Whole-genome-based phylogeny of African swine fever virus

Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning

In 2007, an outbreak of African swine fever (ASF), a deadly disease of domestic swine and wild boar caused by the African swine fever virus (ASFV), occurred in Georgia and has since spread globally. Historically, ASFV was classified into 25 different genotypes. However, a newly proposed system recategorized all ASFV isolates into 6 genotypes exclusively using the predicted protein sequences of p72. However, ASFV has a large genome that encodes between 150-200 genes, and classifications using a single gene are insufficient and misleading, as strains encoding an identical p72 often have significant mutations in other areas of the genome. We present here a new classification of ASFV based on comparisons performed considering the entire encoded proteome. A curated database consisting of the protein sequences predicted to be encoded by 220 reannotated ASFV genomes was analyzed for similarity between homologous protein sequences. Weights were applied to the protein identity matrices and averaged to generate a genome-genome identity matrix that was then analyzed by an unsupervised machine learning algorithm, DBSCAN, to separate the genomes into distinct clusters. We conclude that all available ASFV genomes can be classified into 7 distinct biotypes.

Target capture sequencing for the first Nigerian genotype I ASFV genome

African swine fever (ASF) is a contagious viral disease that affects domestic pigs and wild boars, causing significant economic losses globally. After the first Nigerian outbreak in 1997, there have been frequent reports of ASF in pig-producing regions in the country. To facilitate control, it is important to understand the genotype and phylogenetic relationship of ASF viruses (ASFVs). Recent genetic analysis of Nigerian ASFV isolates has revealed the presence of both genotypes I and II; this is based on analysis of a few selected genes. Phylogenetic analysis of ASFV whole genomes highlights virus origins and evolution in greater depth. However, there is currently no information on the ASFV genome from Nigerian isolates. Two ASFV-positive samples were detected during a random survey of 150 Nigerian indigenous pig samples collected in 2016. We assembled near-complete genomes of the two ASFV-positive samples using in-solution hybrid capture sequencing. The genome-wide phylogenetic tree assigned these two genomes into p72 genotype I, particularly close to the virulent Benin 97/1 strain. The two ASFVs share 99.94 and 99.92 % genomic sequence identity to Benin97/1. This provides insight into the origin and relationship of ASFV strains from Nigeria and Italy. The study reports for the first time the determination of near-complete genomes of ASFV using in-solution hybrid capture sequencing, which represents an important advance in understanding the global evolutionary landscape of ASFVs.

African Swine Fever Virus Gene B117L Encodes a Small Protein Endowed with Low-pH-Dependent Membrane Permeabilizing Activity

African swine fever virus (ASFV) is causing a devastating pandemic in domestic and wild swine in Central Europe to East Asia, resulting in economic losses for the swine industry. The virus contains a large double-stranded DNA genome that contains more than 150 genes, most with no experimentally characterized function. In this study, we evaluate the potential function of the product of ASFV gene B117L, a 115-amino-acid integral membrane protein transcribed at late times during the virus replication cycle and showing no homology to any previously published protein. Hydrophobicity distribution along B117L confirmed the presence of a single transmembrane helix, which, in combination with flanking amphipathic sequences, composes a potential membrane-associated C-terminal domain of ca. 50 amino acids. Ectopic transient cell expression of the B117L gene as a green fluorescent protein (GFP) fusion protein revealed the colocalization with markers of the endoplasmic reticulum (ER). Intracellular localization of various B117L constructs also displayed a pattern for the formation of organized smooth ER (OSER) structures compatible with the presence of a single transmembrane helix with a cytoplasmic carboxy terminus. Using partially overlapping peptides, we further demonstrated that the B117L transmembrane helix has the capacity to establish spores and ion channels in membranes at low pH. Furthermore, our evolutionary analysis showed the high conservation of the transmembrane domain during the evolution of the B117L gene, indicating that the integrity of this domain is preserved by the action of the purifying selection. Collectively our data support a viroporin-like assistant role for the B117L gene-encoded product in ASFV entry. IMPORTANCE ASFV is responsible for an extensively distributed pandemic causing important economic losses in the pork industry in Eurasia. The development of countermeasures is partially limited by the insufficient knowledge regarding the function of the majority of the more than 150 genes present on the virus genome. Here, we provide data regarding the functional experimental evaluation of a previously uncharacterized ASFV gene, B117L. Our data suggest that the B117L gene encodes a small membrane protein that assists in the permeabilization of the ER-derived envelope during ASFV infection.

