Phylogenetic analysis and molecular epidemiology
Whole-genome sequencing and phylogenetic analysis were carried out for
all 174 H3N2 viruses isolated from both nasal and tracheal swab samples
during the study period. Together with 179 reference H3 SIV genome
sequences retrieved from the existing databases (GenBank, GISAID), a
maximum likelihood phylogenetic tree of 353 concatenated genomes of H3
SIVs was constructed. All tattoo codes indicating farm of origin and
sampling dates of the H3 isolates were labelled in the tree (Figure 3).
The 174 sequences of the H3N2 virus isolates can be grouped into 9
clusters, numbered 1-9, of closely related virus sublineages within the
concatenated phylogenetic tree. Genetically similar viruses were
detected in pigs from multiple farms on the same sampling occasion. For
example, all H3N2 viruses collected on 3rd July 2014
formed a subcluster of taxa with closely related evolutionary history
(subcluster 5). Interestingly, in subcluster 5, 18 nearly identical H3N2
viruses were isolated at the abattoir from pigs originating from 13
different farms in 3 different provinces (Guangdong, Hunan and Jiangxi).
Similarly, in subcluster 4, there were 17 highly related H3N2 viruses
isolated from pigs originated from 5 different farms in 2 provinces
(Jiangxi and Guangdong) on one sampling date 7thJanuary 2016. A similar phenomenon was found in virus subclusters 6, 7
and 8. It was highly improbable that a genetically identical virus was
simultaneously circulating in multiple farms and provinces at the same
time period. Thus, the phylogeny was strongly suggestive of a virus from
a common source which transmitted to swine from other farms during
transportation or while being held within the abattoir prior to
slaughter.
One of these farms GD101 had similar but not identical viruses isolated
on 2nd July 2015 and 7th September
2016, suggesting that this virus sub-lineage was persisting within the
farm for over two years.