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.