Discussion
This study presents an update on ASFV circulating in Nigeria based on the characterization of three genes of the ASFV from samples collected during suspected ASF disease outbreaks between 2016- 20180. Phylogeny of ASFV identified genotype I and Ia from samples analyzed based on theB646L and E183L genes which show high stability of these regions of the virus. However, sequence analysis of the hypervariable CVR encoded within B602L gene revealed six ASFV genotype I variants, three of which were new (Tet-21b, Tet-31 & Tet-34) and never reported in Nigeria nor any of the West African countries. Earlier genetic studies had recovered 11 ASFV genotype I variants in Nigeria (Tet-15, Tet-17a, Tet-17b, Tet-20a, Tet-20b, Tet-21a, Tet-22, Tet-27, Tet-29, Tet-32, Tet-36, Tet-48) (Owolodun et al., 2010; Luka et al., 2016) (Table 2). With 3 newly recovered variants in this study, 14 ASFV genotype I TRS variants have now been recovered in Nigeria. Interestingly, earlier ASFV genotype I variants like Tet-36 recovered from the first outbreak in 1997 have been displaced by newer TRS variants. In this study, Tet-15, Tet-27, and Tet-34 were the most widely distributed ASFV variants co-circulating in Benue and Plateau States. (Table 2, Fig.1). These findings differ from the previous studies that reported Tet-36 as the dominant variant between 2003 and 2007 and Tet-20b was the most widespread TRS variant from 2007 to 2015(Luka et al., 2016). Tet-15 was first reported in Kaduna State in 2014 at a live pig market, but the variant has now spread to two other States based on the results from this study (Table 2). It is likely, Tet-15 spread from the live pig market in Kaduna State to Benue and Plateau States via trading of live pigs. Tet-27 was first recovered in 2003, the TRS variant has persisted and was recovered in several sites in Benue State in 2018 (Luka et al., 2016; Owolodun et al., 2010)(Table 2). Multiple variants of ASFV genotype I have been recovered in some countries in West and Central Africa. For instance, multiple ASFV genotype I variants have been recovered in Ivory Coast (4), Benin (4), Burkina Faso (7), Ghana (6), and Cameroon (4) (Luka et al., 2016; Couacy‐Hymann et al., 2019; Wade et al., 2019). These findings suggest the CVR of B602Lof ASFV genotype I is prone to mutations in West and Central Africa. Furthermore, these mutations occur despite no documented evidence of the presence of sylvatic or tick ASFV transmission cycle in West and Central Africa (Luka et al., 2017). ASF outbreaks frequently occur in Nigeria with severe clinical outcomes, thereby affecting pig farmers’ financial income and threatening food security. In this study, ASF outbreaks were reported in eight out of 30 pig-producing states of Nigeria (Fig 1). Although the number of outbreaks may be higher but were underreported due to a lack of financial compensation to pig farmers. Rather, farmers rapidly sell-off or slaughter sick pigs leading to further spread of the disease in Nigeria (Fasina et al., 2010). The ASF outbreaks between 2016 and 2018 in this study were both in intensively reared exotic pigs and free ranged NIP. Based on data collected, Plateau and Benue States seem to be hotspots of ASF in Nigeria as they have the highest number of recorded outbreaks. Epidemiological data collected in this study showed that basic biosecurity measures such as proper quarantine before the introduction of new stock and traffic control were not observed, leading to the introduction and spread of ASF in the affected pig farms. For instance, the ASF outbreak in Imo State was attributed to the illegal introduction of pigs into Nigeria from Cameroon, while that of Abia State was exacerbated by inadequate sanitary and biosecurity measures. Outbreaks in both States occurred in a cluster of pig farms. Clustering/communal pig farming is common practice in Nigeria, whereby pig farms are located close to each other, and farmers have access to each other’s farms, share farmworkers and equipment. The ASF outbreaks reported in Zing, Taraba State affected 101 pig farmers leading to the death of 3,354 NIP breed (Fig 1). Although, field investigation did not reveal the source of the outbreak, nevertheless, the extensive husbandry system contributed to the spread of ASFV in the community. Interestingly, some of the NIPs survived the ASF outbreak with lower mortality rates of 45.6% compared to 73.7-80% for exotic breeds as recorded in this study. Some of the NIPs that survived the ASF outbreak were still alive and identified by farmers during a field visit to Zing, Taraba State, for another research study in 2019. Previously, studies in Nigeria have observed tolerance of NIP to ASFV, sometimes with no clinical signs or reduced death rates during outbreaks (Oluwole & Omitogun, 2014). Studies in the Democratic Republic of Congo and Mozambique, reported indigenous pigs in endemic areas infected with the ASFV remained asymptomatic(Patrick et al., 2020 Penrinth et al.,2004; Patrick et al., 2020). Several risk factors have been identified as being responsible for the spread of ASFV in Nigeria, namely: poor husbandry system, live pigs trading and slaughtering of pigs on the farm and, movement of ASF infected and recovered animals (Fasina et al., 2012). Other factors include external sourcing of replacement stock, presence of ASF-infected farms within the neighbourhood of other farms and exchange of feed and farm tools by farmers and their workers (Olugasa & Ijagbone, 2007; Awosanya et al., 2015). This study further confirms the importance of these risk factors in the spread and sustenance of the virus in the pig populations in Nigeria.