Table 4 Overview of recent studies on genetic diversity of P. knowlesi

Individual gene studies

 Fong et al. (2016) [137]

Gamma protein region II (PkγRII), Duffy binding protein α region II

Erythrocyte invasion

Pen. Malaysia, Sabah, Sarawak

H

79

Purifying selection for PkγRII

2 distinct geographical clusters between Pen. Malaysia and Malaysian Borneo

 Loh et al. (2016) [138]

Circumsporozoite (csp), SSU rRNA, merozoite surface protein 1 (msp1), cytochrome c oxidase subunit 1 (cox1)

Sporozoite development and hepatocyte invasion (csp), erythrocyte invasion (msp1)

Singapore, Thailand, Pen. Malaysia, Sarawak

H

24

–

cox1 showed differentiation among P. knowlesi isolates based on geographical region

 Yusof et al. (2016) [139]

A-type 18S SSU rRNA, cox1

–

Pen. Malaysia, Sabah, Sarawak

H, Mf

210

–

Neutrality test indicated population expansion

 Ahmed et al. (2016) [140]

Normocyte binding protein Xa (NBPXa)

Erythrocyte invasion

Pen. Malaysia, Sarawak, Sabah

H

56

Purifying selection

3 clusters: Type 1 and 2 found in Pen. Malaysia and Malaysian Borneo whereas Type 3 found only in Pen. Malaysia

 Grigg et al. (2016) [141]

Dihydrofolate-reductase (dhfr)

Folate biosynthesis pathway and pyrimethamine resistance marker

Sabah

H

446

dN/dS ratio indicated potential purifying selection

1/3 of the infections were with P. knowlesi dhfr mutants. No mutations were found at 4 aa sites that deemed critical for pyrimethamine binding among all isolates, indicating no evidence of drug selective pressure in humans

 Rawa et al. (2016) [142]

Rhoptry-associated protein 1 (rap1)

Parasitophorous vacuole formation following erythrocyte invasion

Pen. Malaysia

H

34

Purifying selection

2 clusters were identified

 Yap et al. (2017) [143]

Merozoite surface protein 1 42 kDa region (msp1₄₂)

Erythrocyte invasion

Pen. Malaysia, Sabah, Thailand, India

H, Macaque

39

Purifying selection within Malaysia isolates

–

 Chua et al. (2017) [144]

Apical membrane antigen 1 (ama1)

Erythrocyte invasion

Sabah

H

36

Purifying selection

–

De Silva et al. (2017) [145]

Merozoite surface protein 1 (msp3)

Erythrocyte invasion

Pen. Malaysia

H

48

Purifying selection in Domain B

2 clusters were identified

 Ahmed et al. (2018) [146]

msp1

Erythrocyte invasion

Pen. Malaysia, Sabah, Sarawak, Thailand

H, Macaque

76

Purifying selection

3 clusters were identified: Malaysian Borneo cluster, Thailand human and Thailand macaque cluster, and mixture of Pen. Malaysia and Thailand isolates cluster

 Ahmed et al. (2018) [147]

Merozoite surface protein 1 paralog (msp1p)

–

Pen. Malaysia, Sarawak

H

40

Purifying selection

4 distinct geographical clusters within Malaysia

 Ahmed et al. (2018) [148]

Thrombospondin-related adhesive protein (trap)

Sporozoite motility to mosquito’s salivary gland and invasion to host hepatocytes

Pen. Malaysia, Malaysian Borneo

H

40

Positive selection/balancing selection

–

 Ahmed et al. (2018) [149]

P. knowlesi 6-cysteine protein (pk41)

Surface antigen

Pen. Malaysia, Sarawak

H

39

Purifying selection

3 clusters: 2 clusters of Sarawak human isolates and third cluster consisted of lab isolates

 Yap et al. (2018) [150]

msp1₄₂

Erythrocyte invasion

Pen. Malaysia, Sabah, Sarawak

H

83

Purifying selection, Neutrality test indicated balancing selection in Malaysian Borneo isolates but not in Pen. Malaysia

2 distinct geographical clusters between Pen. Malaysia and Malaysian Borneo

 Fong et al. (2019) [151]

Erythrocyte-binding protein region 2 (pkβII)

Erythrocyte invasion

Pen. Malaysia, Malaysian Borneo

H

65

Purifying selection

2 distinct geographical clusters between Pen. Malaysia and Malaysian Borneo

Ahmed et al. (2019) [152]

Merozoite surface protein 4 (msp4)

Surface antigen

Pen. Malaysia, Sarawak, the Philippines

H

36

Purifying selection in Exon II

2 distinct geographical clusters between Pen. Malaysia and Malaysian Borneo

 Ahmed and Quan (2019) [153]

Merozoite surface protein 7D (msp7D)

Erythrocyte invasion (putative function)

Pen. Malaysia, Sarawak

H

37

Positive selection in central region but purifying selection found in 5’ and 3’ regions

–

 Ahmed et al. (2019) [154]

Merozoite surface protein 8 (msp8)

Erythrocyte invasion (putative function)

Pen. Malaysia, Sarawak

H

43

Purifying selection

2 distinct geographical clusters between Pen. Malaysia and Malaysian Borneo

 Chong et al. (2020) [155]

csp

Sporozoite development and hepatocyte invasion

Pen. Malaysia, Sarawak, Sabah, Singapore

H

212

Purifying selection

–

 Ng et al. (2021) [156]

ama1

Erythrocyte invasion

Pen. Malaysia, Sarawak

H

41

Purifying selection

2 clusters distinguished between Pen. Malaysia and Sarawak

Microsatellite genotyping, whole-genome sequence analyses and other polymorphic marker studies

 Lee et al. (2011) [48]

Mitochondrial (mt) genome, csp

Sporozoite development and hepatocyte invasion (csp)

Sarawak

H, Mf, Mn

82 csp, 54 mt genome

–

Mitochondrial genome analyses suggested that P. knowlesi underwent population expansion approximately 30,000–40,000 years ago and possibility of increased parasite admixture between macaque troops

 Divis et al. (2015) [68]

Microsatellites (10 loci)

–

Pen. Malaysia, Sabah, Sarawak

H, Mf, Mn

599

–

2 clusters associated with either Mn or Mf

Assefa et al. (2015) [157]

Whole-genome

–

Sarawak

H

53

16/2381 (0.67%) genes showed signs of balancing selection with highest Tajima’s D value in csp

3 clusters: 2 clusters of Sarawak human isolates and third cluster consisted of lab isolates

Evidence of long-term population expansion

 Pinheiro et al. (2015) [158]

Whole-genome

–

Sarawak

H

7

–

2801/4623 genes (60.8%) are dimorphic (2 clusters)

 Divis et al. (2017) [159]

Microsatellites (10 loci)

–

Pen. Malaysia, Sabah, Sarawak

H, Mf, Mn

182

–

3 clusters: 2 Malaysian Borneo cluster associated with either Mn or Mf and 1 Pen. Malaysia cluster

 Benavente et al. (2017) [160]

Whole-genome (nuclear, mitochondria, and apicoplast genomes)

–

Pen. Malaysia, Sarawak

H, Mf, Mn

60 (nuclear genome),

114 (mt and apicoplast genomes)

–

3 clusters: 2 Malaysian Borneo cluster associated with either Mn or Mf and 1 Pen. Malaysia cluster

Evidence of genomic regions with shared polymorphisms between 2 Malaysian Borneo subpopulation clusters

 Divis et al. (2018) [161]

Whole-genome (nuclear, mitochondria, and apicoplast genomes)

–

Pen. Malaysia, Sarawak

H, Mf, Mn

80 (nuclear genome), 129 (mt genome), 65 (apicoplast genome)

–

High heterogeneity in the level of intercluster divergence was distributed across the genome, with long contiguous chromosomal blocks having high or low divergence

 Benavente et al. (2019) [162]

Whole-genome

–

Pen. Malaysia, Sabah, Sarawak

H, Mf, Mn

103

–

NBPXb gene showed genetics exchanges between some Mn- and Mf-associated isolates

DBPβ and NBPXa presented genetic exchange events with Mn-Pk into the Peninsular subpopulation

 Saleh Huddin et al. (2019) [163]

Microsatellites (7 loci)

–

Pen. Malaysia

H, Mf

173

–

No significant genetic differentiation was seen between human and long-tailed macaque in Pen. Malaysia

 Hocking et al. (2020) [164]

Whole-genome

–

Pen. Malaysia

H

28

215/4742 (4.53%) genes showed signs of balancing selection

3 subclusters were observed within Pen. Malaysia isolates

 Divis et al. (2020) [165]

Bi-allelic SNP

–

Sabah, Sarawak

H, Mf, Mn

1492

2 clusters associated with either Mn or Mf.Cluster associated with Mf was the predominant (70%) infections.Majority of the recent cases were found to be grouped in Mf-associated cluster