Asian Variant Research Articles

A Catalogue of Structural Variation across Ancestrally Diverse Asian Genomes

Structural variants (SVs) are significant contributors to inter-individual genetic variation associated with traits and diseases. Current SV studies using whole-genome sequencing (WGS) have a largely Eurocentric composition, with little known about SV diversity in other ancestries, particularly from Asia. Here, we present a WGS catalogue of 73,035 SVs from 8392 Singaporeans of East Asian, Southeast Asian and South Asian ancestries, of which ~65% (47,770 SVs) are novel. We show that Asian populations can be stratified by their global SV patterns and identified 42,239 novel SVs that are specific to Asian populations. 52% of these novel SVs are restricted to one of the three major ancestry groups studied (Indian, Chinese or Malay). We uncovered SVs affecting major clinically actionable loci. Lastly, by identifying SVs in linkage disequilibrium with single-nucleotide variants, we demonstrate the utility of our SV catalogue in the fine-mapping of Asian GWAS variants and identification of potential causative variants. These results augment our knowledge of structural variation across human populations, thereby reducing current ancestry biases in global references of genetic variation afflicting equity, diversity and inclusion in genetic research.

Functional characterization of single nucleotide polymorphic variants of DNA repair enzyme NEIL1 in South Asian populations

The base excision repair (BER) pathway is a precise and versatile mechanism of DNA repair that is initiated by DNA glycosylases. Endonuclease VIII-like 1 (NEIL1) is a bifunctional glycosylase/abasic site (AP) lyase that excises a damaged base and subsequently cleaves the phosphodiester backbone. NEIL1 is able to recognize and hydrolyze a broad range of oxidatively-induced base lesions and substituted ring-fragmented guanines, including aflatoxin-induced 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxyaflatoxin B1 (AFB1-FapyGua). Due to NEIL1’s protective role against these and other pro-mutagenic lesions, it was hypothesized that naturally occurring single nucleotide polymorphic (SNP) variants of NEIL1 could increase human risk for aflatoxin-induced hepatocellular carcinoma (HCC). Given that populations in South Asia experience high levels of dietary aflatoxin exposures and hepatitis B viral infections that induce oxidative stress, investigations on SNP variants of NEIL1 that occur in this region may have clinical implications. In this study, the most common South Asian variants of NEIL1 were expressed, purified, and functionally characterized. All tested variants exhibited activities and substrate specificities similar to wild type (wt)-NEIL1 on high-molecular weight DNA containing an array of oxidatively-induced base lesions. On short oligodeoxynucleotides (17-mers) containing either a site-specific apurinic/apyrimidinic (AP) site, thymine glycol (ThyGly), or AFB1-FapyGua, P206L-NEIL1 was catalytically comparable to wt-NEIL1, while the activities of NEIL1 variants Q67K and T278I on these substrates were ≈2-fold reduced. Variant T103A had a greatly diminished ability to bind to 17-mer DNAs, limiting the subsequent glycosylase and lyase reactions. Consistent with this observation, the rate of excision by T103A on 17-mer oligodeoxynucleotides containing ThyGly or AFB1-FapyGua could not be measured. However, the ability of T103A to excise ThyGly was improved on longer oligodeoxynucleotides (51-mers), with ≈7-fold reduced activity compared to wt-NEIL1. Our studies suggest that NEIL1 variant T103A may present a pathogenic phenotype that is limited in damage recognition, potentially increasing human risk for HCC.

Genomic analysis of lumpy skin disease virus asian variants and evaluation of its cellular tropism

Lumpy skin disease virus (LSDV) is a poxvirus that mainly affects cattle and can lead to symptoms such as severe reduction in milk production as well as infertility and mortality, which has resulted in dramatic economic loss in affected countries in Africa, Europe, and Asia. In this study, we successfully isolated two strains of LSDV from different geographical regions in China. Comparative genomic analyses were performed by incorporating additional LSDV whole genome sequences reported in other areas of Asia. Our analyses revealed that LSDV exhibited an ‘open’ pan-genome. Phylogenetic analysis unveiled distinct branches of LSDV evolution, signifying the prevalence of multiple lineages of LSDV across various regions in Asia. In addition, a reporter LSDV expressing eGFP directed by a synthetic poxvirus promoter was generated and used to evaluate the cell tropism of LSDV in various mammalian and avian cell lines. Our results demonstrated that LSDV replicated efficiently in several mammalian cell lines, including human A549 cells. In conclusion, our results underscore the necessity for strengthening LSD outbreak control measures and continuous epidemiological surveillance.

