swine farms worldwide. It has been detected in several countries in Europe, Asia and North America; yet, it has not been reported in South America. In November 2019, an enteric disease outbreak in a pig farm located in San Martin, Peru; was reported along with submission of three intestinal samples from pigs who succumbed to the disease. Samples were processed for molecular detection by qRT-PCR, viral isolation and further sequencing analysis. A taqman-based RT-PCR was performed to differentiate among the most relevant swine enteric coronaviruses described to date. All samples were positive to Porcine Deltacoronavirus with a cycle threshold (Ct) value between 9-14, revealing a high viral load, while testing negative to Porcine Epidemic diarrhea and Transmissible Gastroenteritis viruses. Following detection, viral isolation was performed using PK-15 and Vero cell lines. After 5 days of inoculation, no cytopathic effect was observed. A second blind passage allowed the observation of cytopathic effect on PK-15 cells, while it remained absent in Vero cells. A fluorescence test using an anti-N monoclonal antibody confirmed viral replication. One sample was processed for whole genome sequencing (NGS). In short, raw reads were imported into CLC genomics and assembled de novo. Out of 479k reads generated from the sample, 436k assembled into a 25501 bp contig which was 99.5% identical to a reference Porcine Deltacoronavirus strain from US within the North American phylogroup. Yet, there are relevant differences at the nucleotide and amino acid levels compared to previously described Porcine Deltacoronavirus strains. Altogether, our findings represent the first report of Porcine Deltacoronavirus in South America, its genomic characterization, which provides information of its evolutionary origin. Thus, this study offers new insights into the molecular epidemiology of Porcine Deltacoronavirus infections in the swine industry.
Edwardsiella ictaluri is an emerging bacterial pathogen that affects farmed tilapia ( Oreochromis spp.). This study reports the arrival, establishment, and widespread findings of E. ictaluri in farmed tilapia in Vietnam. Among 26 disease outbreaks from 9 provinces in Northern Vietnam during 2019–2021, 19 outbreaks originated from imported seeds, while outbreaks in seven farms were from domestic sources. Clinically sick fish showed the appearance of numerous white spots in visceral organs, and accumulative mortality reached 30%–65%. Twenty-six representative bacterial isolates recovered from 26 disease outbreaks were identified as E. ictaluri based on a combination of phenotypic tests, genus- and species-specific polymerase chain reaction assays, 16S rRNA and gyrB sequencing, and phylogenetic analysis. All isolates harbored the same virulence gene profiles esrC +, evpC +, ureA-C +, eseI-, escD-, and virD4-. Antimicrobial susceptibility tests revealed that 80.8%–100% of isolates were multidrug resistant, with resistance to 4–8 antimicrobials in the groups of penicillin, macrolides, sulfonamides, amphenicols, and glycopeptides. The experimental challenge successfully induced disease that mimicked natural infection. The median lethal doses (LD 50) of the tested isolates (n = 4) were 42–61 colony forming units/fish, indicating their extremely high virulence. This emerging pathogen is established and has spread to various geographical locations, causing serious impacts on farmed tilapia in northern Vietnam. It is likely that this pathogen will continue to spread through contaminated stocks (both imported and domestic sources) and persist. Thus, increased awareness, combined with biosecurity measures and emergent vaccination programs is essential to mitigate the negative impact of this emerging disease on the tilapia farming industry.
In the last decades fungal pathogens are causing devastating population declines across a broad range of taxa. A newly emerging fungal disease, sea turtle egg fusariosis, caused by members of the Fusarium solani species complex (FSSC), has been reported to be responsible for hatching failure in sea turtles around the world. However, this has not been reported in other non-marine turtle species. Herein we report high hatching failure from eggs symptomatic of fusariosis in the yellow-spotted Amazon river turtle ( Podocnemis unifilis), inhabiting a pristine environment in the Ecuadorian Amazon. We assessed hatching success from eggs symptomatic and asymptomatic of fusariosis ( n = 680 eggs), tested for Fusarium infection by PCR amplifying the TEF-1α gene (n= 68 turtle internal egg swab samples) and sequenced eight amplicons for screening of FSSC membership on an Illumina Miseq. Hatchability was 72% for asymptomatic eggs, whilst only 8% of symptomatic eggs hatched. Eight percent of asymptomatic and 58% of symptomatic eggs tested positive for Fusarium spp. and sequencing revealed that nine sequence variants from three asymptomatic and four symptomatic eggs corresponded to F. keratoplasticum, F. solani and F. falciforme, the three major FSSC pathogens already reported in sea turtle egg fusariosis. Our study therefore suggests that observed hatching failure of eggs showing symptoms of fusariosis is at least partially caused by Fusarium pathogens within FSSC in a freshwater turtle. This report highlights that fusariosis is more widespread among the Testudines order than previously reported and is not limited to sea environments, which is of particular conservation concern.
