Contrasting and dynamic patterns of population structure for
both P. falciparum and P. vivax
As previously described, for P. falciparum, low to moderate
genetic differentiation was seen between the Wosera 2005 (ESP1) and
Madang 2006 studies (Jennison et al., 2015; Schultz et al., 2010)
(Figure 3). Comparisons were not done between Pf 2005/6 and otherPf populations as it was not possible to calibrate data through
combining allele calls before binning (see Materials and Methods).
Post-LLIN, there remains low to moderate genetic differentiation between
ESP (2012-2013) and Madang (2014) (Figure 3). However, there was little
genetic differentiation of East Sepik P. falciparum populations
pre-LLIN (ESP2 2005) compared to post-LLIN (2012-13), nor between Madang
2010 and 2014 populations (Figure 3). For P. vivax , a different
pattern can be seen, with low genetic differentiation between provinces
pre-LLIN, which increases in the post LLIN-studies (Figure 3). Similar
to P. falciparum , within province genetic differentiation between
the different time points does not increase post-LLIN.
Population genetic structure was further investigated by Bayesian
cluster analysis using STRUCTURE (Pritchard et al., 2000). Haplotypes or
populations with ancestry in more than one cluster are considered
admixed and indicates that substantial gene flow occurs between defined
geographic areas. Our analysis identified three P. vivax and
three P. falciparum clusters (Figure 4, S7, S8 and S9). The
clustering patterns show that the P. falciparum populations in
later years are more mixed than the populations of 2005/2006, where
populations clustered according to geographical locations including
amongst the three catchment areas within Madang Province (Figure 4)
(Schultz et al., 2010){Schultz, 2010 #16}. On the contrary, P.
vivax populations were very diverse and displayed little population
structure in all time points, despite the increase in differentiation
between ESP and MAD post-LLIN populations (Figures 4 and 5).
For P. vivax , as we observed significant mLD post-LLIN in ESP,
local phylogenetic analysis was conducted. This supports focal
transmission as shown by the clustering of haplotypes from the same
village: Sunuhu (Figure 5). The STRUCTURE analysis also shows some
evidence of this inbred cluster (Figure 4B). Interestingly, this village
had the highest prevalence in the region in the 2012-13 survey (36%
infected with P. vivax by qPCR compared to 0.5-9% in other
villages (Kattenberg et al., 2020). In Sunuhu, clonal and closely
related haplotypes (≤2 unmatched alleles) were observed in 48% (11/23)
of the haplotypes from that village (see supplementary file 1). The 11
closely related haplotypes were observed throughout the village, were
not clustered in neighbouring households, and were not associated with
participant characteristics (p>0.05), such as age and sex
(Table S3).