Cryptosporidium parvum is a major zoonotic pathogen responsible for outbreaks of severe diarrhea in humans and calves. Almost all investigations of cryptosporidiosis outbreaks caused by C. parvum have focused on its IIa subtype family in industrialized nations. From December 2018 to April 2019, approximately 200 neonatal calves on a large cattle farm in Hebei Province, China presented watery diarrhea and over 40 died. To investigate the cause of the outbreak, 179 and 223 fecal specimens were collected during and after the diarrhea outbreak from the farm, including 40 and 56 from neonatal calves, respectively. Among them, 18 fecal specimens from ill calves during the peak of the outbreak were analyzed for four common enteric pathogens using enzymatic immunoassay (EIA), 75 additional specimens from neonatal calves were tested for rotavirus by EIA, and all specimens were analyzed for Cryptosporidium spp. using PCR and sequencing techniques. Of the initial 18 specimens from sick calves, ten were positive for C. parvum, five for rotavirus, and one for coronavirus. The overall prevalence of rotavirus in neonatal calves was 20.0% (15/75), with no significant differences during (21.6% or 8/37) and after (18.4% or 7/38) the outbreak. In contrast, the prevalence of C. parvum was significantly higher during the outbreak (60.0%, 24/40) than after the outbreak (30.4%, 17/56). C. parvum infection was associated with the occurrence of watery diarrhea in neonatal calves (odds ratio = 11.19), while no association was observed between C. bovis infection and diarrhea. All C. parvum isolates were identified as subtype IIdA20G1. Older animals were infected with C. bovis, C. ryanae, C. occultus, and C. andersoni. This is one of the few reports of outbreaks of severe diarrhea caused by C. parvum IId subtypes in calves. More attention should be directed toward preventing the dissemination of C. parvum in China.

African swine fever (ASF) has spread across many countries in Europe since the introduction into Georgia in 2007. We report here on the first cases of ASF in wild boar detected in Germany close to the border with Poland. In addition to the constant risk of ASF virus (ASFV) spread through human activities, movements of infected wild boar also represent a route of introduction. Since ASF emerged in Western Poland in November 2019, surveillance efforts, in particular examination of wild boar found dead, were intensified in the regions of Germany bordering with Poland. The first case of ASF in wild boar in Germany was therefore detected by passive surveillance and confirmed on 10th September 2020. By 24th September 2020, 32 cases were recorded. Testing of samples from tissues of carcasses in different stages of decomposition yielded cycle threshold values from 18 to 36 in the OIE-recommended PCR which were comparable between the regional and national reference laboratory. Blood swabs yielded reliable results, indicating that the method is suitable also under outbreak conditions. Phylogenetic analysis of the ASFV whole-genome sequence generated from material of the first carcass detected in Germany, revealed that it groups with ASFV genotype II including all sequences from Eastern Europe, Asia and Belgium. However, some genetic markers including a 14 bp tandem repeat duplication in the O174L gene were confirmed that have so far been detected only in sequences from Poland (including Western Poland). Epidemiological investigations that include estimated postmortem intervals of wild boar carcasses of infected animals suggest that ASFV had been introduced into Germany in the first half of July 2020 or even earlier.

Porcine circovirus 4 (PCV4), a novel and unclassified member of the genus Circovirus, was first reported in China in 2019. Aimed at providing more evidence about the active circulation of PCV4, this study screened 335 pooled internal organs and detected the virus (i) at the rates of 3.28%, (ii) from both clinical healthy and clinical sick pigs of various age groups, and (iii) in six out of nice provinces of Korea. The complete genomic sequence of a Korean PCV4 strain (E115) was 1,770 nucleotides in length and had 98.5% to 98.9% identity to three PCV4 strains available at GenBank up to date. Utilizing a set of bioinformatic programs, it was revealed that the Korean PCV4 strain contained several genomic features of (i) a palindrome stem-loop structure with conserved nonanucleotide, (ii) packed overlapping ORFs oriented in different directions, and (iii) two intergenic regions in between genes encoding putative replication- associated protein (Rep) and capsid (Cap) proteins. This study also predicted the presence of essential elements known so far for the replication of circoviruses, for example, the origin of DNA replication, endonuclease and helicase domains of Rep, the nuclear localization signal on the putative Cap protein. Finally, based on the phylogeny inferred from sequences of the putative Rep protein, it was suggested that PCV4 belong to genus Circovirus of family Circoviridae and losely related to three previous known porcine circoviruses of PCV1, PCV2 and PCV3.