BRCA1 deficiency enhances the aggressiveness of breast cancer cells expressing HPV16 oncoproteins.

The precise etiology of breast cancer is not completely understood, although women with BRCA1 gene mutations have a significantly increased risk of developing the disease. In addition, sporadic breast cancer is frequently associated with decreased BRCA1 gene expression. Growing evidence of Human papillomaviruses (HPVs) infections in breast tumors has raised the possibility of the involvement of HPVs in the pathogenesis of breast cancer. We investigated whether the effects of HPV oncoproteins E6 and E7 were influenced by the expression levels of BRCA1. HPV16E6E7 (prototype or E6D25E/E7N29S Asian variant type) were stably expressed in MDA-MB231 breast cancer cells, wild type for BRCA1, or with BRCA1 knocked down. Expression of HPV16E6E7 oncogenes did not affect BRCA1 levels and the abundance of HPV16E6E7 was not altered by BRCA1 knockdown. BRCA1 levels did not alter HPV16E6E7-dependent degradation of G1-S cell cycle proteins p53 and pRb. However, we found that the expression of G2-M cell cycle protein cyclin B1 enhanced by HPV16E6E7 was impacted by BRCA1 levels. Especially, we found the correlation between BRCA1 and cyclin B1 expression and this was also confirmed in breast cancer samples from a Thai cohort. We further demonstrated that the combination of HPV oncoproteins and low levels of BRCA1 protein appears to enhance proliferation and invasion. Transactivation activities of HPV16E6E7 on genes regulating cell proliferation and invasion (TGF-β and vimentin) were significantly increased in BRCA1-deficient cells. Our results indicate that a deficiency of BRCA1 promotes the transactivation activity of HPV16E6E7 leading to increase of cell proliferation and invasion. HPV infection appears to have the potential to enhance the aggressiveness of breast cancers, especially those deficient in BRCA1.

Mitochondrial genetic diversity and phylogenetic relationships of Echinococcus multilocularis in Europe

The cestode Echinococcus multilocularis is the causative agent of alveolar echinococcosis, a fatal zoonotic parasitic disease of the northern hemisphere. Red foxes are the main reservoir hosts and, likely, the main drivers of the geographic spread of the disease in Europe. Knowledge of genetic relationships among E. multilocularis isolates at a European scale is key to understanding the dispersal characteristics of E. multilocularis. Hence, the present study aimed to describe the genetic diversity of E. multilocularis isolates obtained from different host species in 19 European countries. Based on the analysis of complete nucleotide sequences of the cob, atp6, nad2, nad1 and cox1 mitochondrial genes (4,968 bp), 43 haplotypes were inferred. Four haplotypes represented 62.56 % of the examined isolates (142/227), and one of these four haplotypes was found in each country investigated, except Svalbard, Norway. While the haplotypes from Svalbard were markedly different from all the others, mainland Europe appeared to be dominated by two main clusters, represented by most western, central and eastern European countries, and the Baltic countries and northeastern Poland, respectively. Moreover, one Asian-like haplotype was identified in Latvia and northeastern Poland. To better elucidate the presence of Asian genetic variants of E. multilocularis in Europe, and to obtain a more comprehensive Europe-wide coverage, further studies, including samples from endemic regions not investigated in the present study, especially some eastern European countries, are needed. Further, the present work proposes historical causes that may have contributed to shaping the current genetic variability of E. multilocularis in Europe.

Asian flush gene variant increases mild cognitive impairment risk: a cross-sectional study of the Yoshinogari Brain MRI Checkup Cohort.

