Diversity and emergence of new variants of African swine fever virus Genotype I circulating in domestic pigs in Nigeria (2016–2018)

Abstract

Background African swine fever (ASF) is the most lethal disease of pigs caused by ASF virus (ASFV) with severe economic implications and threat to the swine industry in endemic countries. Between 2016 and 2018, several ASF outbreaks were reported throughout pig producing states in Nigeria. Objectives Thereafter, this study was designed to identify the ASFV genotypes responsible for these outbreaks within the study period (2016–2018). Methods Twenty‐two ASFV‐positive samples by polymerase chain reaction were selected. The samples were collected during passive surveillance in eight states of Nigeria were characterised using 3 partial genes sequences of the virus namely, p72 capsid protein of the B646L, p54 envelope protein of E183L and the central variable region (CVR) within B602L of ASFV. Results Phylogenetic and sequences analysis based on p72 and p54 revealed ASFV genotype I as the circulating virus. Sequence analysis of the CVR of B602L revealed genetic variations with six ASFV tandem repeat sequence (TRS) variants namely, Tet‐15, Tet‐20a, Tet‐21b, Tet‐27, Tet‐31 and Tet‐34, thus increasing the overall genetic diversity of ASFV in Nigeria. Three of the TRS variants, Tet‐21b, Tet‐31 and Tet‐34, were identified for the first time in Nigeria. The new TRS variants of ASFV genotype I were identified in Enugu, Imo, Plateau and Taraba states, while co‐circulation of multiple variants of ASFV genotype I was recorded in Plateau and Benue states. Conclusions The high genetic diversity, emergence and increasing recovery of new variants of genotype I in Nigeria should be a concern given that ASFV is a relatively stable DNA virus. The epidemiological implications of these findings require further investigation.

Full genome sequence analysis of African swine fever virus isolates from Cameroon

“…The I196L, MGF360-16R and MGF360-18R The Cameroon 2018 isolate contained 19 copies of the tetra amino acid repeats in the CVR (Table 2) and these were identical to isolates obtained from across Cameroon between 2010 to 2020, corresponding to Variant A in a previous study (13). Cameroon 1994 contained 28 tetra amino acid repeats that was mostly closely related to sequences obtained from Nigeria with 27 tetra amino acid repeats in 2003, 2004, 2015 and 2018 and with 29 repeats that was obtained in 2006 (11,14,30). The assembled sequence of the Cameroon 1982 CVR was identical to sequence AAQ08102 submitted to NCBI in 2003, but different to CAJ90777 (7) and inspection of the reads aligned to the final assembled 1982 genome suggested a mixed population in the sample.…”

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

“…Following these outbreaks, ASF remained endemic in a number of countries in West Africa including Ghana, Nigeria, Senegal, Togo and Guinea Bissau, possibly via free-ranging populations of pigs [31,32]. Recently, a number of ASF outbreaks have been reported in Côte d'Ivoire [33], Ghana (2019, 2020; 2021) [34], Sierra Leone (2020) [35], and Nigeria [36,37]. Despite many ASF outbreaks, until 2020, only the ASFV p72 genotype I strains have been reported from West Africa [38,39].…”

“…Using genotyping tools, ASFV genotype I strains circulating in Nigeria have been well characterized. Based on the central variable region (CVR) of the B602L gene, 21 variants of ASFV genotype I have been recovered in Nigeria from 1997-2022 [37,47,48].…”

Full genome sequence analysis of African swine fever virus isolates from Cameroon

“…The CMR2018/lab1 isolate contained 19 copies of the tetra amino acid repeats in the CVR ( Table 2 ) and these were identical to isolates obtained from across Cameroon between 2010 to 2020, corresponding to Variant A in a previous study [ 13 ]. CAM1994/1 contained 28 tetra amino acid repeats that was mostly closely related to sequences obtained from Nigeria with 27 tetra amino acid repeats in 2003, 2004, 2015 and 2018 and with 29 repeats that was obtained in 2006 [ 11 , 14 , 30 ]. The assembled sequence of the CAM1982 CVR was identical to sequence AAQ08102 submitted to NCBI in 2003, but different to CAJ90777 [ 7 ] and inspection of the reads aligned to the final assembled 1982 genome suggested a mixed population in the sample.…”

“…ASFV isolates from Western Africa are predominately B646L genotype I [11][12][13][14] with a single outbreak of genotype II in Nigeria in 2020 [15]. With the exception of some isolates from Senegal which are CD2v serogroup 1, these viruses are all CD2v serogroup 4 [12].…”