Animal tuberculosis (TB) is a widespread infectious disease caused by the Mycobacterium tuberculosis bacteria belonging to the Mycobacterium tuberculosis complex (MTC) that can persist in reservoir wildlife hosts. Wild boar (sus scrofa) are a key reservoir for MTC and an increasing trend in wild boar density is expected to lead to an increase in TB prevalence with spill-over to livestock. MTC infection is presently controlled through a variety of strategies, including culling. African swine fever (ASF) is a virulent, viral infection which affects wild boar and is spreading across Eurasia and Oceania. ASF infection leads to near 100% mortality at the individual level, can cause a dramatic decrease in population density and may therefore lead to TB control. In this study we develop a mathematical model to examine the impact of ASF introduction into a wild boar population that supports endemic TB. Our model results indicate that an ASF infection will reduce wild boar population density and lead to a decrease in the prevalence of TB. If ASF persists in the local host population the model predicts the long-term decline of TB prevalence in wild boar. If ASF is eradicated, or fades-out in the local host population, the model predicts a slower recovery of TB prevalence in comparison to wild boar density after an ASF epidemic. This may open a window of opportunity to apply TB management to maintain low TB prevalence.

In May 2020, Deng et al. (2020) published their article providing the evidence that no SARS-CoV-2-specific antibodies were detected in 1,914 samples which excluded the possibility of 35 animal species as intermediate host for SARS-CoV-2 in Transboundary and Emerging Diseases. In order to ensure the stability of SARS-CoV-2-specific antibodies in storage serum samples, we strongly suggest that standard serum banks should be established.

This study reports the development of multiplex real-time PCR assays for differential detection of capripoxvirus (CaPV), parapoxvirus (PaPV), and foot-and-mouth disease virus (FMDV) in sheep, goats and cattle. Three multiplex assays were developed, a capripox (CaP) rule-out assay for simultaneous detection and differentiation of CaPV and PaPV, a FMD rule-out assay for simultaneous detection and differentiation of FMDV and PaPV, and a FMD/CaP rule-out assay for simultaneous detection and differentiation of CaPV, PaPV and FMDV. All multiplex assays included -actin gene ACTB as an internal positive control to monitor PCR inhibition and accuracy of nucleic acid extractions. The optimized assays were highly specific to the target viruses (CaPV, PaPV, and FMDV) with no cross-reactivity against other differential viruses. Using positive control plasmids as template, the limit of detection (LOD) of the multiplex assays were estimated as 2 (CaPV), 7 (PaPV), and 15 (FMDV) copies per assay. The amplification efficiency (AE) and correlation co-efficient (R2), estimated from the standard curves (Ct vs. log10 template dilution), were 94-106% and >0.99, respectively, for CaP and FMD rule-out assays, 96-116% (AE) and >0.98 (R2), respectively, for CaP/FMD rule-out assays and 91-102% and >0.99, respectively, for the corresponding singleplex assays. The diagnostic sensitivity (DSe) of the multiplex assays was assessed on 35 (CaPV), 36 (PaPV) and 39 (FMDV) clinical specimens collected from experimentally (CaPV and FMDV) and naturally (PaPV) infected animals, and all tested positive (DSe 100%) except two FMDV specimens that were tested negative (37/39; DSe 95%). The newly developed multiplex assays offer a valuable tool for differential detection of clinically indistinguishable CaPV, PaPV, and FMDV in suspected animals and animals with mixed infections.

Recently, a wound dressing formulation, (Tri-Solfen®, Medical Ethics Pty Ltd, Australia; TS) registered for use in ruminant husbandry in Australia, was registered for Foot-and-Mouth Disease (FMD) therapy in large ruminants in Laos, following clinical observations of improved welfare and healing following treatment of FMD lesions. In November 2019, an FMD outbreak in Cameroon provided an opportunity for a field trial, comparing clinical responses and recoveries to treatments on a sample of cattle (n = 36) comprising three equal groups of animals (n = 12), comparing responses to three treatments:(i) the application to lesions of TS, (ii) the administration of parenteral oxytetraycline commonly used for FMD in Cameroon; and (iii) an untreated control group (C). Appetite scores, lesion healing scores, and changes in dimensions of lesions, were recorded over a 15-day study period. Cattle treated with TS achieved both superior appetite and lesion healing scores with more rapid reduction in dimensions of lesions than other groups. Farmer observations indicated the TS treatment group had a more rapid return to eating with cessation of excessive salivation, and more rapid return of mobility (walking) with absence of overt lameness. The findings indicate that although mortality is usually low in FMD outbreaks, the disease is a debilitating and painful disorder with negative animal welfare impacts that should be addressed. All farmers expressed their desire that the product be made available for use in their region and modelling indicates that TS therapy imposes no additional financial burden on farmers, with the treatment likely to be provided at a similar or reduced cost to current treatment choices. As use of antibiotics for treatment of a viral disease potentially increases pressures for development of antimicrobial resistance and residues in the food chain, TS as an alternative non-antimicrobial therapy should be promoted for wider use in FMD outbreaks.