The East Asian-specific genetic diversity, the rs671 variant of aldehyde dehydrogenase 2, causes the "Asian flush" phenomenon following alcohol consumption, resulting in an alcohol avoidance phenotype. The variant is suggested as a risk factor for Alzheimer's disease; however, its association with mild cognitive impairment (MCI), an effective target for secondary prevention of dementia, remains unclear. This cross-sectional study examined 430 individuals aged 60-80 years (251 women) without overt cognitive impairment in Yoshinogari, Japan. The effect of the rs671 variant on MCI, defined by scores <26 or <25 on the Japanese version of the Montreal Cognitive Assessment, was evaluated using multivariate logistic regression. The models included APOEε4, sex, age, education, history of habitual drinking, Brinkman index, hypertension, diabetes, and subclinical magnetic resonance imaging findings and consistently estimated the risk of the rs671 variant. Subsequently, stratified analyses by history of habitual drinking were performed based on an interactive effect between rs671 and alcohol consumption, and the rs671 variant significantly influenced MCI in participants who did not drink habitually, with odds ratios ranging from 1.9 to 2.1 before and after adjusting for covariates, suggesting an association independent of hippocampal atrophy and small vessel dysfunction. Conversely, no such association with the rs671 variant was observed in participants with a history of habitual alcohol use. Instead, hippocampal atrophy and silent infarcts were associated with MCI. This is the first study to demonstrate an association between the rs671 variant and MCI morbidity. The findings highlight the need for race-specific preventive strategies and suggest potential unrecognized mechanisms in dementia development.

Nonlinear relationship between body mass index and serum uric acid: An observational and Mendelian randomization study among Chinese adults

Background and aimsConflicting evidence exists on the relationship between body mass index (BMI) and serum uric acid (SUA), and importantly, the causal role of BMI in SUA remains unclear. We aimed to evaluate the BMI-SUA relationship and its causality among Chinese adults using observational and Mendelian randomization (MR) analyses. Methods and resultsStudy included 6641 adults from East China. A genetic risk score based on 14 BMI-associated East Asian variants was formulated. One-sample MR and non-linear MR analyses assessed the causal link between BMI_GRS and SUA levels. Mean BMI levels were 24.8 (SD 3.4) and 24.3 (SD 3.6) kg/m2 in men and women, respectively. Spline models revealed gender-specific BMI-SUA associations: a reverse J-shape for men and a J-shape for women (P-values for nonlinearity <0.05). In men, BMI showed a positive correlation with SUA levels when BMI was below 29.6 kg/m2 (beta coefficient 19.1 [95 % CI 15.1, 23.0] μmol/L per 1-SD increase in BMI), while in women, BMI exhibited a negative correlation with SUA levels when the BMI was less than 21.7 kg/m2 (beta coefficient −12.9 [95 % CI -21.6, −4.1] μmol/L) and a positive correlation when BMI exceeded 21.7 kg/m2 (beta coefficient 13.3 [95 % CI 10.9, 15.8] μmol/L). Furthermore, MR analysis suggested non-linear BMI-SUA link in women but not men. ConclusionOur study indicates a non-linear correlation between BMI and SUA in both genders. It is noteworthy that in women, this correlation may have a causal nature. Nevertheless, further longitudinal investigations are required to authenticate our findings.

Asian Zika virus can acquire generic African-lineage mutations during in utero infection

ABSTRACT The Zika virus 2015 epidemic showed an unusual phenotype for human flaviviruses, specifically fetal infection. We previously showed that in utero inoculation with the Asian Zika virus isolated from the human sample causes persistent infection in porcine fetuses. Here, we characterized the evolution of the Asian Zika virus in the fetal brain and placenta. Interestingly, the Asian Zika virus acquired generic African lineage K101R (A408G) and R1609 K (G4932A) mutations during in utero infection. Both African mutations were nonsynonymous and had a high frequency of nearly 100% in the fetal brain. Then, we synthetically generated the wild-type Asian variant and fetal brain-specific variant with generic African-lineage K101R and R1609 K mutations. In mosquito C6/36 cells, but not in human and pig cells, the fetal brain-specific variant showed higher virus loads compared to the Asian wild-type prototype. While in utero infection with both variants caused comparable virus loads in the placenta and amniotic fluids, fetuses injected with the fetal brain-specific variant had the trend to higher virus loads in lymph nodes. Also, introduced K101R and R1609 K mutations were stable and had high nearly 100% frequency at 28 days after in utero inoculation in both directly injected and trans-infected fetuses. These findings evoke concerns because Zika persists in pig herds and mosquitoes on farms in Mexico. It will be essential to identify how persistent in utero infection affects virus evolution and whether in utero-emerged Zika variants have the potential for shedding into the environment, more efficient transmission, and more aggressive infection phenotypes.

