Impact of natural selection on global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection

Human genomic diversity has been shaped by both ancient and ongoing challenges from viruses. The current coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a devastating impact on population health. However, genetic diversity and evolutionary forces impacting host genes related to SARS-CoV-2 infection are not well understood. We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (angiotensin converting enzyme 2 [ACE2], transmembrane protease serine 2 [TMPRSS2], dipeptidyl peptidase 4 [DPP4], and lymphocyte antigen 6 complex locus E [LY6E]). We analyzed data from 2,012 ethnically diverse Africans and 15,977 individuals of European and African ancestry with electronic health records and integrated with global data from the 1000 Genomes Project. At ACE2, we identified 41 nonsynonymous variants that were rare in most populations, several of which impact protein function. However, three nonsynonymous variants (rs138390800, rs147311723, and rs145437639) were common among central African hunter-gatherers from Cameroon (minor allele frequency 0.083 to 0.164) and are on haplotypes that exhibit signatures of positive selection. We identify signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage compared with the chimpanzee genome. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19. Our study provides insights into global variation at host genes related to SARS-CoV-2 infection, which have been shaped by natural selection in some populations, possibly due to prior viral infections.

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronaviruses are enveloped, positive-sense, and single-stranded RNA viruses, many of which are zoonotic pathogens that crossed over into humans. Seven coronavirus species, including SARS-CoV-2, have been discovered that, depending on the virus and host physiological condition, may cause mild or lethal respiratory disease. There is considerable variation in disease prevalence and severity across populations and communities. Importantly, minority populations in the United States appear to have been disproportionally affected by COVID-19 (1, 2). For example, in Chicago, more than 50% of COVID-19 cases and nearly 70% of COVID-19 deaths are in African Americans (who make up 30% of the population of Chicago) (1). While social and economic factors are largely responsible for driving COVID-19 health disparities, investigating genetic diversity at host genes related to SARS-CoV-2 infection could help identify functionally important variation, which may play a role in individual risk for severe COVID-19 infection.In this study, we focused on four key genes playing a role in SARS-CoV-2 infection (3). The ACE2 gene, encoding the angiotensin-converting enzyme-2 protein, was reported to be a main binding site for severe acute respiratory syndrome coronavirus (SARS-CoV) during an outbreak in 2003, and evidence showed stronger binding affinity to SARS-CoV-2, which enters the target cells via ACE2 receptors (3, 4). The ACE2 gene is located on the X chromosome (chrX); its expression level varies among populations (5); and it is ubiquitously expressed in the lung, blood vessels, gut, kidney, testis, and brain, all organs that appear to be affected as part of the COVID-19 clinical spectrum (6). SARS-CoV-2 infects cells through a membrane fusion mechanism, which in the case of SARS-CoV, is known to induce down-regulation of ACE2 (7). Such down-regulation has been shown to cause inefficient counteraction of angiotensin II effects, leading to enhanced pulmonary inflammation and intravascular coagulation (7). Additionally, altered expression of ACE2 has been associated with cardiovascular and cerebrovascular disease, which is highly relevant to COVID-19 as several cardiovascular conditions are associated with severe disease. TMPRSS2, located on the outer membrane of host target cells, binds to and cleaves ACE2, resulting in activation of spike proteins on the viral envelope and facilitating membrane fusion and endocytosis (8). Two additional genes, DPP4 and LY6E, have been shown to play an important role in the entry of SARS-CoV-2 virus into host cells. DPP4 is a known functional receptor for the Middle East respiratory syndrome coronavirus (MERS-CoV), causing a severe respiratory illness with high mortality (9, 10). LY6E encodes a glycosylphosphatidylinositol-anchored cell surface protein, which is a critical antiviral immune effector that controls coronavirus infection and pathogenesis (11). Mice lacking LY6E in hematopoietic cells were susceptible to murine coronavirus infection (11).Previous studies of genetic diversity at ACE2 and TMPRSS2 in global human populations did not include an extensive set of African populations (5, 12–14). No common coding variants (defined here as minor allele frequency [MAF] > 0.05) at ACE2 were identified in any prior population studies. However, few studies included diverse indigenous African populations whose genomes harbor the greatest diversity among humans. This leads to a substantial disparity in the representation of African ancestries in human genetic studies of COVID-19, impeding health equity as the transferability of findings based on non-African ancestries to African populations can be low (15). Including more African populations in studying the genetic diversity of genes involved in SARS-CoV-2 infection is extremely necessary. Additionally, the evolutionary forces underlying global patterns of genetic diversity at host genes related to SARS-CoV-2 infection are not well understood. Using methods to detect natural selection signatures at host genes related to viral infections helps identify putatively functional variants that could play a role in disease risk.We characterized genetic variation and studied natural selection signatures at ACE2, TMPRSS2, DPP4, and LY6E in ethnically diverse human populations by analyzing 2,012 genomes from ethnically diverse Africans (referred to as the “African diversity” dataset), 2,504 genomes from the 1000 Genomes Project (1KG), and whole-exome sequencing of 15,977 individuals of European ancestry (EA) and African ancestry from the Penn Medicine BioBank (PMBB) dataset (SI Appendix, Fig. S1). The African diversity dataset includes populations with diverse subsistence patterns (hunter-gatherers, pastoralists, agriculturalists) and speaking languages belonging to the four major language families in Africa (Khoesan; Niger–Congo, of which Bantu is the largest subfamily; Afroasiatic; and Nilo-Saharan). We identify functionally relevant variation, compare the patterns of variation across global populations, and provide insight into the evolutionary forces underlying these patterns of genetic variation. In addition, we perform an association study using the variants identified from whole-exome sequencing at the four genes and clinical traits derived from electronic health record (EHR) data linked to the subjects enrolled in the PMBB. The EHR data include diseases related to organ dysfunctions associated with severe COVID-19, such as respiratory, cardiovascular, liver, and renal complications. Our study of genetic variation in genes involved in SARS-CoV-2 infection provides data to investigate infection susceptibility within and between populations and indicates that variants in these genes may play a role in comorbidities relevant to COVID-19 severity.     

