Characterization of a Novel African Swine Fever Virus p72 Genotype II from Nigeria

Ambagala, Aruna; Goonewardene, Kalhari; Lamboo, Lindsey; Goolia, Melissa; Erdelyan, Cassidy N G; Fisher, Mathew; Handel, Katherine; Lung, Oliver; Blome, Sandra; King, Jacqueline; Forth, Jan Hendrik; Calvelage, Sten; Spinard, Edward; Gladue, Douglas P.; Masembe, Charles; Adedeji, Adeyinka Jeremy; Olubade, Toyin; Maurice, Nanven A.; Ularamu, Hussaini; Luka, Pam Dachung

doi:10.3390/v15040915

Cited by 16 publications

(25 citation statements)

References 56 publications

(67 reference statements)

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“…Genes annotated as “ACD ####” were given less weight because they are hypothetical proteins with no known function. Genes within the five MGF families (MGF100, MGF110, MGF300, MGF360, and MGF505) were given less weight since they are highly variable and often contain homopolymer stretches of G/C or A/T that can result in indels that lead to deletions, truncations, and fusions [ 10 , 22 ] and reviewed in [ 37 ]. The weighted gene-level percent identity distance matrices were then averaged into a single genome-genome percent identity matrix, and clustered based on similarity using DBSCAN.…”

Section: Resultsmentioning

confidence: 99%

“…Numerous reports have documented the existence of variations stemming from the genotype 2 strain whose origin can be traced back to Georgia. Genotype 2 variants have been identified in various regions across the globe, including Europe, Asia, Hispaniola, and Africa [ 3 , 6 , 7 , 8 , 9 , 10 ]. Indeed, some of these strains have mutations across the genome, genetic rearrangements, and deletions.…”

Section: Introductionmentioning

confidence: 99%

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Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning

Dinhobl,

Spinard,

Tesler

et al. 2023

Viruses

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning

Dinhobl,

Spinard,

Tesler

et al. 2023

Viruses

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“…For virus isolation, GUS PCR positive samples were filtered with Minisart ® 0.22 µm Syringe Filters (Sartorius, Goettingen, Germany) and inoculated into primary porcine alveolar macrophage (PAM) and primary porcine leukocyte (PPL) cultures prepared from heparinized whole blood collected from a healthy pig, as described previously [ 29 , 30 ]. The cultures were incubated at 37 °C in a 5% CO 2 incubator for 7 days, and observed daily under an inverted light microscope for hemadsorption (HAD).…”

Section: Methodsmentioning

confidence: 99%

Characterization of an African Swine Fever Virus Field Isolate from Vietnam with Deletions in the Left Variable Multigene Family Region

Ambagala,

Goonewardene,

Kanoa

et al. 2024

Viruses

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In this paper, we report the characterization of a genetically modified live-attenuated African swine fever virus (ASFV) field strain isolated from Vietnam. The isolate, ASFV-GUS-Vietnam, belongs to p72 genotype II, has six multi-gene family (MGF) genes deleted, and an Escherichia coli GusA gene (GUS) inserted. When six 6–8-week-old pigs were inoculated with ASFV-GUS-Vietnam oro-nasally (2 × 105 TCID50/pig), they developed viremia, mild fever, lethargy, and inappetence, and shed the virus in their oral and nasal secretions and feces. One of the pigs developed severe clinical signs and was euthanized 12 days post-infection, while the remaining five pigs recovered. When ASFV-GUS-Vietnam was inoculated intramuscularly (2 × 103 TCID50/pig) into four 6-8 weeks old pigs, they also developed viremia, mild fever, lethargy, inappetence, and shed the virus in their oral and nasal secretions and feces. Two contact pigs housed together with the four intramuscularly inoculated pigs, started to develop fever, viremia, loss of appetite, and lethargy 12 days post-contact, confirming horizontal transmission of ASFV-GUS-Vietnam. One of the contact pigs died of ASF on day 23 post-contact, while the other one recovered. The pigs that survived the exposure to ASFV-GUS-Vietnam via the mucosal or parenteral route were fully protected against the highly virulent ASFV Georgia 2007/1 challenge. This study showed that ASFV-GUS-Vietnam field isolate is able to induce complete protection in the majority of the pigs against highly virulent homologous ASFV challenge, but has the potential for horizontal transmission, and can be fatal in some animals. This study highlights the need for proper monitoring and surveillance when ASFV live-attenuated virus-based vaccines are used in the field for ASF control in endemic countries.

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“…Yet, as of early 2020, only ASFV isolates belonging to genotype 1 have been observed in Cameroon ( 6 , 7 ). However, in 2020, Nigeria, which shares a border to the west of Cameroon, reported an outbreak caused by a unique genotype 2 strain, highlighting the need for continued ASFV surveillance programs in the area ( 5 , 8 – 10 ).…”

Section: Announcementmentioning

confidence: 99%