Toxoplasmosis is a zoonotic disease caused by the ubiquitous coccidia Toxoplasma gondii. Rodents play an important role in maintaining its life cycle, as they are one of the main diet sources for felids (wild and domestic), the unique definitive hosts. However, reports of toxoplasmosis in porcupines (Rodentia Order) are uncommon, with gaps concerning its pathophysiology. South America is the continent with the greatest genetic diversity of rodents and T. gondii. A free-ranging hairy dwarf porcupine was admitted to a wildlife rescue center with a history of trauma. During rehabilitation, the animal presented neurological symptoms (sporadic episodes of hind limbs paresis) and died five months later. The main findings during necropsy were brain congestion and severe incisor overgrowth associated with maxillary perforation. The histopathological exam showed moderate encephalitis, with variable-sized round cysts, positive for PAS stain and immunohistochemistry for T. gondii. Additionally, two cysts were observed in the medulla of the adrenal gland. Molecular techniques were performed to characterize the parasite load by qPCR (Cq=30) and the genotype by PCR-RFLP with 11 markers, which revealed a new genotype. This case adds to the body of knowledge in comparative pathology of Neotropical Rodentia and reports a new genotype circulating in South America.
For the first time we built a correlative model for predicting the distribution of H. marginatum, one of the main vector of Crimean-Congo Haemorrhagic fever virus (CCHFV), at high resolution in a recently colonized area, namely south of France. Field tick collections were conducted on horses from 2016 to 2021 in 14 French southern departments, which resulted in a first map of H. marginatum on the national territory. Such updated presence/absence data, as well as the mean number of H. marginatum per examined animal (mean parasitic load) as a proxy of the tick abundance, were correlated to multiple parameters that described the climate and habitats characterizing each collection site, as well as movements of horses as a possible source of tick diffusion and new establishment. Our model highlighted the importance of warm temperatures all along the year, as well as dry conditions during summer and moderate annual humidity for the establishment of H. marginatum. A predominance of open natural habitats in the environment was also identified as a supporting factor, in opposition to artificial and humid habitats that were determined as unsuitable. Based on this model, we predicted the current suitable areas for the establishment of the tick H. marginatum in South of France, with a relatively good accuracy using internal and external validation methods. Concerning tick abundance, some correlative relationships were similar than in the occurrence model but the type of horse movements were also pointed out as an important factor explaining the mean parasitic load, leading to differential exposure to ticks. The limitations of estimating and modelling H. marginatum abundance in a correlative model are discussed.
During the European emergence of Schmallenberg virus (SBV) in 2011, examination of Culicoides spp. showed that SBV infected midges were present across Denmark. However, SBV associated malformations in ruminant species have not been reported in Denmark. In April 2021, seven calves with severe congenital generalized arthrogryposis and reduced body weight originating from a narrow region of the Jutlandic peninsula were submitted for examination. Analysis of fetal brain tissue for SBV viral RNA and pleural effusion for fetal anti-SBV antibodies identified SBV as the cause of the congenital syndrome. Backwards calculation from the calving dates indicated the occurrence of an unnoticed emergence of SBV in Denmark from early August 2020 and during the late summer and autumn. As SBV associated malformations may lead to dystocia urging for fetotomy or Cesarean section, veterinarians performing obstetric intervention are first line personnel in recognition of SBV emergence in domestic ruminants.
CDC estimates 1 million dogs are imported into the United States annually. With the movement of large numbers of animals into the United States the risk of disease importation is a concern, especially for emerging diseases. Dogs that arrive to the United States ill or dead are investigated by public health authorities to ensure dogs are not infected with diseases of concern (such as rabies). We identified factors associated with illness and death in imported dogs and estimated the initial investigation cost to public health authorities. Dog importation data from the CDC’s Quarantine Activity Reporting System were reviewed from 2010–2018. The date of entry, country of origin, port of entry, transportation method, and breed were extracted to examine factors associated with illness and death in dogs during international travel. Costs for public health investigations were estimated from data collected by the Bureau of Labor Statistics and Office of Personal Management. Death or illness was more likely to occur in brachycephalic breeds (aOR=3.88, 95%CI 2.74–5.51). Transportation of dogs via cargo (aOR=2.41, 95%CI 1.57–3.70) or as checked baggage (aOR=5.74, 95%CI 3.65–9.03) were also associated with death or illness. On average, 19 dog illnesses or deaths were reported annually from 2010–2018. The estimated annual cost to public health authorities to conduct initial public health assessments ranged from $2,071–$104,648. Current regulations do not provide adequate resources or mechanisms to monitor the rates of morbidity and mortality of imported dogs. There are growing attempts to assess animal welfare and communicable disease importation risks; however, responsibility for dogs’ health and well-being is overseen by multiple agencies. A joint federal agency approach to identify interventions that reduce dog morbidity and mortality during flights while continuing to protect U.S. borders from public health and foreign animal disease threats could be beneficial.