Introduction
Tilapia lake virus (TiLV) is an emerging virus that has greatly affected
global tilapia farming industry and food security (Food and Agriculture
Organization of the United Nations, 2017; Jansen et al., 2019). TiLV was
discovered in Israel in 2014 (Eyngor et al., 2014; Bacharach et al.,
2016) following the first report of a novel disease in Ecuador, called
syncytial hepatitis of tilapia (Ferguson et al., 2014). Since then, TiLV
outbreaks have been reported in many other countries, including Peru
(Pulido et al., 2019), Ecuador (Subramaniam et al., 2019), Egypt (Fathi
et al., 2017; Nicholson et al., 2017), India (Behera et al., 2018),
Thailand (Dong, Siriroob et al., 2017; Surachetpong et al., 2017),
Malaysia (Abdullah et al., 2018; Amal et al., 2018), Bangladesh (Chaput
et al., 2020), Tanzania (Mugimba et al., 2018), Uganda (Mugimba et al.,
2018), the USA (Ahasan et al., 2020), Colombia (Tsofack et al., 2017),
Indonesia (Koesharyani et al., 2018), Chinese Taipei (World Organisation
for Animal Health, 2017a), Mexico (World Organisation for Animal Health,
2019), and Philippines (World Organisation for Animal Health, 2017b).
High mortality rates (20–90%), and rapid spread of the virus have
threatened the livelihoods of millions of tilapia farmers on the global
scale (Food and Agriculture Organization of the United Nations, 2017;
Jansen et al., 2019).
TiLV is a negative-sense single-stranded RNA virus with a 10-segment
genome (Bacharach et al., 2016). The gene on segment 1 is predicted to
code for the PB1 protein (Bacharach et al., 2016), which shows a very
low, but detectible, similarity to the polymerase proteins of influenza
(Bacharach et al., 2016). Other segments, however, showed no detectible
similarities to any known genes in the NCBI database, indicating that it
is a new virus that is distantly related to all known viruses. Indeed,
TiLV is currently classified as the only member of a new genusTilapinevirus (International Committee on Taxonomy of Viruses,
2019), the sole genus in the family Amnoonviridae .Amnoonviridae is a recently established family in the orderArticulavirales , which also contains the influenza virus (the
family Orthomyxoviridae ) (International Committee on Taxonomy of
Viruses, 2019).
A number of genome sequences of TiLVs have been reported, and analyses
of these sequences have led to better understanding of how the virus
evolves and spreads across regions (Bacharach et al., 2016; Surachetpong
et al., 2017; Pulido et al., 2019; Ahasan et al., 2020; Chaput et al.,
2020). Most of the reported sequences are, however, not whole genomes,
and a recent study has shown that reassortment is very common for TiLV
(Chaput et al., 2020) – a phenomenon in which multiple strains of
viruses with segmented genomes co-infect the same host cell and exchange
their genetic materials (McDonald et al., 2016; Lowen, 2018). This means
that analysis of individual genomic segments might not give a full
picture of how TiLV evolves, and on the other hand, analysis of whole
genomes without taking reassortment into account might yield an
erroneous history of the virus.
Here, we report eight new whole genomes of TiLVs from Thailand, sampled
between 2014–2019. Furthermore, their sampling dates distribute
relatively evenly across the entire sampling period, providing us
sufficient temporal information for dating the early origin of TiLV, and
how it evolves and spreads through time. Together with nine publicly
available whole genome sequences of TiLVs, phylogenetic analyses were
performed to investigate the emergence of TiLV, and how it spread
globally.