Genetic diversity and population structure of tomato brown rugose fruit virus (ToBRFV) variants from Antalya province, Turkey

In this study, bioinformatic analyses were carried out according to the fully coded CP and MP gene regions of the agent, using six novel tomato brown rugose fruit virus (ToBRFV) variants obtained from the production greenhouses in Antalya, where the infection was first detected in Turkey and global variants. Molecular evolutionary analyses using both CP and MP gene regions showed that all variants were distributed in three major clades. Population dynamics studies for both gene regions have shown that there was very low nucleotide diversity and haplotype diversity. The low haplotype diversity for the CP and MP genes indicated almost no recombination status. A strong negative selection was determined for CP and MP gene regions, dN/dS= 0.0877 and dN/dS=0.2104, respectively. Neutrality test results revealed that ToBRFV populations are in an expansion phase. Pairwise comparisons were performed between populations separated in the geographic hierarchy as American, European, and Asian variants, and the findings showed intense gene flow and high genetic similarity (FST&lt;0,33 and migration rate &gt;1). The results of this study reveal the recent population structure of the virus and suggest that necessary precautions should be taken in the international seed trade against contaminated seeds.

Detection of Asian genetic components in autochthonous human Echinococcus multilocularis infections from endemic Warmia-Masuria (north-eastern Poland)

Alveolar echinococcosis is a life-threatening zoonotic disease caused by the larval stage of the cestode Echinococcus multilocularis. People are aberrant intermediate hosts accidentally infected with the parasite eggs via faecal-oral route, usually by the consumption of unwashed fruit and vegetable or direct contact with definitive hosts. The recently reported presence of Asian admixture in E. multilocularis tapeworms from Polish red foxes prompted the question of metacestode descent in the human population. In this study, a Maximum Likelihood tree based on partial sequences of E. multilocularis mitochondrial genes cox1, cob, and nad2 coupled with a hierarchical clustering analysis of microsatellite EmsB profiles and supplemented by Sammon's nonlinear mapping with k-means clustering revealed Asian genetic components, to date associated only with the sylvatic cycle, in two autochthonous samples from alveolar echinococcosis patients living in endemic Warmia-Masuria, north-eastern Poland. The red fox is the most likely source of contamination in the environment shared by people and wildlife that led to these infections. Our results confirm that Asian genetic variants participate in the synanthropic cycle in north-eastern Poland and indicate that they may be present in the human population in other areas where Asian genetic variants were detected in red foxes.

Abstract 5521: Racial and ethnic disparities for intravascular large B-cell lymphoma: A Surveillance, Epidemiology, and End Results (SEER) database analysis with emphasis on Hispanics

Abstract Background: Intravascular large b-cell lymphoma (IVLBCL) is a rare but highly aggressive subtype of non-Hodgkin lymphoma (NHL). IVLBCL is a clonal proliferation with selective growth within the blood vessel. It has been primarily described in Asian and European populations, and a median age presentation is in the sixth to seventh decades without a sex predilection. The US incidence is 0.95 in 1 million, but is thought to be higher, as the diagnosis is mainly done postmortem. Meanwhile, the incidence rate of IVBCL in Hispanics (HI) remained unknown. This study looks at demographics, treatment patterns, and outcomes of patients with IVLBCL in the US, examining disparities by HI vs Non-Hispanic (NH). Methods: Data were analyzed on IVLBCL patients reported to the SEER 18 database between 2000 and 2018. SEER 18 contains the most comprehensive population-based cancer information in the US, covering approximately 27% of the US population and 36% of HI alone. The racial groups analyzed were NH whites, HI whites, blacks, and Asians/PIs (Pacific Islanders). Patient characteristics, age-adjusted incidence rate, and survival rate were compared across ethnic groups. Kaplan-Meier and Cox regression analyses compared overall survival (OS) between HI and NH. Multivariate analysis and propensity score matching were performed, with adjustment for age, stage and B-symptoms. Results: We identified 164 patients with IVLBCL, of which 10% were HI. 41% of HI were male vs 44% of NH. HI were diagnosed at an older age, 72. vs 69 y.o., compared to NHI (p=0.907). Most of NH and HI were diagnosed between 60-80 y.o. (p=0.322), 53.1% and 47.1%, respectively. Regarding race, HI and NH were mainly identified as whites (88% vs 78%), followed by Asians (6% vs 17%) (p=0.013). For HI, 53% presented B symptoms compared to 16% of NH (p=&amp;lt;0.001). On survival analysis, the survival probability at 2, 5 and 10 years of HI vs NH was (0.540 vs 0.505), (0.432 vs 0.425), and (0.443 vs 0.237), respectively. The median survival time was 0.8 years for HI and 1.9 years for NH. The 10 year OS probability was not significantly different for HI vs NH (p=0.66).On multivariate analysis, when adjusted for age, those patients who were 60 to 80 y.o. had worse OS compared to those younger than 60 y.o., with HR 1.4 (95% CI: 0.7 - 2.1). Conclusion: In our study, despite a lower percentage of patients identified as Asian in our HI population, there is a significant difference in the presence of B-symptoms between HI and NH, going against the traditional description of an Asian variant with increased systemic symptoms. Despite this finding, it demonstrated similar outcomes in the 10 years survival analysis for HI and NH. Standardized treatment may explain why no variation was reported in OS. Our analysis shows that ethnic variations do not seem to affect oncological outcomes in IVLBCL for HI in the US. Citation Format: Daniela Urueta Portillo, Daniel Rosas, Joel E. Michalek, Qianqian Liu, Adolfo E. Diaz Duque. Racial and ethnic disparities for intravascular large B-cell lymphoma: A Surveillance, Epidemiology, and End Results (SEER) database analysis with emphasis on Hispanics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5521.

Discovery of Brassica Yellows Virus and Porcine Reproductive and Respiratory Syndrome Virus in Diaphorina citri and Changes in Virome Due to Infection with 'Ca. L. asiaticus'.

Detection of new viruses or new virus hosts is essential for the protection of economically important agroecosystems and human health. Increasingly, metatranscriptomic data are being used to facilitate this process. Such data were obtained from adult Asian citrus psyllids (ACP) (Diaphorina citri Kuwayama) that fed solely on mandarin (Citrus ×aurantium L.) plants grafted with buds infected with 'Candidatus Liberibacter asiaticus' (CLas), a phloem-limited bacterium associated with the severe Asian variant of huanglongbing (HLB), the most destructive disease of citrus. Brassica yellows virus (BrYV), the causative agent of yellowing or leafroll symptoms in brassicaceous plants, and its associated RNA (named as BrYVaRNA) were detected in ACP. In addition, the porcine reproductive and respiratory syndrome virus (PRRSV), which affects pigs and is economically important to pig production, was also found in ACP. These viruses were not detected in insects feeding on plants grafted with CLas-free buds. Changes in the concentrations of insect-specific viruses within the psyllid were caused by coinfection with CLas. IMPORTANCE The cross transmission of pathogenic viruses between different farming systems or plant communities is a major threat to plants and animals and, potentially, human health. The use of metagenomics is an effective approach to discover viruses and vectors. Here, we collected buds from the CLas-infected and CLas-free mandarin (Citrus ×aurantium L. [Rutaceae: Aurantioideae: Aurantieae]) trees from a commercial orchard and grafted them onto CLas-free mandarin plants under laboratory conditions. Through metatranscriptome sequencing, we first identified the Asian citrus psyllids feeding on plants grafted with CLas-infected buds carried the plant pathogen, brassica yellows virus and its associated RNA, and the swine pathogen, porcine reproductive and respiratory syndrome virus. These discoveries indicate that both viruses can be transmitted by grafting and acquired by ACP from CLas+ mandarin seedlings.

Zika Virus Infection Damages the Testes in Pubertal Common Squirrel Monkeys (Saimiri collinsi).

During the Zika virus (ZIKV) outbreak and after evidence of its sexual transmission was obtained, concerns arose about the impact of the adverse effects of ZIKV infection on human fertility. In this study, we evaluated the clinical-laboratory aspects and testicular histopathological patterns of pubertal squirrel monkeys (Saimiri collinsi) infected with ZIKV, analyzing the effects at different stages of infection. The susceptibility of S. collinsi to ZIKV infection was confirmed by laboratory tests, which detected viremia (mean 1.63 × 106 RNA copies/µL) and IgM antibody induction. Reduced fecal testosterone levels, severe testicular atrophy and prolonged orchitis were observed throughout the experiment by ultrasound. At 21 dpi, testicular damage associated with ZIKV was confirmed by histopathological and immunohistochemical (IHC) analyses. Tubular retraction, the degeneration and necrosis of somatic and germ cells in the seminiferous tubules, the proliferation of interstitial cells and an inflammatory infiltrate were observed. ZIKV antigen was identified in the same cells where tissue injuries were observed. In conclusion, squirrel monkeys were found to be susceptible to the Asian variant of ZIKV, and this model enabled the identification of multifocal lesions in the seminiferous tubules of the infected group evaluated. These findings may suggest an impact of ZIKV infection on male fertility.

Effects of mexiletine on a race-specific mutation in Nav1.5 associated with long QT syndrome.

Mutations in cardiac Nav1.5 have been associated with LQT syndrome, Brugada syndrome, and sudden arrhythmia death syndrome. Genetic studies showed that Nav1.5 mutations vary across race-ethnic groups. The Nav1.5 mutation P1090L was linked with familial long QT syndrome (LQTS) and was identified as an ethnic-specific variant in Asians. To explore the role of the P1090L in the LQT syndrome, we characterized the effects of the mutation on the Nav1.5 channel function. We found that the P1090L mutation altered the gating process of the channel and exhibited an enhanced window current. Treatment with mexiletine reversed the depolarization shift of the steady-state inactivation produced by the mutation. Mexiletine modified the recovery and development of inactivation of the mutation and reduced the mutated channel's availability. We characterized that the P1090L is a gain-of-function, the mutation presented a larger window current and increased channel availability. Treatment with mexiletine rescued the dysfunctional inactivation of the mutation. The results might potentially enable a mechanism-based approach to the treatment of LQTS.

Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population.

Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.

CFTR genotype analysis of Asians in international registries highlights disparities in the diagnosis and treatment of Asian patients with cystic fibrosis

Cystic fibrosis (CF) is not well-characterized in Asians, potentially resulting in delayed diagnosis and poor prognosis. We characterized CF in Asian subgroups to address these disparities. De-identified ethnicity and CFTR variant data were obtained from the United States, United Kingdom, and Canadian CF registries. We measured the prevalence of CF, CFTR variant allele frequencies, effectiveness of screening panels, and eligibility for modulator therapies. The prevalence of CF was 1 in 74,982 people (Canada) to 1 in 13,340 people (United Kingdom) for South Asians and 1 in 256,541 (Canada) to 1 in 52,563 (United Kingdom) for other Asians, suggesting 26,000 to 146,000 patients with CF in South Asia. p.(F508del) variant was markedly less frequentin Asians than in non-Hispanic Whites. Splicing and nonsense variants occurred at high allelic frequencies in Asians, resulting in 41% to 49% of South Asians and 21% to 39% of other Asians being ineligible for CFTR modulator therapies. Hologic/EU2v1 panels failed to identify 37% to 47% of South Asian and 23% to 46% of other Asian patients with CF. Among Asians, CF appears to be more common in South Asians. A significant CF population may exist in South Asia. CFTR variants in South and other Asians markedly differ from non-Hispanic Whites causing inequities in newborn screening, diagnosis, and treatment. New strategies are necessary to mitigate these health care disparities.

Bilirubin metabolism and UDP-glucuronosyltransferase 1A1 variants in Asians: Pathogenic implications and therapeutic response.

In the Asian general population, at least six single-nucleotide variants (SNVs) in the UDP-glucuronosyltransferase (UGT) 1A1 gene have been identified: -3279T>G, -53A(TA)6 TAA>A(TA)7 TAA, 211G>A, 686C>A, 1091C>T, and 1456T>G. Each of these six SNVs was observed in at least four ethnic groups of the 12 Asian populations studied. In East Asian populations, the descending frequency of these six SNVs was as follows: -3279G>[-53A(TA)7 TAA, 211A]>(686A, 1091T)>1456G. Because of the presence of linkage disequilibrium and the expulsion phenomenon, when the SNVs -3279G, -53A(TA)7 TAA, 211A, and 686A were simultaneously involved, 15 instead of the estimated 81 genotypes were observed. Those carrying 686AA or 1456GG developed Gilbert's syndrome or Crigler-Najjar syndrome type 2. Both -53A(TA)7 TAA/A(TA)7 TAA and 211AA are the main causes of Gilbert's syndrome in East Asian populations. In East Asian populations, the 211AA genotype is the main cause of neonatal hyperbilirubinemia, whereas -53A(TA)7 TAA/A(TA)7 TAA exerts a protective effect on hyperbilirubinemia development in neonates fed with breast milk. Both 211A and -53A(TA)7 TAA are significantly associated with adverse drug reactions induced by irinotecan (one of the most widely used anticancer agents) in Asians. However, at least three common SNVs (-3279G, -53A(TA)7 TAA, and 211A) should be comprehensively analyzed. This study investigated the clinical significance of these six SNVs and demonstrated that examining UGT1A1 variants in Asian populations is considerably challenging.

Molecular characteristics and genetic evolutionary analyses of circulating parvoviruses derived from cats in Beijing

BackgroundFeline parvovirus (FPV) is a member of the family Parvoviridae, which is a major enteric pathogen of cats worldwide. This study aimed to investigate the prevalence of feline parvovirus in Beijing of China and analyze the genetic features of detected viruses.ResultsIn this study, a total of 60 (8.5%) parvovirus-positive samples were detected from 702 cat fecal samples using parvovirus-specific PCR. The complete VP2 genes were amplified from all these samples. Among them, 55 (91.7%) sequences were characterized as FPV, and the other five (8.3%) were typed as canine parvovirus type 2 (CPV-2) variants, comprised of four CPV-2c and a new CPV-2b strain. In order to investigate the origin of CPV-2 variants in cats, we amplified full-length VP2 genes from seven fecal samples of dogs infected with CPV-2, which were further classified as CPV-2c. The sequences of new CPV-2b/MT270586 and CPV-2c/MT270587 detected from feline samples shared 100% identity with previous canine isolates KT156833 and MF467242 respectively, suggesting the CPV-2 variants circulating in cats might be derived from dogs. Sequence analysis indicated new mutations, Ala91Ser and Ser192Phe, in the FPV sequences, while obtained CPV-2c carried mutations reported in Asian CPV variants, showing they share a common evolutionary pattern with the Asian 2c strains. Interestingly, the FPV sequence (MT270571), displaying four CPV-specific residues, was found to be a putative recombinant sequence between CPV-2c and FPV. Phylogenetic analysis of the VP2 gene showed that amino acid and nucleotide mutations promoted the evolution of FPV and CPV lineages.ConclusionsOur findings will be helpful to further understand the circulation and evolution of feline and canine parvovirus in Beijing.

Variant landscape of the RYR1 gene based on whole genome sequencing of the Singaporean population

The RYR1 gene codes for a ryanodine receptor which is a calcium release channel in the skeletal muscle sarcoplasmic reticulum. It is associated with Malignant Hyperthermia (MH) and congenital myopathies including Central Core Disease (CCD), Multiminicore Disease (MMD) and Congenital Fibre-Type Disproportion (CFTD). There is currently little information on the epidemiology of RYR1 variants in Asians. Our study aims to describe the RYR1 variant landscape in a Singapore cohort unselected for RYR1-associated conditions. Data was retrieved from the SG10K pilot project, where whole genome sequencing was performed on volunteers unselected and undetermined for RYR1-associated conditions. Variants were classified based on pathogenicity using databases ClinVar and InterVar. Allele frequencies of pathogenic variants were compared between Chinese, Indians and Malays. Using databases ExAC, GnomAD and GenomeAsia 100k study, we further compared local allele frequencies to those in Europe, America and Asia. Data was analysed using R Commander. Significant P value was set at p < 0.05. Majority of the RYR1 variants were missense mutations. We identified four pathogenic and four likely pathogenic RYR1 variants. All were related to the aforementioned RYR1-associated conditions. There were 6 carriers of RYR1 pathogenic variants amongst 4810 individuals, corresponding to an allele frequency of 0.06%. The prevalence of pathogenic variants was the highest amongst Indians (4 in 1127 individuals) (p = 0.030). Majority of pathogenic and likely pathogenic mutations were missense and located in mutational hotspots. These variants also occurred at higher frequencies in Asians than globally. This study describes the variant landscape of the RYR1 gene in Singapore. This knowledge will facilitate genetic screening for RYR1-related conditions.

Visceral leishmaniasis in Kazan

In Tatarstan, cases of infections that did not occur before began to be noted. One of them is leishmaniasis, a protozoal vector-borne infection caused by intracellular parasites of the genus Leishmania transmitted by mosquitoes. With this type of infection, mainly the internal organs (visceral form) or the skin and mucous membranes (cutaneous form) are affected. In the CIS, it is registered in the countries of Central Asia and the Caucasus. In Kazan, over the past 2 years, 2 cases of visceral leishmaniasis were detected, imported from Georgia and Tajikistan. In both cases, the patients were children: in the first, the Mediterranean-Central Asian variant was diagnosed, in the second, the Indian variant.