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PLOS One logoLink to PLOS One
. 2023 Dec 12;18(12):e0294891. doi: 10.1371/journal.pone.0294891

Prevalence and molecular heterogeneity of glucose-6-phosphate dehydrogenase (G6PD) deficiency in the Senoi Malaysian Orang Asli population

Danny Xuan-Rong Koh 1, Mohamed Afiq Hidayat Zailani 2, Raja Zahratul Azma Raja Sabudin 2,*, Sanggari Muniandy 1, Nur Awatif Akmal Muhamad Hata 3, Siti Noor Baya Mohd Noor 3, Norhazilah Zakaria 3, Ainoon Othman 4, Endom Ismail 5
Editor: Germana Bancone6
PMCID: PMC10715666  PMID: 38085718

Abstract

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked genetic disorder characterized by reduced G6PD enzyme levels in the blood. This condition is common in populations exposed to malaria; an acute febrile disease caused by Plasmodium parasites. G6PD-deficient individuals may suffer from acute hemolysis following the prescription of Primaquine, an antimalarial treatment. The population at risk for such a condition includes the Senoi group of Orang Asli, a remote indigenous community in Malaysia. This study aimed to elucidate the G6PD molecular heterogeneity in this subethnic group which is important for malaria elimination. A total of 662 blood samples (369 males and 293 females) from the Senoi subethnic group were screened for G6PD deficiency using a quantitative G6PD assay, OSMMR2000-D kit with Hb normalization. After excluding the family members, the overall prevalence of G6PD deficiency in the studied population was 15.2% (95% CI: 11–19%; 56 of 369), with males (30 of 172; 17.4%) outnumbering females (26 of 197; 13.2%). The adjusted male median (AMM), defined as 100% G6PD activity, was 11.8 IU/gHb. A total of 36 participants (9.6%; 26 male and 10 female) were deficient (<30% of AMM) and 20 participants (5.4%; 4 male and 16 female) were G6PD-intermediate (30–70% of AMM). A total of 87 samples were genotyped, of which 18 showed no mutation. Seven mutations were found among 69 genotyped samples; IVS11 T93C (47.1%; n = 41), rs1050757 (3’UTR +357A>G)(39.1%; n = 34), G6PD Viangchan (c.871G>A)(25.3%; n = 22), G6PD Union (c.1360C>T)(21.8%; n = 19), c.1311C>T(20.7%; n = 18), G6PD Kaiping (c.1388G>A)(8.0%; n = 7), and G6PD Coimbra (c.592C>T)(2.3%; n = 2). Our analysis revealed 27 hemizygote males, 18 heterozygote females, 7 homozygote females, and 2 compound heterozygote females. This study confirms the high prevalence of G6PD deficiency among the Senoi Malaysian Orang Asli, with a significant degree of molecular heterogeneity. More emphasis should be placed on screening for G6PD status and proper and safe use of Primaquine in the elimination of malaria among this indigenous population.

Introduction

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common genetic disorder that affects more than 500 million people worldwide [1]. G6PD acts as a key house-keeping enzyme that oxidizes glucose-6-phosphate to 6-phosphogluconolactone in the pentose phosphate pathway and reduces nicotinamide adenine dinucleotide phosphate (NADP) to nicotinamide adenine dinucleotide phosphate-oxidase (NADPH), a crucial reducing agent in the protection of red blood cells against oxidative stress [1]. This X-linked hereditary condition affects the entire world, but it is more prevalent, particularly in parts of the African continent, the Middle East, and Southeast Asia, where it often overlaps with the geographical distribution of malaria infection [2].

In Malaysia, the overall prevalence of G6PD deficiency among males was 4.7%, which was detected in three main ethnics in Malaysia including Chinese (6.0%) which was the most predominant, followed by Malays (4.6%) and Indian (1.3%) [3,4]. The Orang Asli was the indigenous population of Peninsular Malaysia that formed a national minority. They were formed of three groups, namely Senoi, Proto Malay, and Negrito, which were further divided into six different subethnics in each group [5].

The Senoi population represents the largest group of the Orang Asli in Malaysia (54.9%), followed by the Proto Malay (42.3%) and Negrito (2.8%) [6]. These indigenous groups inhabit remote areas including the tropical rainforest and traditionally adopt a hunter-gatherer lifestyle with self-subsistence culture such as jungle farming. Their lifestyle habit and geographical distributions both resulted in constant exposure to neglected tropical and infectious diseases such as malaria and soil-transmitted helminth infection among the Orang Asli population [7,8]. A previous epidemiological study revealed that the endemicity of malaria among the Orang Asli population was 24.2%, with at least 3.7 times more in the Orang Asli children under 12 years [9].

Malaria is an acute febrile infection caused by Plasmodium parasites. It is a medical emergency as the infection may rapidly progress to life-threatening complications such as cerebral malaria, pulmonary edema, acute renal failure, and severe anemia. If the infected individuals do not receive prompt and appropriate treatment, these conditions can be fatal [10,11]. Currently, Primaquine is the most widely used anti-malarial drug in the world [12,13], capable of treating and eliminating P. vivax liver stage infection and gametocytocidal activity for P. falciparum [14]. However, in G6PD-deficient patients, this medication may cause oxidative stress resulting in acute hemolysis.

The Orang Asli population is highly susceptible to mosquito bites and malaria infection due to their isolated settlements in tropical forests and traditions of hunting and foraging for food in the jungle. Despite the high susceptibility and endemicity of malaria among the Orang Asli in Malaysia, there is a scarcity of molecular studies of the G6PD variants that may impede a successful radical cure of malaria infection.