Changes in Running Speeds in a 100 KM Ultra-Marathon Race

The purpose of this study was to determine if runners who completed a 100 km ultramarathon race in the fastest times changed their running speeds differently compared to those runners who ran an overall slower race. Times were taken from the race results of the 1995 100 km IAU World Challenge in Winschoten, Netherlands. Race times and 10 km split times were analyzed. Runners (n = 67) were divided into groups of ten with the last group consisting of seven runners. The mean running speed for each 10 km segment was calculated using each runner’s 10 km split times. Mean running speed was calculated using each runner’s race time. The first 10 km split time was normalized to 100, with all subsequent times adjusted accordingly. The mean running speed for each group at each 10 km split was then calculated. The faster runners started at a faster running speed, finished the race within 15 % of their starting speed, and maintained their starting speed for longer (approximately 50 km) before slowing. The slower runners showed a greater percentage decrease in their mean running speed, and were unable to maintain their initial pace for as long. It is concluded that the faster runners: 1) ran with fewer changes in speed, 2) started the race at a faster running speed than the slower runners, and 3) were able to maintain their initial speed for a longer distance before slowing.

Key Points

Faster runners in the 100 km race;

• ran with fewer changes in running speed compared to the slower runners;
• started the race at a faster running speed than the slower runners;
• were able to maintain their initial running speed for longer distances than slower runners.

Key words: Pacing strategy, peak performance, ultra-endurance     

The guanine-thymine dinucleotide repeat polymorphism within the tenascin-C gene is associated with achilles tendon injuries

BACKGROUND: Although there is a high incidence of tendon injury as a result of participation in physical activity, the mechanisms responsible for such injuries are poorly understood. Investigators have suggested that some people may have a genetic predisposition to develop tendon injuries; in particular, genes on the tip of the long arm of chromosome 9 might, at least in part, be associated with this condition. The tenascin-C gene, which has been mapped to chromosome 9q32-q34, encodes for a structural component of tendons. HYPOTHESIS: The tenascin-C gene is associated with Achilles tendon injury. STUDY DESIGN: Case control study; Level of evidence, 3. METHODS: A total of 114 physically active white subjects with symptoms of Achilles tendon injury and 127 asymptomatic, physically active white control subjects were genotyped for the guanine-thymine dinucleotide repeat polymorphism within the tenascin-C gene. RESULTS: A significant difference in the allele frequencies of this polymorphism existed between the 2 groups of subjects (chi(2) = 51.0, P = .001). The frequencies of the alleles containing 12 repeats (symptomatic group, 18.9% vs control group, 10.2%) and 14 repeats (symptomatic group, 9.2% vs control group, 0.8%) were significantly higher in the symptomatic group, while the frequencies of the alleles containing 13 repeats (symptomatic group, 8.8% vs control group, 24.0%) and 17 repeats (symptomatic group, 7.5% vs control group, 20.1%) were significantly lower in this same group. Subjects who were homozygous or heterozygous for the underrepresented alleles (13 and 17 repeats) but who did not possess an overrepresented allele (12 and 14 repeats) may have a lower risk of developing Achilles tendon injuries (odds ratio, 6.2; 95% confidence interval, 3.5-11.0; P < .001). CONCLUSIONS: The guanine-thymine dinucleotide repeat polymorphism within the tenascin-C gene is associated with Achilles tendon injury. Alleles containing 12 and 14 guanine-thymine repeats were overrepresented in subjects with tendon injuries, while the alleles containing 13 and 17 repeats were underrepresented. CLINICAL RELEVANCE: Persons who have variants of the tenascin-C gene with 12 and 14 guanine-thymine repeats appear to have a 6-fold risk of developing Achilles tendon injuries.     

24‐Month HIV‐free survival among HIV‐exposed Infants in Lesotho: the PEAWIL cohort study

IntroductionFollowing the implementation of the provision of lifelong antiretroviral therapy to all HIV‐positive pregnant or breastfeeding women for prevention of mother‐to‐child transmission (PMTCT) of HIV by the Kingdom of Lesotho in 2013, we assessed the effectiveness of this approach by evaluating 24‐month HIV‐free survival among HIV‐exposed infants (HEIs).MethodsWe conducted a prospective observational cohort study that enrolled HIV‐positive and HIV‐negative pregnant women, with follow‐up of women and their infants for 24 months after delivery. Participant recruitment started in June 2014 and follow‐up ended in September 2018. Trained nurses collected study information through patient interviews and chart abstraction at enrolment and every three to six months thereafter. Maternal HIV testing, infant mortality, HIV transmission and HIV‐free survival rates were computed using Kaplan–Meier estimation. Cox regression hazard models were used to identify factors associated with infant HIV infection and death.ResultsBetween June 2014 and February 2016, we enrolled 653 HIV‐positive and 941 HIV‐negative pregnant women. Twenty‐seven HIV‐negative women acquired HIV during follow‐up. Ultimately, 634 liveborn HEI (382 (52%) male, 303 (48%) female, 3 missing) and 839 who remained HIV‐unexposed (HUIs) (409 (49.0%) male, 426 (51.0%) female, 4 missing) were followed; 550 HEIs and 701 HUIs completed the 24‐month follow‐up period. Of 607 (95.7%) HEIs who were tested for HIV at least once during follow‐up, 17 were found to be HIV‐positive. Two (9.5%) of 21 infants born to mothers who acquired HIV infection during follow‐up were HIV‐positive compared to 15 (2.4%) of 613 HEI born to women with known HIV infection. The risk of HIV transmission from HIV‐positive mothers to their infants by 24 months of age was 2.9% (95% CI: 1.8 to 4.7). The estimated 24‐month mortality rate among HEIs was 6.0% (95% CI: 4.4 to 8.2) compared to 3.8% (95% CI: 2.6 to 5.3) among HUIs (Log‐rank p = 0.065). HIV‐free survival at 24 months was 91.8% (95% CI: 89.2 to 93.7). Lower maternal age and birth weight were independently associated with increased HIV infection or death of infants.ConclusionsThe implementation of lifelong ART for PMTCT in the Lesotho public health system resulted in low HIV transmission, but survival of HEI remains lower than their HIV uninfected counterparts.     

