Aims: This study was aimed to investigate predictive prevalence of rs11385942 and rs657152 single nucleotide polymorphisms (SNPs) in the world populations since these were associated with severe COVID-19. 

Methods: Genetic data of rs11385942 and rs657152 SNPs of the 26 populations were obtained from the 1000 Genomes project. Phenotypes were assigned as high-risk, medium-risk or no-risk based on the carrying of characteristics risk alleles. 

Results: It was demonstrated that the prevalence of risk allele associated with rs11385942 SNP for developing severe COVID-19 was significantly different in various ethnic groups (Chi-square test, p<0.00001) with highly prevalent in South Asia (29.6%; 95% CI 27%-32%), followed by Europe (8.1%; 95% CI 6%-10%), Africa (5.3%; 95% CI 4%-7%), America (4.6%; 95% CI 3%-6%) and East Asia (0.5%; 95% CI 0%-1%), respectively. However, prevalence of risk allele associated with rs657152 SNP was not significantly different in various ethnic groups (Chi-square test, p=0.06) but was highly prevalent in South Asia (46.1%; 95% CI 44%-48%), followed by Africa (43.6%; 95% CI 43%-44%), Europe (36.8%; 95% CI 36%-37%), East Asia (36.3%; 95% CI 35%-38%) and America (30.5%; 95% CI 30%-31%), respectively. High-risk phenotypes associated with carrying two copies of rs11385942 variant alleles were significantly different in various ethnic groups (Chi-square test, p=0.005) with highly prevalent in South Asia (9.4%; 95% CI 7%-12%), followed by Africa (0.6%; 95% CI 0%-1%) and America (0.3%; 95% CI 0%-1%), respectively. 

Conclusion: Genetic associations of rs11385942 and rs657152 with severe COVID-19 should urgently assess in different ethnicities for pathogenesis of this pandemic disease.

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was discovered in Wuhan, China, in early 2019 and since then rapidly evolved into a global pandemic [1,2]. As of 4th July 2020, there were approximately 10.1 million confirmed SARS-CoV-2 cases worldwide, with total deaths over 0.5 million [3]. Interestingly, COVID-19 has varied clinical manifestations, having only mild symptoms with the large majority of infected patients while many patients didn’t have no symptoms at all [2,4]. Mortality rates were predominantly higher in the subgroup of patients who had severe respiratory failure considered as severe COVID-19 which may requires early and prolonged support by mechanical ventilation [2,5].

The pathogenesis of COVID-19 and associated respiratory failure is poorly understood to date. Although, higher mortality is consistently associated with older age, male sex and comorbidities [6-8], however, genetic risk factors associated with severity of COVID-19 has not yet been fully clarified. A recent genome-wide association study (GWAS) attempted to delineate host genetic factors contributing to severe COVID-19 with respiratory failure [2]. This study after analyzing 8,582,968 single-nucleotide polymorphisms (SNPs) and conducted a meta-analysis of the two case–control panels involving 1980 patients at seven hospitals in the Italian and Spanish epicenters of the SARS-CoV-2 pandemic in Europe, identified two novel SNPs i.e., rs11385942 and rs657152 with severe COVID-19. The rs11385942 SNP at locus 3p21.31, had association signal spanned six genes SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6 and XCR1 whereas the rs657152 SNP at locus 9q34.2, the association signal coincided with the ABO blood group locus [2]. This study concluded that these two SNPs (rs11385942 and rs657152) were associated with severe COVID-19 as genetic susceptibility locus.

These findings emphasized that it should explore at the population levels to identify risk phenotypes associated with carrying these SNPs risk alleles for identifying people who may be at greater risk for severe COVID-19 in different ethnicities. The current study was therefore aimed to investigate predictive prevalence of the rs11385942 and rs657152 SNPs and associated risk phenotypes susceptible to severe COVID-19 in the world populations using 1000 Genomes genetic data.

Study participants

This study utilized all genetic data pertaining rs11385942 and rs657152 obtained from five continental groups, the Americas (AMR), Europe (EUR), Africa (AFR), South Asia (SAS) and East Asia (EAS) participated in the 1000 Genomes project as described elsewhere [9,10]. In the continent of America four ethnic groups (CLM= Colombian in Medellin, Colombia; MXL= Mexican Ancestry in Los Angeles, California; PEL= Peruvian in Lima, Peru; PUR= Puerto Rican in Puerto Rico) consisting of 347 healthy volunteers were participated in the 1000 Genomes project. Similarly, in the Europe five ethnic groups (CEU= Utah residents with Northern and Western European ancestry; FIN=Finnish in Finland; GBR= British in England and Scotland; IBS=Iberian populations in Spain; TSI= Toscani in Italy) consisting of 503 healthy volunteers were participated in the 1000 Genomes project. In the Africa seven ethnic groups (ACB=African Caribbean in Barbados; ASW=African Ancestry in Southwest US; ESN= Esan in Nigeria; GWD=Gambian in Western Division, The Gambia; LWK=Luhya in Webuye, Kenya; MSL=Mende in Sierra Leone; YRI= Yoruba in Ibadan, Nigeria) consisting of 661 healthy volunteers were participated in the 1000 Genomes project. In the South Asia five ethnic groups (BEB, Bengali in Bangladesh; GIH= Gujarati Indian in Houston, TX; ITU= Indian Telugu in the UK; PJL= Punjabi in Lahore, Pakistan; STU= Sri Lankan Tamil in the UK) consisting of 489 healthy volunteers were participated in the 1000 Genomes project. In the East Asia five ethnic groups (CDX= Chinese Dai in Xishuangbanna, China; CHB=Han Chinese in Bejing; CHS=China, Southern Han Chinese, China; JPT= Japanese in Tokyo, Japan; KHV= Kinh in Ho Chi Minh City, Vietnam) consisting of 504 healthy volunteers were participated in the 1000 Genomes project.