Iwai et al. (2001) and Wang et al. (2008) were among the first to report cases of G6PD deficiency among the Orang Asli [14,15]. However, both studies did not provide detailed subethnicity information. A study was conducted among Temiar, a subethnic group of the Senoi Orang Asli, and discovered that the population’s G6PD incidence was 52.4% (36.2% in males, 29.8% in females) [16]. Another study which was conducted on the Negrito, the smallest Orang Asli group showed that the ethnicity had a 9% prevalence, with the highest incidence coming from the Lanoh subethnic group of Negrito Orang Asli (28%) [17]. However, these studies were conducted using a fluorescent spot test (FST), a qualitative method that was proven to have a lack of sensitivity to detect G6PD deficiency, particularly in females heterozygotes and those with moderate enzyme activity ranging between 20 to 60% of the normal mean [3,18,19].

In addition, a previous study successfully identified three novel single nucleotide polymorphisms (SNP) in the 3’ untranslated region (3’UTR) among the deficient Negritos, which were rs112950723, rs111485003, and rs1050757G [20]. Further investigation on these SNPs revealed that only the rs1050757G significantly changed the secondary structure of the mutant transcript, whereas the rs112950723 and rs111485003 did not affect mRNA folding [21]. Nonetheless, according to this study, additional experimental research is needed to reliably determine the role of mRNA secondary structure on G6PD deficiency. This study aimed to characterize the genetic profile of the Senoi Orang Asli and to elucidate the G6PD molecular heterogeneity in this subethnic group.

Materials and methods

Study design

This was a cross-sectional study involving all subethnic groups of the Senoi Orang Asli population in Peninsular Malaysia, namely Che Wong, Mah Meri, Jah Hut, Semaq Beri, Semai, and Temiar. The ethical approval for this study was obtained from the Universiti Kebangsaan Malaysia (UKM) Medical Centre Ethics Committee (UKM1.5.3.5/244) and the Malaysian Department of Orang Asli Development (JHEOA.PP.30.052Jld.6(13)).

A total of 662 consenting volunteers consisting of 369 males and 293 females of the Senoi subethnic were enrolled in this study. The inclusion criteria were healthy Senoi Orang-Asli individuals of pure, single subethnic lineage for three generations. Individuals with an unclear or mixed subethnics lineage as well as those with any systemic or blood disease were excluded from this study. All participants were informed about the nature of the study, and written consent was obtained from each individual prior to sample collection.

Sample collection and processing

Six ml venous blood sample was collected from each participant in ethylene diamine tetra acetic acid (EDTA) tubes using sterile venipuncture techniques. The blood samples were stored in an insulated container with ice packs and were sent to the laboratory at the Haematology Unit, Department of Diagnostic Laboratory Services (JPMD), UKM Medical Centre (UKMMC) within 24 hours post-collection.

In the laboratory, the G6PD activity of the samples was measured using a quantitative method, OSMMR2000-D assay kit with hemoglobin (Hb) normalization (OSMMR; R&D Diagnostics, N. Dimopoulos S.A, Greece). Five microliters of the blood sample were mixed with 75 μl of elution buffer. The mixture and 75 μl of the kit’s reagent were put in a separate well of a microplate. This microplate preparation was then steadily warmed to 37°C for 20 minutes in an incubator. A NanoVueTM spectrophotometer (Harvard Bioscience Inc., Holliston, Massachusetts, USA) was used for Hb evaluation by adding 15 μl of the sample into the reagent and was read at 405 nm in a single measurement mode.

A total of 80 μl of the color reagent mixture provided by the manufacturer in the OSMMR kit was then added to the sample. Following mixing, the microplate was once more read in kinetic mode at 550 nm and readings were taken at 0 and 15 minutes. The total change in optical density was calculated from the readings and the final results were expressed in IU/gHb. The adjusted male median (AMM) was determined, and the value was defined as 100% G6PD activity. The 30% and 70% cut-off values were established and used for the diagnosis of G6PD deficiency among the population. These cut-off values were based on the recent World Health Organization (WHO) recommendation for phenotypic classification of G6PD deficiency, as well as corresponded to the safe cut-off points for receiving antimalarial treatment including Primaquine and Tafenoquine. This approach was also adopted by the majority of comparable studies in previous years [21,22].

For all G6PD-deficient samples with activities below 70% of AMM and a subset of G6PD-normal as identified by the G6PD OSMMR2000-D kit assay (n = 69), molecular analysis was performed using the DNA sequencing method to characterize their mutations. The genomic DNA of these samples was extracted from peripheral blood leucocytes using the QIAamp DNA Blood Mini Kit (Qiagen Diagnostics GmbH, Hilden, Germany). Then, the extracted DNA was amplified through the polymerase chain reaction (PCR) technique using specific primer sets (Table 1) with specific PCR conditions (Table 2).

Table 1. Primers design sets for molecular analysis of G6PD mutation.

Target exon Primer design (5’ to 3’) Annealing Temperature (°C) PCR product size (bp)
9, 10 F: CCT CAA CCC CGG AGA AGT CA
R: TGA AGA ACA TGC CCG GCT TC
56.0 869
11, 12, 13, and 3’ untranslated region (UTR) F: ACG TGA AGC TCC CTG ACG C
R: CCA TGG AGT GCA GAG TTG GT
64.5 965
1 F: TAA AAA CAC AAG CCC CGC CC
R: CTC AAG CAC AAC AAA CAG CGT
4.4 900
2 F: GAA TAC ACC AAT GCT TTG AGT
R: GCT CAA CTT AGC AGA GCC TGT
56.0 489
3, 4 F: TCG GGG CTC TTC TGT CTG TA
R: GCT GGT AAT GGG GGT CTC AA
61.4
558
5 F: TGT CTC CCA GGC CAC CCC AGA G
R: GAC ACG CTC ATA GAG TGG TG
64.5 305
6 F: GAG GAG GTT CTG GCC TCT ACT
R: AGA TCC TGT TGG CAA ATC TGC AG
55.6 464
7, 8 F: GAC AAG GGT GAC CCC TCA CA
R: CTG TGC TCA GAG GTG GTG ACT T
64.4 793

Table 2. Conditions for polymerase chain reaction (PCR) technique.

Temperature (°C) Steps Duration (s) Cycle
95.0 Initial denaturation 300 1
98.0 Denaturation 60
Refer to Table 1 Annealing 60 30
72.0 Extension 60
72.0 Final extension 600 1
10.0 Storage Infinite -

The PCR products were then purified using the QIAquick PCR Purification Kit (Qiagen Diagnostics GmbH, Hilden, Germany) followed by a quality and purity analysis using a similar spectrophotometer. An automated Sanger DNA sequencing was performed on the purified PCR products by services from Apical Scientific Pvt. Ltd (previously known as First BASE Laboratories Pvt. Ltd, Selangor, Malaysia).

Data analysis

All data were collated and analyzed using Microsoft® 365 Excel Spreadsheet Software (Microsoft Corporation, WA, USA). The adjusted male median (AMM) was calculated from all male participants and defined as 100% G6PD activity. The method for AMM calculation was described by Ley et al. (2017) [23]. From the AMM, 30% and 70% cut-off values were established to classify the G6PD status of the participants. The overall prevalence of G6PD deficiency was calculated by identifying and excluding all related family members. The prevalence among male and female participants was determined and compared accordingly. The results were statistically analyzed using IBM SPSS Statistics 26.0 for Windows. The results of the molecular analysis were analyzed using Applied Biosystem Sequence Scanner Software v2.0 (Thermo Fisher Scientific, Massachusetts, USA).

Results

Study population and distribution of G6PD activity

All 662 venous blood samples of the Senoi Orang Asli were analyzed for G6PD activity (293 males and 369 females). The participants were healthy, afebrile, and free of malaria. There were 102 children aged from 2 to 12 years old, while the remaining 473 samples were adults aged from 13 to 79 years old. The major subethnicities of participants were Temiar (201; 30.3%), followed by Semai (186; 28.1%), and Jah Hut (167; 25.2%), the remaining were Semoq Meri (53; 8.0%), Mah Meri (47; 7.0%) and Che Wong (8; 1.2%).

The AMM of the studied population was 11.8 IU/gHb. Individuals with enzyme levels less than 30% of AMM were classified as deficient, while those with enzyme levels between 30% to 70% were classified as intermediate deficiency. G6PD-normal participants were those with enzyme activity of more than 70% of AMM. Table 3 shows the corresponding values for each phenotypic classification for this study.

Table 3. Classification of G6PD activity in the Senoi Malaysian Orang Asli.

Measurement Parameter G6PD activity (IU/gHb)
Adjusted Male Median (AMM) (100% activity) 11.8
G6PD-deficient (<30% of AMM) < 3.6
G6PD-intermediate (30–70% of AMM) 3.6–8.3
G6PD-normal (>70% of AMM) >8.3

The prevalence of G6PD deficiency was 15.2% (95% Confidence Interval: 11–19%; 56/369), with males (30/172; 17.4%) outnumbering females (26/197; 13.2%). A total of 36 participants (9.6%; 26 male and 10 female) were G6PD-deficient (<30% of AMM) and 20 participants (5.4%; 4 male and 16 female) were G6PD-intermediate (30–70% of AMM). A Chi-square test was performed to compare the proportions of deficient and intermediate individuals between females and males. Results revealed a statistically significant higher proportion of deficient individuals in males as compared to females (p = 0.000459) and a statistically significant higher proportion of intermediate individuals in females as compared to males (p = 0.007). These results with their enzyme levels were summarized in Table 4.

Table 4. Prevalence and distribution of G6PD deficiency among the Senoi Malaysian Orang Asli population.

(n = 369).

Gender Phenotype Prevalence (N, %) G6PD activity (IU/gHb)
Range Mean (±SD)
Male Deficient 26 (7.0%) 0.7–3.3 2.0 (±0.9)
Intermediate 4 (1.1%) 4.0–8.2 6.1 (±2.3)
Normal 142 (38.5%) 8.4–22.0 12.2 (±2.5)
Female Deficient 10 (2.7%) 0.7–3.5 1.5 (±0.9)
Intermediate 16 (4.3%) 3.7–9.3 6.0 (±1.7)
Normal 171 (46.3%) 9.4–23.3 12.9 (±2.9)
Overall Deficient 36 (9.8%)
Intermediate 20 (5.4%)
Normal 313 (84.8%)
Total 56/369 (15.2%) (95% CI: 11–19%)

The spectrum of G6PD mutation

Molecular analysis was performed on 87 samples including all G6PD-deficient and G6PD-intermediate blood samples (n = 56) and a subset of G6PD-normal samples (n = 31). Our analysis revealed 27 hemizygote males, 18 heterozygote females, 7 homozygote females, and 2 compound heterozygote females. A total of 18 genotyped samples showed no mutation (Fig 1).

Fig 1. G6PD activity distributions (% Normal) for Coimbra, Kaiping, Union, Viangchan, and unknown variants among the Senoi Malaysian Orang Asli population.

Fig 1

Seven variants of G6PD mutations were found in 79.3% of the samples (69; 35 males and 34 females). The IVS11 T93C mutations were the highest among them (47.1%; n = 41), followed by rs1050757 (3’UTR +357A>G) (39.1%; n = 34), G6PD Viangchan (c.871G>A) (25.3%; n = 22), G6PD Union (c.1360C>T) (21.8%; n = 19), c.1311C>T (20.7%; n = 18), G6PD Kaiping (c.1388G>A)(8.0%; n = 7), and G6PD Coimbra (c.592C>T) (2.3%; n = 2). The genotype of each G6PD mutation and the distribution of silent mutation and polymorphism among the Senoi Malaysian Orang Asli population were summarized in Tables 5 and 6.

Table 5. G6PD genotypes of the Senoi Malaysian Orang Asli population.

G6PD variant Total subjects (n) Genotypes (n) G6PD activity (IU/gHb)
Range Mean (±SD) 95% CI
G6PD Coimbra (c.592 C>T) 2 Hemizygote (2) 2.8–2.9 2.8 ±0.02 2.7–3.0
G6PD Viangchan (c.871 G>A) 21 + 1a Hemizygote (13) 1.6–4.2 2.8 ±0.71 2.4–3.2
Heterozygote (9) 1.2–7.8 5.6 ±0.91 4.9–6.3
Homozygote (5) 2.6–3.8 3.5 ±0.52 2.8–4.1
Compound heterozygote (1a) 2.9
G6PD Kaiping (c.1388 G>A) 6 + 1b Hemizygote (5) 2.1–2.8 2.4 ±0.28 2.1–2.6
Heterozygote (1) 2.9
Compound heterozygote (1b) 1.4
G6PD Union (c.1360 C>T) 17 + 1a +1b Hemizygote (7) 0.7–1.1 0.9 ±0.11 0.8–1.0
Heterozygote (8) 3.1–7.7 6.3 ±1.41 5.0–7.5
Homozygote (2) 0.7–1.0 0.8 ±0.17 0–2.7
Compound heterozygote (1a + 1b)
Unknown variants 33 Male (17) 0.6–4.0
Female (16) 0.9–7.5

1a A compound heterozygote case of G6PD Viangchan + Union.

1b A compound heterozygote case of G6PD Kaiping + Union.

Table 6. Distribution of silent mutation and polymorphism among the studied population.

Gender Subethnicity c.1311 C>T IVS1193 T>C 3’UTR +357 A>G
Male Jah Hut 1 6 6
Semai 6 10 10
Temiar 0 3 0
Female Jah Hut 2 6 5
Semai 9 12 12
Temiar 0 4 1
Total 18 41 34

Discussion

G6PD deficiency is a public health concern in Malaysia. One of the most serious clinical consequences of this hereditary disease, particularly in newborns, is neonatal hyperbilirubinemia, which requires prompt diagnosis and treatment to prevent kernicterus, an irreversible bilirubin-induced brain damage [22]. Moreover, the use of anti-malarial treatments such as Primaquine in G6PD deficient patients would increase the risk of acute hemolysis [23]. Therefore, based on the WHO guideline to support the treatment of malaria, it was recommended to screen the target population for G6PD deficiency and to ensure the treatment of jaundice for any population with a prevalence of G6PD deficiency greater than 3% among males [24].

The detection of G6PD deficiency was significantly higher in this study compared to previous reports. The higher detection of G6PD deficiency in our study were owing to the use of a quantitative G6PD activity assay, the OSMMR-2000D kit assay, rather than the widely used semiquantitative FST. In numerous earlier research, the OSMMR-2000D kit assay served as the gold standard quantitative G-6-PD enzymatic test. [18,19,2528]. In contrast, the FST has been shown to perform poorly in detecting partial G6PD deficiency among female heterozygotes, with up to 14.8% of subjects misdiagnosed as normal [18].

In regard to the genetic composition, G6PD deficiency exhibits high ethnogeographic variability across the global population [29]. Previous studies proved that each ethnic group in Malaysia has a unique spectrum of G6PD mutations. As an example, in Malay, the most common G6PD variant discovered was G6PD Viangchan (c.871 G>A), accounting for 37.2% of the deficient cases, followed by G6PD Mediterranean (c.563C>T; 26.7%), and G6PD Mahidol (c.487G>A; 15.1%) [3]. Other mutation variants with lower prevalence identified in Malay were G6PD Canton (c.1376G>T), G6PD Chatham (c.1003G>A), and G6PD Andalus (c.1361G>A). This broad spectrum of mutation illustrated the Malay people’s rich history of interaction with neighboring Southeast Asia ethnic groups, outside traders, and Chinese and Indian immigrants [3].

Meanwhile, for Chinese ethnicity in Malaysia, G6PD Canton (c.1376G > T) and G6PD Kaiping (c.1388 G>A) were the most common variants, representing 83.6% of cases. Several other Chinese-specific variants with lower frequencies identified were G6PD Gaohe (c.95A>G), G6PD Nankang (c.517T>C), G6PD Chinese-5 (c.1024C>T), and G6PD Quingyuan (c.392G>T) [4,30]. The finding of multiple variants among the Chinese ethnicity reflected the historical origins of the early Chinese ancestors who immigrated to Malaysia. However, there was a lower prevalence of G6PD deficiency among the Indian ethnicity, where some individuals were found to carry different variants including G6PD Namoru (c.208T>C) and G6PD Mediterranean (c.563C>T) [14].

In contrast, information and studies on the G6PD status and mutations of the indigenous Malaysian Orang Asli are scarcer. In a prior investigation, Wang et al. (2008) discovered a few cases of G6PD Coimbra (c.592 C>T), G6PD Viangchan (c.871 G>A), c.1311C>T, and IVS11 93 T>C in the Orang Asli [15]. Our previous study on five Negrito subethnicities of the Orang Asli in 2011 found that Lanoh had the highest prevalence (28%), followed by Kintak (18%), Bateq (15%), Jahai (3%), and none in Kensiu [16]. G6PD Viangchan, G6PD Coimbra, and rs1050757 make up only a small spectrum of the Negrito, in comparison to the Malay and Chinese. Despite the earlier presence of Orang Asli in Peninsular Malaysia, we believe this smaller and less diversified mutation was caused by the profound consequences of inbreeding homophily [20].

In this present study, we confirmed the high prevalence of G6PD deficiency among the Senoi Malaysian Orang Asli, with a significant degree of molecular heterogeneity. In comparison with the prevalence of the Negrito (9%), Senoi had a higher prevalence of 15.2% [17]. Therefore, according to this finding, Senoi has the highest rate of G6PD deficiency in Malaysia. According to our prevalence study, most of the G6PD-deficient Senoi Orang Asli population had G6PD deficiency with enzyme activity less than 30% of AMM (9.8%, 36/369), while only 5.4% (20/369) of the subjects had intermediate deficiency with enzyme activity between 30% to 80% of AMM.

Seven mutations were found in 69 out of 87 genotyped samples including G6PD Coimbra (c.592C>T), G6PD Kaiping (c.1388G>A), G6PD Union (c.1360C>T), G6PD Viangchan (c.871G>A), c.1311C>T, IVS11 93 T>C, and the 3’ UTR mutation +357A>G (rs1050757) polymorphism. The most common variant among the Senoi Orang Asli was G6PD Viangchan (c.871 G>A) with 22 cases (31.8%) including a case of compound female heterozygote of G6PD Viangchan and G6PD Union variants. The G6PD Kaiping variant was found only among the Jah Hut subethnicity. The exclusivity of this variant supported the idea that this subethnic group had Chinese ancestry [31]. The Senoi population also had 19 cases of the G6PD Union variant. This variant was predominantly found in the Philippines and Papua New Guinea populations, as well as in Thailand, Vietnam, and the Solomon Islands [3034]. This molecular discovery suggested a direct link between this subethnic group and the people of Indochina.

Finally, silent mutation and polymorphism were identified in three different subethnicities of the Senoi Orang Asli, the Jah Hut, Semai, and Temiar. For the 3’ UTR mutation +357A>G (rs1050757) polymorphism, it was discovered in 39.1% (34) of the G6PD deficient individuals, including 18.4% (16) in males and 20.9% (18) in females. Amini et al (2013) had previously reported this mutation in 85.4% of the G6PD-deficient Negrito Orang Asli group, with a strong association with haplotype 1311T/IVS11 93 C [20]. The finding revealed the possibility of intermarriage between the Senoi and the Negrito subethnic groups. However, more expression studies are warranted to ascertain the role of the rs1050757 mutation in the epidemiology of G6PD deficiency in Senoi and Negrito populations. In order to complete the genetic picture of G6PD deficiency in the Malaysian Orang Asli, we recommend molecular screening among the Proto-Malay group of Orang Asli in future studies. By comparing the results and annotating the variants from all groups and ethnicities, we hope to improve G6PD health care and malaria eradication for the Orang Asli population.

Conclusions

We confirmed that the Senoi Malaysian Orang Asli subethnic group has the highest prevalence of G6PD deficiency in Malaysia, with a significant difference in its molecular variants. Our findings highlight the importance of determining G6PD status in all Malaysian Orang Asli populations, for a greater emphasis on the proper and safe use of Primaquine for malaria elimination.

Supporting information

S1 File. G6PD activity of Senoi Malaysian Orang Asli.

The study’s minimal underlying data set.

(PDF)

Acknowledgments

We would like to thank the National University of Malaysia, Universiti Kebangsaan Malaysia (UKM) Medical Centre, and the Department of Orang Asli Development (JKOA) for their approval to conduct this research. Many thanks to all research participants, co-investigators, and laboratory personnel for their hard work on this project.

Data Availability

All relevant data are within the paper and its Supporting Information files.

Funding Statement

RZA received the award that funded this study. This study was funded by the Ministry of Higher Education (MOHE), Malaysia through the Exploratory Research Grant Scheme (Grant number: ERGS/1/2012/STG03/UKM/02/1). The website of funder is https://www.mohe.gov.my/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Decision Letter 0

Germana Bancone

13 Mar 2023

PONE-D-23-01672Prevalence and molecular heterogeneity of glucose-6-phosphate dehydrogenase (G6PD) deficiency in the Senoi Malaysian Orang Asli populationPLOS ONE

Dear Dr. Raja Sabudin,

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Reviewer #1: Kindly see the attached form that has a better formatting

Review of the manuscript: “Prevalence and molecular heterogeneity of glucose-6-phosphate dehydrogenase (G6PD) deficiency in the Senoi Malaysian Orang Asli population” (PONE-D-23-01672)

Summary: This article reports the results of a survey among one of Malaysia’s ethnicity (Senoi Malaysian Orang Asli) on the prevalence and dominant genotypes of G6PD deficiency. A total of 662 participants were screened by phenotypic test and all those identified as deficient (n=87, 13%) were genotyped. Among all phenotypic deficient participants, seven G6PD variants were identified. The authors conclude that the prevalence of G6PD deficiency was very high among the study population.

General: The addressed question is relevant for the local context. My key concerns are:

• The authors report overall prevalence of G6PD deficiency within the target population but do not provide any details on how participants were recruited. If participants were not recruited at random and multiple members of the same family were enrolled, the reported prevalence will be biased. The authors need to report prevalence together with its variation (95% confidence interval or interquartile range)

• The authors do not explain their statistical analysis in the methods section, some information is provided in the results section that needs to be moved accordingly. From the results section I understand that the authors calculated the mean G6PD activity after excluding everyone with activities below the manufacturers recommended range of normal activities (<7.8U/gHb). This mean was then defined as 100% activity and anyone with <10% activity was categorised as severe and anyone with >10% activity and <60% was defined as moderate deficient. I recommend that the authors calculate the adjusted male median (AMM) [1] instead and define anyone with activities below 30% of the AMM as deficient and anyone with activities >30% and <70% of the AMM as having intermediate activities. This is the approach chosen by the majority of comparable articles (for example [2]). I am also unsure why the authors stratify their analysis by age group? I am not aware that G6PD activity would differ between 2–12-year-old and older individuals? The here observed difference is likely due to chance.

• Genotyping only phenotypically deficient individuals introduces a bias. Is there any chance the authors can also genotype a random subset of phenotypically G6PD normal individuals?

Minor comments:

• Can the authors add definitions of G6PD deficiency in the abstract?

• Can the authors add total numbers of males and females enrolled in the abstract to put the proportion of deficinet males and females into perspective?

• In the abstract pervalence of G6PD deficinecy is mentioned twice, in lines 32 and 34, kindly streamline

• In the abstract, can the authors start of by stating that no mutation was found among 18 genotyped and deficnet indidvausl (if I counted correct).

• In the abstract can the authors include how many individuals were found to be hemi/homo or heterozygous?

• Line 38 and following, can the authors add absolute numbers to the proportions?

• Line 48: this statement requires a reference.

• Line 52: replace “disease” by “condition”?

• Line 53: G6PD deficient indivduals can be found in almost all populations, not only the mentioned continents.

• Line 74 states that Primaquine is the most widely used antimalarial and this statement will need a reference.

• Line 77 states: “Despite the high susceptibility and endemicity of malaria among the Orang Asli in Malaysia” – can the authors clarify what susceptoibility refer to?

• Table 3: can the authors add that this table only covers G6PD normals? Why not include deficients as a comparisson as well?

• Line 173: how was the level of significance calculated? Please add this to the methods.

• Table 5: rather than categorising all variants as “moderate” or “severe”, present range of observed activities / variant

• Table 5: In the “total: column there is a mention of “21+2” etc. and it is unclear what this means. Is there a footnote missing?

• Throughout the text the authors refer to a variation as ± (for example 14.33±3.48 in line 36) and this is ambiguous. Can the authors replace this by mean and 95%CI for normal distributed data and median and IQR for not normally distributed data?

• Were all partricipanst afebrile and free of malaria? If yes, kindly add.

• Throughout the entire article, the authors should include manufacturer and country of the manufacturer whenever mentioning a product.

Language: the language of the manuscript must be revised by a native English speaker familiar with the topic

Reference:

1. Domingo, G.J., et al., G6PD testing in support of treatment and elimination of malaria: recommendations for evaluation of G6PD tests. Malar J, 2013. 12: p. 391.

2. Ley, B., et al., Wide range of G6PD activities found among ethnic groups of the Chittagong Hill Tracts, Bangladesh. PLOS Neglected Tropical Diseases, 2020. 14(9): p. 8697--1.

Reviewer #2: This is a well written paper with clear and concise findings. I only have minor edits to suggest before moving this forward to publication.

Ln 24 italicize plasmodium

Ln 31 subethnic group

Ln 76 P. falciparum

Were the quantitative assays run in duplicate? I am unfamiliar with this kit, it might be valuable to include any literature comparing this kit with Point scientific or trinity biotech G6PD spectrophotometric tests.

General comment – be consist with use of sub-ethnic vs subethnic - same goes for subethnicity

How did normal G6PD thresholds match up with the study by Pfeffer et al. “Quantification of glucose-6-phosphate dehydrogenase activity by spectrophotometry: A systematic review and meta-analysis” I’d be interested in seeing if they aligned, given the unique population of this study.

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Reviewer #2: No

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Attachment

Submitted filename: Review Pone D23-01672.docx

PLoS One. 2023 Dec 12;18(12):e0294891. doi: 10.1371/journal.pone.0294891.r002

Author response to Decision Letter 0


4 Sep 2023

Response to Editor's comments:

1. Thank you for the comments. We have checked though the PLOS ONE's style requirements and made necessary amendments, including the file names.

2. We apologize for the tehcnical issue. We have now removed the funding-related text from the manuscript (the Acknowledgement section). Thank you, we agreed with the current Funding Statement and no further updates are required from our side.

3. We have uploaded our study’s minimal underlying data set as Supporting Information file 1 (S1_file.pdf). We have fully anonymized the data and removed any potentially identifying patient information. Thank you.

Response to Reviewer 1:

1. Thank you for your valuable comments. The authors have exluded the family members in calculation of the overall prevalence to prevent bias. We have recalculated and provided a revised prevalence, as well as its variation (95% confidence interval). These results were written in abstract as well as in the body of the manuscript.

In the abstract:

“…The overall prevalence of G6PD deficiency was 15.2% (95% Confidence Interval: 11-19%; 56 of 369) , with males (30 of 172; 17.4%) outnumbering females (26 of 197; 13.2%). The adjusted male median (AMM), defined as 100% G6PD activity, was 11.8 IU/gHb. A total of 36 participants (9.6%; 26 male and 10 female) were severely deficient (<30% of AMM) and 20 participants (5.4%; 4 male and 16 female) were G6PD-intermediate (30 - 80% of AMM).”

2. Thank you for this comment. We have added the explaination on statistical analysis in the methods section (Data analysis) as suggested.

We appreciate the Reviewer’s recommendation. We have amended our calculation using the adjusted male median (AMM). We have also used the cut-off threshold of 30% and 70% as per advised.

We agreed with the comments given regarding the age. We have amended our manuscript and did not stratify the analysis by age group.

3. We have genotyped a random subset of phenotypically G6PD normal individuals. We have now included this point in our manuscript.

“Molecular analysis was performed on 87 samples including all G6PD-deficient blood samples (n=56) and subset of G6PD-normal sample (n=31).”

MINOR

Thank you for the excellent comments. We have amended our manuscript accordingly:

1. We have added definitions of G6PD deficiency in the abstract.

“Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked genetic disorder characterized by reduced G6PD enzyme level in the blood.”

2. We have added the total numbers of males and females enrolled in the abstract.

“…A total of 662 blood samples (369 males and 293 females).”

3. We have amended the lines mentioned and streamlined the details.

4. Excellent suggestion. We have included this point as suggested. Yes, the number given (n=18) was correct.

“A total of 87 samples were genotyped, of which 18 showed no mutation.”

5. We have included the number of participants with the hemi/homo or heterozygous in the abstract as suggested.

“Our analysis revealed 27 hemizygote males, 18 heterozygote females, 7 homozygote females, and 2 compound heterozygote females.”

6. In lines 38 (abstract), the authors have added absolute numbers to the proportions as requested.

“…Seven mutations were found among 69 genotyped samples; IVS11 T93C (47.1%; n=41), rs1050757 (3’UTR +357A>G)(39.1%; n=34), G6PD Viangchan (c.871G>A)(25.3%; n=22), G6PD Union (c.1360C>T)(21.8%; n=19), c.1311C>T(20.7%; n=18), G6PD Kaiping (c.1388G>A)(8.0%; n=7), and G6PD Coimbra (c.592C>T)(2.3%; n=2).

7. The authors have added a suitable reference for this statement.

Luzzatto L, Ally M, Notaro R. Glucose-6-phosphate dehydrogenase deficiency. Blood. 2020;136(11): 1225–1240. doi: 10.1182/blood.2019000944

8. We have replaced the word “disease” with “condition”.

9. We agreed with this comment, and we have amended the sentence accordingly to address this point.

“This X-linked hereditary condition affects the entire world, but it is more prevalent particularly in parts of the African continent, the Middle East, and Southeast Asia, where it often overlaps with the geographical distribution of malaria infection.”

10. We have added a reference for this statement.

Camarda G, Jirawatcharadech P, Priestley RS, Saif A, March S, Wong MH, Leung S, et al. Antimalarial activity of primaquine operates via a two-step biochemical relay. Nature communications. 2019 Jul 19;10(1):3226.

11. We have added a sentence to further clarify the point of high susceptibility.

“…The Orang Asli population is highly susceptible to mosquito bites and malaria infection due to their isolated settlements in tropical forests and traditions of hunting and foraging for food in the jungle….”

12. Thank you for this excellent comment. We have amended the table accordingly (Refer Tables 3 and 4).

13. We have added the method for calculation of significance in the “Data Analysis” section.

14. We have amended the table and presented the range of observed activities as suggested (Refer Table 5).

15. We have added the footnote missing from the table.

“Footnote: 1a refers to a compound heterozygote case of G6PD Viangchan + Union, and 1b refers to a compound heterozygote case of G6PD Kaiping + Union”

16. Thank you for the comment. We have included the 95%CI for our AMM value and G6PD levels for all genotypes in Table 5. However, for other values throughout the text, we would like to respectfully propose using the mean and standard deviation (SD) (example: 14.33±3.48 ) as measures of variation, rather than the 95% confidence interval (CI), to represent our data. We believe that the mean and SD provide a clear and concise way to describe the central tendency and spread of our data, without the additional complexity introduced by the CI. The use of these statistics aligns with common reporting practices in our field and maintains the readability of our manuscript.

17. Yes, all participants were afebrile and free of malaria. We have added this information in the “Result” section.

“The participants were healthy, afebrile, and free of malaria.”

18. We have checked the entire manuscript and included the details of the manufacturer and country of the manufacturer for all products mentioned. All details were provided in the first mention, and these details were not included in subsequent mention throughout the manuscript (aligned with the journal’s guideline).

For language improvement, we have conducted a thorough grammar check and revision of the manuscript to ensure its clarity and readability. We have included the relevant references given in our reference list.

Response to Reviewer 2:

1. Thank you. We have amended all mentioned points accordingly, including Lines 24,31,76, as suggested.

2. The quantitative assays were not run in duplicate for our study. While trying our best, we have included a statement in addresing this point with inclusion of several relevant references.

“In numerous earlier research, the OSMMR-2000D kit assay served as the gold standard quantitative G-6-PD enzymatic test. [18,19,25 – 28].”

3. We have checked through the manuscript and be consistent in using subethnic and subethnicity (13 replacements).

4.Thank you for your high interest. We appreciate your comment.

In our study, the normal threshold for 100% G6PD activity corresponded to a slightly higher value of 11.8 IU/gHb. The mentioned paper by Pfeffer et al. (2020) stated that a universal threshold of 100% G6PD activity was defined as 9.4 IU/gHb. However, the authors also highlighted that caution is stricly advised in comparing findings based on absolute G6PD activity measurements across studies due to variability in laboratory methods, with possible contribution of unmeasured population factors. We have briefly included this interesting point and the mentioned reference in our manuscript as well.

“The normal threshold for 100% G6PD activity, the AMM, of our study corresponded to a slightly higher value of 11.8 IU/gHb compared to a universal threshold of 9.4 IU/gHb, as described by a meta analysis study of Pfeffer et al. (2020) [25]. However, as described by the article, researchers should strongly cautioned against drawing conclusions solely on absolute G6PD activity from different studies, due to interlaboratory variability and possible unmeasured population factors.”

Attachment

Submitted filename: Response to Reviewers.docx

Decision Letter 1

Germana Bancone

18 Sep 2023

PONE-D-23-01672R1Prevalence and molecular heterogeneity of glucose-6-phosphate dehydrogenase (G6PD) deficiency in the Senoi Malaysian Orang Asli populationPLOS ONE

Dear Dr. Raja Sabudin,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

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Reviewer #1: Yes

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Please see attachment for better formatting

Re-Review of the manuscript: “Prevalence and molecular heterogeneity of glucose-6-phosphate dehydrogenase (G6PD) deficiency in the Senoi Malaysian Orang Asli population” (PONE-D-23-01672_R1)

Summary: Most of my comments have been addressed (many thanks), I have some comments around the involved statistics, kindly see below, line numbers refer to the manuscript with highlighted changes.

Statistics:

• Line 164 to 168. Why do the authors calculate the mean G6PD activity and the AMM? This is a bit confusing. It would be easier to just calculate and report the AMM.

• Line 168: the authors describe how they assessed differences in G6PD activities using a paired T-test and this is the wrong test. A paired test requires paired measurements (for example by testing the same person with two different assays) but I don’t think this is given here. Also, G6PD activity is probably not normally distributed, and this is one of the requirements for a T-test. The authors should consider using the Mann-Whitney U test instead.

• Line 195: The authors report the mean G6PD activity for children and adults stratified. I cannot understand how this distinction could be useful (please also see my previous comments). Unless the current literature is wrong, G6PD activity does not change much once an individual has reached one year of age. Any observed differences between children and adults are therefore likely due to chance. Consider removing this element?

• Line 196 – 197: Rather than comparing mean activities between age groups and gender, it would be better to compare proportions of deficient and intermediate individuals between females and males. The authors could consider a Chi-square test for this.

• Lines 208 – 211: Can the authors show how genotype and phenotype are associated? Perhaps in a figure where G6PD activities for each genotype (and for genotypically unknown/normal participants) is displayed. For an example see [1] figure 2

Minor comments:

• Line 197: Change this sentence so it reads “The prevalence of G6PD deficiency…”

• Line 239: Pfeffer et al do not describe a universal G6PD cut-off, please remove this statement

1. Pfeffer, D.A., et al., Genetic Variants of Glucose-6-Phosphate Dehydrogenase and Their Associated Enzyme Activity: A Systematic Review and Meta-Analysis. Pathogens, 2022. 11(9).

Reviewer #2: (No Response)

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Reviewer #1: Yes: Benedikt Ley

Reviewer #2: No

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While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2023 Dec 12;18(12):e0294891. doi: 10.1371/journal.pone.0294891.r004

Author response to Decision Letter 1


5 Oct 2023

Statistic:

1. Thank you for your comments. The authors agreed with the point given and have removed the calculation of the mean as suggested. The authors have only reported the AMM.

(Deleted sentence -Line 164-168)

2. Thank you for your insightful comments. The mentioned line (Line 168) reported on mean G6PD activity. This sentence, based on the first remark, has been removed by the authors. As a result, neither the paired T-test nor the Mann-Whitney U test was performed in this revised version.

3. The authors agreed with this comment and have removed this element from the manuscript.

(Deleted sentence -Line 195-197)

4. The authors agreed with this comment and have performed a Chi-square test to compare the proportions of deficient and intermediate individuals between females and males. The following sentences were added:

(Line 191-195)

“A Chi-square test was performed to compare the proportions of deficient and intermediate individuals between females and males. Results revealed no significant difference (p = 0.111) in the proportion of deficient individuals between the two categories. However, there was a statistically significant variation in the proportion of intermediate individuals between males and females in the studied population (p = 0.007).

5. Thank you for this comment. The authors have added a figure to display the association between genotype and phenotype, guided by the given example.

(Fig 1. G6PD activity distributions (% Normal) for Coimbra, Kaiping, Union, Viangchan, and unknown variants among the Senoi Malaysian Orang Asli population.)

Minor comments:

• Line 187: The sentence was amended to “The prevalence of G6PD deficiency was 15.2%”.

• Line 237-242: The statement was removed

Decision Letter 2

Germana Bancone

13 Nov 2023

Prevalence and molecular heterogeneity of glucose-6-phosphate dehydrogenase (G6PD) deficiency in the Senoi Malaysian Orang Asli population

PONE-D-23-01672R2

Dear Dr. Raja Sabudin,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Germana Bancone, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Before publication, I would invite the authors to revise their calculation of Chi squared when comparing G6PD deficient phenotypes between sex. According to my calculation based on numbers provided, both the "severe" phenotype and the intermediate phenotype are significantly different between male and females.

On a correlated note, while defined in the results as activity <30%, the use of term "severe" for G6PD deficiency in this context does not seem appropriate. I would suggest the authors use just "deficient" and "intermediate".

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: (No Response)

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #3: No

**********

Acceptance letter

Germana Bancone

4 Dec 2023

PONE-D-23-01672R2

Prevalence and molecular heterogeneity of glucose-6-phosphate dehydrogenase (G6PD) deficiency in the Senoi Malaysian Orang Asli population

Dear Dr. Raja Sabudin:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

If we can help with anything else, please email us at customercare@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Dr. Germana Bancone

Academic Editor

PLOS ONE

Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 File. G6PD activity of Senoi Malaysian Orang Asli.

    The study’s minimal underlying data set.

    (PDF)

    Attachment

    Submitted filename: Review Pone D23-01672.docx

    Attachment

    Submitted filename: Response to Reviewers.docx

    Data Availability Statement

    All relevant data are within the paper and its Supporting Information files.


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