Antimicrobial resistance and molecular typing of Salmonella in the chicken production chain in Hubei Province, China

Salmonella is a significant foodborne zoonotic pathogen that endangers both human and animal health. The goal of this research is to gain a preliminary understanding of Salmonella contamination and antimicrobial resistance in the chicken production chain in Hubei Province, China. 1149 animal and environmental samples were collected from chicken farms, slaughterhouses, and retail markets in six cities across Hubei Province in China from 2019 to 2020, yielding Salmonella isolation rates of 4.68% (28/598), 12.21% (47/385), and 9.64% (16/166), respectively. Seventeen distinct serotypes were detected among 53 non-clonal Salmonella strains, of which Meleagridis (26.42%, 14/53) was the dominant serotype. Almost half of the strains (49.06%, 26/53) were multi-drug resistant (MDR). Whole-genome sequencing (WGS) showed that 10 resistance genes (tetA, blaTEM, parC, qnrS1, floR, aac(6′)-Iy, aph(6)-Id, aph(3″)-Ib, aac(6′)-Iaa and sul2) and 7 categories of virulence genes were present in all three links in 22 non-clonal dominant serotype strains. It was shown that Salmonella in the chicken production chain in Hubei Province had a high resistance rate to Tetracycline (TET, 73.58%), Ofloxacin (OFL, 69.81%), Florfenicol (FFC, 60.38%) and Ampicillin (AMP, 39.62%) which was consistent with the widespread use of these drugs in the husbandry industry in China. Salmonella ST types determined by MLST and serotypes determined by WGS had a one-to-one correlation. Minimum spanning tree analysis revealed that there was cross contamination of Salmonella in farms and slaughterhouses, slaughterhouses and markets, animal samples and environmental samples. This work provides useful information for the prevention and control of contamination and antimicrobial resistance of Salmonella in the chicken production chain, as well as demonstrating the dependable role of WGS in Salmonella molecular typing.

In vitro and in vivo antiviral activity of nucleoside analogue cHPMPC against African swine fever virus replication

African swine fever virus (ASFV) causes a haemorrhagic disease affecting wild boar and domestic pigs which can result in morbidity and fatality rates of up to 100%. ASFV is a large double-stranded DNA virus which replicates predominantly in the cell cytoplasm and codes for its replication and transcription machinery. No vaccine is widely available and control depends on early detection, culling of infected herds and adherence to biosecurity measures. In this study the small molecule nucleoside analogue, cyclic cidofovir (cHPMPC), was evaluated for its ability to inhibit replication of four different ASFV genotypes in primary porcine macrophages. Time of addition studies demonstrated that cHPMPC effectively inhibits ASFV replication and late gene expression when added pre-infection or early post-infection but not when added at late times, suggesting the drug target may be the virus DNA polymerase, or the RNA polymerase involved in late transcription. Oral administration of cHPMPC delayed onset of clinical signs and significantly reduced viral titres in blood and tissues of treated pigs. These results indicate that cHPMPC is a promising compound for further development to control ASFV outbreaks.

Research progress on the proteins involved in African swine fever virus infection and replication

African swine fever (ASF) is an acute, hemorrhagic and highly contagious infectious disease caused by African swine fever virus (ASFV), which infects domestic pigs or wild boars. It is characterized by short course of disease, high fever and hemorrhagic lesions, with mortality of up to 100% from acute infection. Up to now, the lack of commercial vaccines and effective drugs has seriously threatened the healthy economic development of the global pig industry. ASFV is a double-stranded DNA virus and genome varies between about 170-194 kb, which encodes 150-200 viral proteins, including 68 structural proteins and more than 100 non-structural proteins. In recent years, although the research on structure and function of ASFV-encoded proteins has been deepened, the structure and infection process of ASFV are still not clear. This review summarizes the main process of ASFV infection, replication and functions of related viral proteins to provide scientific basis and theoretical basis for ASFV research and vaccine development.