Allele frequency and determination of risk phenotypes

Allele and genotype frequency of rs11385942 and rs657152 were obtained from the 1000 Genomes project Phase III in line with Fort Lauderdale principles 11. Since no genotype information was available for rs657152 SNP, therefore, phenotypes were assigned based on the carrying of rs11385942 risk allele only. Participants carrying two copies of rs11385942 SNP were predicted to consider as high-risk phenotypes. In a comparative fashion, participants carrying one copy of the rs11385942 SNP were predicted to consider as medium-risk phenotypes. However, participants carrying no mutation of the rs11385942 SNP were predicted to consider as no-risk/normal phenotypes. 

Prevalence of rs657152 risk allele is presented as descriptive statistics as frequency and with 95% CI calculation in five continental groups consisting of 26 populations participated in 1000 Genomes project. However, prevalence of rs11385942 risk allele as well as associated risk phenotypes as determined by the method described above is presented as descriptive statistics also as frequency and with 95% CI calculation in five continental groups consisting of 26 populations participated in 1000 Genomes project.

All the genetic data of human presented in this study were obtained from 1000 Genomes project Phase III in line with Fort Lauderdale principles. By this principle, no further human ethics approval is required to publish any results using 1000 Genomes project data as it has already published elsewhere [9,10].

All data analysis was primarily carried out by principal investigator. However, all data analysis was also carried out by an independent reviewer anonymously. Finally, the author double checked analyzed data provided by this independent researcher and amended it if found any anomalies.

The datasets generated during and/or analysed during this current study are available in the 1000 Genomes data repository (https://www.internationalgenome.org/).

Using rs11385942 SNP data from 1000 Genomes project, it was found that the variant allele was prevalent in 9.5% (95% CI 9%-10%) of the total 26 populations participated in this genomic project. It was also found that variant allele was prevalent highest in South Asia (29.6%; 95% CI 27%-32%), followed by Europe (8.1%; 95% CI 6%-10%), Africa (5.3%; 95% CI 4%-7%), America (4.6%; 95% CI 3%-6%) and East Asia (0.5%; 95% CI 0%-1%), respectively as shown in Figure 1. The risk allele associated with the rs11385942 SNP was prevalent significantly different in various ethnicities as assessed by Chi-square test, p<0>

However, as described in Method section, high-risk phenotypes due to carrying two copies of the rs11385942 variant alleles were highly prevalent in South Asia (9.4%; 95% CI 7%-12%), followed by Africa (0.6%; 95% CI 0%-1%) and America (0.3%; 95% CI 0%-1%), respectively as shown in Figure 2. No high-risk phenotypes were found in East Asia and European population. The high-risk phenotypes associated with the rs11385942 SNP was prevalent significantly different in various ethnicities as assessed by Chi-square test, p=0.005. However, medium-risk phenotypes were found highest in South Asia (40.3%; 95% CI 36%-45%), followed by Europe (16.1%; 95% CI 13%-19%), Africa (9.4%; 95% CI 7%-12%), America (8.6%; 95% CI 6%-12%) and East Asia (1%; 95% CI 0%-2%), respectively as shown in Figure 2. Medium-risk phenotypes associated with the rs11385942 SNP was also prevalent significantly different in various ethnicities as assessed by Chi-square test, p<0>

Using rs657152 SNP data from 1000 Genomes project, it was found that the variant allele was prevalent in 38.6% (95% CI 38%-39%) of the total 26 populations participated in this genomic project. It was also found that variant allele was prevalent highest in South Asia (46.1%; 95% CI 44%-48%), followed by Africa (43.6%; 95% CI 43%-44%), Europe (36.8%; 95% CI 36%-37%), East Asia (36.3%; 95% CI 35%-38%) and America (30.5%; 95% CI 30%-31%), respectively as shown in Figure 3. Although the risk allele associated with the rs657152 SNP was not prevalent significantly different in various ethnicities (Chi-square test, p=0.06) but was considerably high in different ethnic groups.