The COL5A1 genotype is associated with range of motion measurements

There is an interest in identifying the intrinsic risk factors, including altered musculotendinous flexibility, that may be associated with musculotendinous injuries. We have recently shown that a sequence variant, namely the BstUI restriction fragment length polymorphism (RFLP), within the COL5A1 gene is associated with chronic Achilles tendinopathy. Mutations within COL5A1 have been implicated in Ehlers Danlos syndrome, a condition that is characterized by joint hypermobility. The aim of this study was to investigate the association of sequence variants within COL5A1 and musculotendinous range of motion (ROM). The sit and reach (SR) and the passive straight leg raise (SLR) were measured on 119 Caucasian subjects with either a past, current or no history of Achilles tendon injuries. The subjects were genotyped for four sequence variants within the 3′‐UTR of the COL5A1 gene. Gender (P=0.016), age (P=0.011) and the BstUI RFLP (P=0.010) jointly contributed significantly to the optimal SLR model which accounted for 19.3% of the variance. The factors contributing significantly to SR, which accounted for 28.8% of the variance, were weight (P=0.004), age (P<0.001) and the BstUI RFLP (P=0.001). These data suggest that the COL5A1 BstUI RFLP is independently associated with lower limb ROM within the cohort investigated in this study.     

The -55 C/T polymorphism within the UCP3 gene and performance during the South African Ironman Triathlon

Uncoupling protein 3 is believed to be involved in total body energy expenditure, including the regulation of fat and glucose metabolism. These biochemical processes may distinguish top ultra-endurance triathletes from slower competitors. The aim of this study was to determine whether the uncoupling protein 3 gene is associated with the performance capacity of ultra-endurance Ironman triathletes. Two triathlete groups consisting of the 89 fastest and 89 slowest Caucasian, male triathletes who completed either the 2000 or 2001 South African Ironman triathlon events were genotyped for the -55 C/T polymorphism within the uncoupling protein 3 gene. A control group consisting of 92 Caucasian males who had not trained for or participated in an ultra-endurance athletic event was also genotyped. There was no significant difference in the genotype (CC, CT and TT) frequency distribution of the -55 C/T polymorphism within the uncoupling protein 3 gene between the fast triathlete, slow triathlete and control groups. In addition, no significant differences were observed between the frequencies of the C and T alleles between the three groups. The two triathlete groups were combined and grouped according to their genotype. No particular genotype or allele was associated with the time taken by the triathletes to complete the entire triathlon, or either the swim, cycle or run legs of the event. Thus no association was found between the -55 C/T polymorphism within the uncoupling protein 3 gene and the ultra-endurance performance of triathletes who completed either the 2000 or 2001 South African Ironman triathlons.     

The COL5A1 gene and Achilles tendon pathology

PURPOSE: There is an increase in the incidence of Achilles tendon injuries as a result of the participation in physical activity. It has been suggested that some individuals have a genetic predisposition to Achilles tendon pathology (ATP). The aim of this study was to determine whether the alpha 1 type V collagen (COL5A1) gene, which encodes for a tendon protein, is associated with the symptoms of ATP. METHODS: One-hundred and eleven Caucasian subjects diagnosed with ATP and 129 Caucasian control (CON) subjects were genotyped for the BstUI and DpnII restriction fragment length polymorphisms (RFLPs) within the COL5A1 gene. RESULTS: There was a significant difference in the allele frequencies of the COL5A1 BstUI RFLP between the ATP and CON subjects (P=0.006). The frequency of the A2 allele was significantly higher in the CON group (29.8%) than in the ATP group (18.0%) (odds ratio of 1.9; 95% confidence interval (CI) 1.3-3.0; P=0.004). This allele had a stronger protective role when only the 72 patients diagnosed with chronic Achilles tendinopathy were analyzed (odds ratio of 2.6; 95% CI 1.5-4.5). CONCLUSIONS: The COL5A1 BstUI RFLP is associated with ATP and more specifically, chronic Achilles tendinopathy. Individuals with an A2 allele of this gene are less likely of developing symptoms of chronic Achilles tendinopathy.