Infection with African swine fever virus (ASFV) causes a highly lethal hemorrhagic disease in domestic and Eurasian wild pigs. Thus, it is a major threat to pig populations worldwide and a cause of substantial economic losses. Recently, less virulent ASFV strains emerged naturally, which showed higher experimental virulence in wild boar than in domestic pigs. The reason for this difference in disease progression and outcome is unclear but likely involves different immunological responses. Unfortunately, besides the importance of CD8α+ lymphocytes, little is known about the immune responses against ASFV in suids. Against this background, we used a multicolor flow cytometry platform to investigate the T-cell responses in wild boar and domestic pigs after infection with the moderately virulent ASFV strain “Estonia2014” in two independent trials. CD4–/CD8α+ and CD4+/CD8α+ αβ T-cell frequencies increased in both subspecies in various tissues, but CD8α+ γδ T cells differentiated and responded in wild boar only. Proliferation in CD8α+ T cells was found 10 days post infectionem only. Frequencies of T-bet+ T cells increased in wild boar but not in domestic pigs. Of note, we found a considerable loss of perforin expression in cytotoxic T cells, 5 and 7 dpi. Both subspecies established a regulatory T-cell response 10 dpi. In domestic pigs, we show increasing levels of ICOS+ and CD8α+ invariant Natural Killer T cells. These disparities in T-cell responses might explain some of the differences in disease progression in wild boar and domestic pigs and should pave the way for future studies.

Peste des Petits Ruminants (PPR) is a highly contagious viral disease that mainly affects goats and sheep in Asia, Africa and the Middle East. The PPR virus (PPRV) can be classified into four genetically distinct lineages (I, II, III, and IV). All have been historically present in Africa, except the Asian lineage IV that has been spreading across the globe and Africa for the last decades. Previous studies have identified the presence of the lineage IV in Nigeria since 2010. In this study, samples were taken from 268 small ruminants with PPR symptoms across Nigeria in 2017-2018 to provide an update on the distribution and genetic diversity of the lineage IV in the country. Sequence from a portion of the PPRV nucleoprotein (N) gene could be obtained from 72 samples, and all but one belonged to lineage IV. Phylogenetic analysis identified at least 5 lineage IV sub-clusters in Nigeria, re-grouping samples across multiple regions. Our results suggest an extensive endemic circulation of PPRV lineage IV across Nigeria and across borders with neighbouring countries, highlighting the difficulty of the control of this disease in the region.

The variety and widespread of coronavirus in natural reservoir animals is likely to cause epidemics via interspecific transmission, which has attracted much attention due to frequent coronavirus epidemics in recent decades. Birds are natural reservoir of various viruses, but the existence of coronaviruses in birds, especially in central China, has been barely studied. The majority of bird coronaviruses belongs to the genus of Deltacoronavirus. To explore the diversity of bird deltacoronaviruses in central China, we tested fecal samples from 415 birds in Hunan Province, China. As the result, we have identified four novel deltacoronavirus stains (HNU1-1, HNU1-2, HNU2 and HNU3) with divergent S genes abounding in common magpies in mainland China. Comparative genomic analysis on the four complete viral genomic sequences showed that these novel magpie deltacoronaviruses containing three different S genes homologous to those of deltacoronaviruses discovered in swine and sparrows. The S genes of HNU1-1 and HNU1-2 showed 93.8% amino acid sequence identities to that of thrush coronavirus HKU12, and the S genes of HNU2 and HNU3 showed 71.1% amino acid sequence identities to White-eye coronavirus HKU16 and sparrow coronavirus HKU17, respectively. Recombination analysis showed that frequent recombination events of the S genes occurred among different deltacoronavirus strains. Two novel putative cleavage sites at the junctions between nonstructural proteins in the HNU CoVs were found. Bayesian phylogeographic analysis showed that the south coast of China might have played a key role in seeding the bird deltacoronavirus epidemics. The results demonstrated that common magpie in China carries diverse deltacoronaviruses with novel genomic features, which indicate an important source of environmental coronaviruses in the biosphere closed to human communities. These findings may contribute to prevention and control the potential coronavirus epidemics.

African swine fever virus (ASFV) can survive in soy-based products for 30 days with T ½ ranging from 9.6-12.9 days in soybean meals and soy oil cake. As the US imports soy-based products from several ASFV-positive countries, knowledge of the type and quantity of these specific imports, and their ports of entry (POE), is necessary information to manage risk. Using the data from the International Trade Commission Harmonized Tariff Schedule website in conjunction with pivot tables, we analyzed imports across air, land, and sea POE of soy-based products from 43 ASFV-positive countries to the US during 2018 and 2019. In 2018, 104,366 metric tons (MT) of soy-based products, specifically conventional and organic soybean meal, soybeans, soy oil cake and soy oil were imported from these countries into the US via seaports only. The two largest suppliers were China (52.7 %, 55,034 MT) and the Ukraine (42.9%, 44,775 MT). In 2019, 73,331 MT entered the US and 54.7% (40,143 MT) came from the Ukraine and 8.4% (6,182 MT) from China. Regarding POE, 80.9% to 83.2% of soy-based imports from China entered the US at the seaports of San Francisco, CA and Seattle, WA, while 89.4% to 100% entered from the Ukraine via the seaports of New Orleans, LA and Charlotte, NC. Analysis of five-year trends (2015 to 2019) of the volume of soy imports from China indicated reduction over time (with a noticeably sharp decrease between 2018 and 2019), and seaport utilization was consistent. In contrast, volume remained high for Ukrainian soy imports, and seaport utilization was inconsistent. Overall, this exercise introduced a new approach to collect objective data on an important risk factor, providing researchers, government officials, and industry stakeholders a means to objectively identify and quantify potential channels of foreign animal disease entry into the US.

Myxomatosis is an emergent disease in Iberian hare, having been considered a rabbit disease for decades. Genome sequencing of the strains obtained from affected Iberian hares showed to be distinct from the classical strains that circulated in rabbits since the virus introduction in Europe, in 1952. The main genomic difference concerns the presence of an additional 2.8Kb region disrupting the M009L gene and adding a set of genes with homology to the MYXV genes M060R, M061, M064 and M065R originated in poxviruses. After the emergence of this recombinant virus (MYXV-Tol or ha-MYXV), in the summer of 2019, the recombinant MYXV was not detected in rabbit surveys suggesting apparent species segregation with the MYXV classic strains persistently circulating in rabbits. Recently, a group of six unvaccinated European rabbits (Oryctolagus cuniculus cuniculus) from a backyard rabbitry in the South Portugal, developed signs of myxomatosis (anorexia, dyspnoea, oedema of eyelids, head, ears, external genitals and anus, and skin myxomas in the base of the ears), five of them dying within 24-48 hours of symptoms onset. Molecular analysis revealed that only the recombinant myxoma virus was present. This is the first documented report of a recombinant myxoma virus (ha-MYXV)  in farm rabbits associated with high mortality, which aggravates the concern for the future of the Iberian hare and wild rabbits and the safety of the rabbit industry against which the existing vaccines may not be fully protective.

Beijing genotype Mycobacterium tuberculosis strains associate with increased virulence, resistance, and/or higher transmission rates. This study describes a specific Beijing strain predominantly identified in the Panamanian province of Colon with one of the highest incidence of tuberculosis in the country. Retrospective Mycobacterial Interspersed Repetitive-Unit/Variable-Number of Tandem Repeats analysis of 42 isolates collected between January-August 2018, allowed to identify a cluster (Beijing A) with 17 (40.5%) Beijing isolates. Subsequent prospective strain-specific PCR based surveillance from September 2019 to March 2020, confirmed the predominance of the Beijing A strain (44.1%) in this province. Whole genome sequencing revealed higher-than-expected diversity within the cluster, suggesting long-term prevalence of this strain and low number of cases caused by recent transmission. The Beijing A strain belongs to the Asian African 3 (Bmyc13, L2.2.5) branch of the modern Beijing sublineage, with their closest isolates corresponding to cases from Vietnam, probably introduced in Panama between 2000 and 2012.

There is some evidence that West Nile virus (WNV), which causes encephalomyelitis in equids, is an emerging disease in Europe. The aim of this study was to perform a systematic review and meta-analysis to determine the seroprevalence of West Nile virus in equids in European countries between 2001 and 2018. Two electronic databases, PubMed and Scopus, were searched for relevant publications published from 2001 to 2018 using predetermined keywords. A total of 1484 papers was initially found. After applying the eligibility criteria, 39 papers were finally included in the systematic review. Analysis of 28,089 equids from 16 European countries revealed a pooled seroprevalence of 8% (95% CI 5–12%, P<0.001, I2 = 99.3%) in Europe. The pooled seroprevalence was slightly higher in Mediterranean basin countries than other countries and when calculated for samples collected between 2001 and 2009 compared to 2010 to 2018. Differences in study design (e.g. sampling associated with recent outbreaks of WNV) contributed to a high degree of variability among studies. Further studies with harmonized study design and reporting of the results are recommended to better estimate and monitor European seroprevalence of West Nile virus in equids.

Bovine viral diarrhea virus (BVDV) is a major cause of economic loss in the cattle industry, worldwide. Infection results in reduce productive performance, growth retardation, reduced milk production, and increased susceptibility to other diseases leading to early culling of animals. There are two main measures used to control the spread of BVDV: the elimination of persistently infected (PI) animals and vaccination. Currently, modified live or inactivated vaccines are used in BVDV vaccination programs, but there are safety risks or insufficient protection, respectively, with these vaccines. Here we report the development and efficacy of the first targeted subunit vaccine against BVDV. The core of the vaccine is a fusion of the BVDV structural protein, E2, to a single-chain antibody, APCH, together termed, APCH-E2. The APCH antibody targets the E2 antigen to the major histocompatibility type II molecule (MHC-II) present on antigen-presenting cells. Industrial production of the vaccine is carried out using the baculovirus expression vector system (BEVS) using single-use manufacturing technologies. This new subunit vaccine induces strong BVDV-specific neutralizing antibodies in guinea pigs and cattle. Importantly, in cattle with low levels of natural BVDV-specific neutralizing antibodies, the vaccine induced strong neutralizing antibody levels to above the protective threshold, as determined by a competition ELISA. The APCH-E2 vaccine induced a rapid and sustained neutralizing antibody response compared to a conventional vaccine in cattle. The development of this subunit targeted vaccine provides cattle and dairy producers with an inexpensive, easily administered, safe, and efficacious BVDV vaccine.

The emergence of mobile mcr genes mediating resistance to colistin is a critical public health issue that has hindered the treatment of serious infections caused by multidrug-resistant pathogens in humans and other animals. We report the emergence of the mcr-9.1 gene in a polymyxin-resistant extended-spectrum β-lactamase (ESBL)-producing Enterobacter kobei infecting a free-living Franciscana dolphin (Pontoporia blainvillei), threatened with extinction in South America. Genomic analysis confirmed a wide resistome with additional presence of genes conferring resistance to clinically relevant β-lactam [blaCTX-M-15, blaACT-9, blaOXA-1 and blaTEM-1B], aminoglycoside [aac(3)-IIa, aadA1, aph(3’‘)-Ib and aph(6)-Id], trimethoprim [dfrA14], tetracycline [tetA], quinolone [aac(6’)-Ib-cr and qnrB1], fosfomycin [fosA], sulphonamide [sul2], and phenicol [catA1 and catB3] antibiotics. The identification of mcr-9.1 in a CTX-M-15-producing pathogen infecting a critically endangered animal is worryingly, due to the restricted therapeutic options, and should be interpreted as a sign of further spread of critical-priority pathogens and their resistance genes in threatened ecosystems.

The raw case fatality rate (CFR, reported number of COVID-19 deaths divided by the number of cases) is a useful indicator to quantify the severity or treatment efficacy in a locality. In many countries, the pandemic showed a two-wave pattern now, namely the daily reported cases once reached a low level and now went up. To our knowledge, no study has compared the CFR for the two waves. In this work, we report that in 53 countries or regions with the highest deaths, the CFR is reduced in 43 countries or regions in the on-going second wave. We discussed the possible reasons. Also, we compare the two-wave pattern of COVID-19 with the weekly influenza positive tests. The influenza activity in pre-pandemic era provided an indicator for climate in a country, since it is well-known that influenza is driven by weather. The sharp drop in 2020 influenza activity is an indicator of the effects of social distancing.

The current COVID-19 pandemic offers a unique opportunity to examine the utility of Internet search data in disease modelling across multiple countries. Google Trends data (GTD) indicating the volume of Internet searching on ‘Coronavirus’ were obtained for a range of European countries along with corresponding incident case numbers. Significant positive correlations between GTD with incident case numbers occurred across European countries, with the strongest correlations being obtained using contemporaneous data for most countries. GTD was then integrated into a lag distributed model; this improved model quality for both the increasing and decreasing epidemic phases.