The results of this study hypothesized that ~10-39% of the world population were being at susceptible to severe COVID-19 due to carrying rs11385942 and rs657152 genetic polymorphisms, warranting urgent future studies to assess these genetic associations with prognosis and severity of COVID-19.

In summary, it was found that ~10-39% of the total 26 populations participated in 1000 Genomes project were identified as being as carrying risk alleles due to rs11385942 and rs657152 SNPs and were predicted to develop severe COVID-19.

Although demographic characteristics e.g., age and sex or comorbidities of COVID-19 patients have been associated with clinical severity of COVID-19, however, genetic associations have not been widely studied. The findings of present study may therefore assist in designing genetic association studies providing evidence that at least two SNPs were predictively associated with severe COVID-19 and were prevalent in considerable proportion of the world populations. 

The rs11385942 on chromosome 3p21.31 covered a cluster of six genes i.e., SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6, and XCR1. Several of these genes have functions that are potentially relevant to COVID-19. For example, SLC6A20 encodes the sodium–imino acid transporter 1 (SIT1) which interacts with angiotensin-converting enzyme 2 (ACE2) functionally [2]. It has already been well-established that ACE2 acts as cell-surface receptor for host entry of SARS-CoV-2 [12-14]. Another example is the C-X-C motif chemokine receptor 6 (CXCR6) encoded by the CXCR6 gene which regulates specific location of lung CD8 T cells throughout the sustained immune response to airway pathogens. As such, a recent GWAS concluded that the rs11385942 SNP on chromosome 3p21.31 locus was involved in COVID-19 susceptibility with a possible enrichment in patients with severe COVID-19 [2]. 

Considerably higher and significantly different frequency of the risk allele and associated risk phenotypes due to carrying homozygous or heterozygous of the rs11385942 SNP among the world populations as identified in the current study suggesting that patients with this variant may develop severe COVID-19 than patients with homozygous for the non-risk allele. The findings of the current study also suggesting that South Asian people are being at greater risk for developing severe COVID-19 than other ethnicities.

The ABO blood groups have also been implicated in susceptibility to SARS-CoV-2 infection as reported in recent preprint studies [15,16]. Recent GWAS confirmed that blood group O was associated with a lower risk of acquiring COVID-19 than that in non-O blood groups. In contrast, blood group A was associated with a higher risk of acquiring COVID-19 than non-A blood groups indicating that the rs657152 on chromosome 9q34.2 coincided with the ABO blood group locus holds considerable risk for population stratification [2]. The findings of present study revealed that the risk allele associated with rs657152 SNP was prevalent substantially high in various ethnicities in which South Asian people being at greater risk for developing severe COVID-19. 

From the findings of current study, it is also hypothesized that these two SNPs i.e., rs11385942 and rs657152 may also involve not only severity of COVID-19 but also SARS-CoV-2 test positivity. This is because, recent findings indicated that SARS-CoV-2 test positivity was significantly different for various ethnic COVID-19 patients [17]. Importantly, only a small proportion of suspected patients were positive for SARS-CoV-2 testing [17-19] rendering that some genetic factors may contribute for this variability in SARS-CoV-2 test positivity. 

The great novelty of the present study is that it is the first study predictively identified risk allele and associated risk phenotypes considering 1000 Genomes genetic data of 26 populations and indicating that the risk allele and also risk phenotypes for developing severe COVID-19 were prevalent significantly different in various ethnicities. The pharmacogenomic considerations of the two SNPs i.e., rs11385942 and rs657152 in the pathogenesis of COVID-19 may ensure precision public health in terms of providing effective prognosis, prevention and controlling measures in advance. These findings warranted urgent clinical studies for assessing these genetic associations with severity of COVID-19 for effective pathogenesis, controlling and prevention of the SARS-CoV-2 pandemic virus.

There are some limitations of this study. Firstly, it is a predictive study, therefore, the association of risk allele due to carrying rs11385942 and rs657152 SNPs with severity of COVID-19 may vary in real-world clinical assessment. Secondly, genotype–phenotype association of current findings may also vary. Thirdly, adjustments for all potential sources of bias e.g., underlying cardiovascular and metabolic factors, demographics i.e., age/sex was not considered for assessing severity of COVID-19. Future clinical studies should consider and adjusted these potential confounders for assessing genetic associations with severity of COVID-19.

Prevalence of risk alleles and associated risk phenotypes due to carrying rs11385942 and rs657152 SNPs was significantly different in various ethnic groups where South Asian people may have greater risk for developing severe COVID-19 as compared to other ethnicities. Genetic associations of rs11385942 and rs657152 SNPs with severe COVID-19 should urgently assess at population levels in different ethnicities for effective pathogenesis, controlling and prevention of the SARS-CoV-2 pandemic virus.

Nothing to declare.

Funding: No funding was available for undertaking this research.

Data availability: All relevant data used in this analysis is freely available upon request.

Author contribution: This is a single authored article; therefore, it was concepted, designed and performed all analysis by MB. This manuscript was drafted by MB also.

Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh.