ADMIXTURE groups shown in Fig 3 and sample equivalency to previously reported groups using STRUCTURE.

(A) Elbow method to identify the optimal number of ancestral populations from ADMIXTURE (K) based on cross-validation error. Red line indicates K = 5 ancestral populations selected following best practices. (B) ADMIXTURE results highlighting the three ancestral populations identified in Knudson et al. 2020 with STRUCTURE [19]. (EPS)</p

Geographic and temporal distribution of 166 monoclonal <i>P</i>. <i>falciparum</i> samples collected along the Pacific Coast of Colombia and Ecuador from 2013 to 2017.

Samples in Colombia originated in three municipalities (Santa Bárbara de Iscuandé in Nariño and Guapi and Timbiquí in Cauca) and were diagnosed at the Guapi diagnostic microscopy post, with the exception of two monoclonal samples that originated in Venezuela. Pie chart divisions are colored by collection year and the area of the pie chart is proportional to the per-location sample count. Samples in Ecuador originated in three sites: Esmeraldas, San Lorenzo and Tobar Donoso. Esmeraldas and San Lorenzo are located 120 kms apart by road and Tobar Donoso is located 40 km east of San Lorenzo but there is no road to reach that locality. The number of samples indicates the number of high-coverage, monoclonal samples, which were used in all subsequent analyses. Map tiles by Stamen Design Toner style, under CC BY 3.0. Data by OpenStreetMap, under OdbL: http://maps.stamen.com/toner/#9/2.6015/-77.5003.</p

Relatedness between parasites along the Pacific Coast of Colombia and Ecuador.

(A) Distribution of pairwise IBD in different transmission intensities: Pacific Coast of Colombia and Ecuador (2013–2017), Guyana [13], Cambodia [33] and Mali [33]. Samples from Western Cambodia belonging to the clonal expansion of K13 C580Y-harboring samples were excluded. (B) Network of 166 monoclonal samples collected from Colombia or Ecuador (2013–2017). Edges connecting nodes correspond to IBD≥0.99. (C) The mean IBD between clusters ranges from 0 to 0.89 and shows the presence of two larger “superclusters” at IBD>0.8. Two Venezuelan samples (17 and 19), show low IBD with Colombian and Ecuadorian samples but intermediate IBD with each other. Single samples (numeric labels) are missing diagonal values as no intra-cluster comparisons could be made.</p

Plot displaying haplotypes surrounding the gene amino acid transporter 1 (aat1).

Samples carrying ancestral alleles isolated in Guapi (SPT26239) and two samples originating in Venezuela are shown at the top and bottom, respectively. (EPS)</p

Comparison of an IBD approach to genetic distance analysis and visualization methods.

(A) ADMIXTURE analysis of the 2014–2017 Colombia-Venezuela samples identifies five major groups, which correspond with the four largest clonal clusters (B, C, D, and I) and one highly related supercluster (F1-F2-F3) in the IBD analysis. In addition to being less granular, these results are dependent on cluster frequency (S4 Fig) and their interpretation is less straightforward than relatedness analysis. (B) Depicting cluster relationships with a neighbor-joining tree based on genetic distance shows more fine-scaled inter-cluster relationships than ADMIXTURE, however, these are qualitative whereas the IBD heat map in Fig 2C provides quantitative relatedness estimates.</p

ADMIXTURE groups using altered clonal cluster frequencies.

(A) Elbow method to identify the optimal number of ancestral populations from ADMIXTURE (K) based on cross-validation error. (B) ADMIXTURE analysis of the Colombia-Venezuela samples with altered cluster frequencies. Cluster C was decreased from a frequency of 0.09 to 0.016 and cluster E1 was increased from a frequency of 0.015 to 0.06. This analysis best supports a division into five groups (K = 5), of which only two fully match with the original analysis. As expected, the cluster that increased in frequency (E1) is fully ascribed to a single ADMIXTURE group (along with E2) whereas the cluster that decreased in frequency (C) is described as “admixed”. (EPS)</p

Recoded genotype information from Echeverry, <i>et al</i> 2013 [17].

(XLSX)</p

Additional file 2 of Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa

Additional file 2. Change on cytokine concentration levels over time in COVID-19 positive individuals. The cytokine concentration levels analysed from plasma of COVID-19 asymptomatic (n = 3), monthly for four months. The quantity of the cytokines for each sampling month is shown by the line graph

Additional file 4 of Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa

Additional file 4. Cytokine concentration levels in COVID-19 patients. Comparison of cytokine concentration levels between COVID-19 symptomatic, asymptomatic patients, pre-COVID-19 health participants, COVID-19 pandemic health individuals and COVID-19 non-survivors. The cytokine concentration levels were measured from plasma of COVID-19 symptomatic (n = 29) and asymptomatic (n = 29), individuals, pre-COVID-19 health participants (100), COVID-19 pandemic health individuals (33) and COVID-19 non-survivors (2). The median quantity of the cytokines is shown by a horizontal line across the scatter plot while the lower and upper dotted lines represent the 25th and 75th percentiles, respectively. Statistical significance between symptomatic and asymptomatic patients were determined by a Kruskal-Wallis test with Dunn’s post hoc. (*: p 0.05)

Additional file 6 of Probing SARS-CoV-2-positive plasma to identify potential factors correlating with mild COVID-19 in Ghana, West Africa

Additional file 6. Coronavirus disease 2019’s fatality rate in the world and Africa. The data was retrieved from WHO COVID-19 dashboard ( https://covid19.who.int/ ). The COVID-19 vaccine was rolled out in December 2020 worldwide and in February/March 2021 in Africa