Clinical Validation of DNA Extraction-Free qPCR, Visual LAMP, and Fluorescent LAMP Assays for the Rapid Detection of African Swine Fever Virus

The global pig industry and food safety are seriously threatened by outbreaks of African swine fever (ASF). To permit early diagnosis of African swine fever virus (ASFV), prevent its spread, and limit its outbreaks, a highly sensitive diagnostic method that can be performed at pig farms is required. Herein, we established DNA extraction-free real-time PCR (qPCR), visual loop-mediated isothermal amplification (LAMP), and fluorescent LAMP assays, which were compared with the results of World Organization for Animal Health (OIE) qPCR to assess ASFV-infected clinical samples. Based on plasmid DNA, the limit of detection for the three assays and OIE qPCR were 5.8 copies/μL. All four assays had good ASFV specificity and showed no cross-reactivity with other tested viruses. These assays were used to diagnose 100 clinical samples. The assays showed good diagnostic consistency, with kappa values of 1.0, 0.84, and 0.88, respectively. Compared with OIE qPCR, the diagnostic specificity/sensitivity of DNA extraction-free qPCR, visual LAMP, and fluorescent LAMP assays were 100%/100%, 100%/87.1%, and 100%/90.32%, respectively. The assays eliminated the need for DNA extraction and are more suitable for ASF diagnosis by inexperienced farmers in low-resource environments, making them a good choice for on-site monitoring of pig farms.

Development Real-Time PCR Assays to Genetically Differentiate Vaccinated Pigs From Infected Pigs With the Eurasian Strain of African Swine Fever Virus

Currently, African swine fever virus (ASFV) represents one of the most important economic threats for the global pork industry. Recently, significant advances have been made in the development of potential vaccine candidates to protect pigs against this virus. We have previously developed attenuated vaccine candidates by deleting critical viral genes associated with virulence. Here, we present the development of the accompanying genetic tests to discriminate between infected and vaccinated animals (DIVA), a necessity during an ASFV vaccination campaign. We describe here the development of three independent real-time polymerase chain reaction (qPCR) assays that detect the presence of MGF-360-12L, UK, and I177L genes, which were previously deleted from the highly virulent Georgia strain of ASFV to produce the three recombinant live attenuated vaccine candidates. When compared with the diagnostic reference qPCR that detects the p72 gene, all assays demonstrated comparable levels of sensitivity, specificity, and efficiency of amplification to detect presence/absence of the ASFV Georgia 2007/1 strain (prototype virus of the Eurasian lineage) from a panel of blood samples from naïve, vaccinated, and infected pigs. Collectively, the results of this study demonstrate the potential of these real-time PCR assays to be used as genetic DIVA tests, supporting vaccination campaigns associated with the use of ASFV-ΔMGF, ASFV-G-Δ9GL/ΔUK, and ASFV-ΔI177L or cell culture adapted ASFV-ΔI177LΔLVR live attenuated vaccines in the field.

Development of Diagnostic Tests Provides Technical Support for the Control of African Swine Fever

African swine fever is a highly contagious global disease caused by the African swine fever virus. Since African swine fever (ASF) was introduced to Georgia in 2007, it has spread to many Eurasian countries at an extremely fast speed. It has recently spread to China and other major pig-producing countries in southeast Asia, threatening global pork production and food security. As there is no available vaccine at present, prevention and control must be carried out based on early detection and strict biosecurity measures. Early detection should be based on the rapid identification of the disease on the spot, followed by laboratory diagnosis, which is essential for disease control. In this review, we introduced the prevalence, transmission routes, eradication control strategies, and diagnostic methods of ASF. We reviewed the various methods of diagnosing ASF, focusing on their technical characteristics and clinical test results. Finally, we give some prospects for improving the diagnosis strategy in the future.