Dominant Genotype Research Articles

Genotyping and Identification of Antigen B Gene Polymorphism of Echinococcus granulosus in Edirne, Thrace, and the First Report of Genotype G2 (Tasmanian Sheep Strain) in Turkey

Echinococcus granulosus is the causative agent of cystic echinococcosis in humans and livestock. It is common worldwide. Cystic echinococcosis is still an important public health problem in Turkey, which is an endemic region. To genotype Echinococcus granulosus isolates and investigate antigen B gene polymorphism in Thrace, Turkey. A cross-sectional study. Seventy-five hydatid cyst materials obtained between June 2020 and May 2021 were included in the study. Hydatid cyst materials were collected from 12 humans from various hospitals in Edirne and 63 from slaughterhouse animals during the same period. Cyst materials were localized in 8 livers and 4 lungs in humans, 23 livers and 17 lungs in cattle, and 13 livers and 10 lungs in sheep. In the first step, the 12S ribosomal RNA gene was amplified by polymerase chain reaction for all samples and run on an agarose gel. Band patterns were used for strain typing. Then, the selected samples that represented each of the band patterns obtained by single-strand conformation polymorphism analysis were sequenced for AgB1, AgB2, mt-CO1, and mt-ND1 genes. Three different genotypes in Edirne, Thrace, Turkey, were observed for Echinococcus granulosus: G1 (domestic sheep strain), G2 (Tasmanian sheep strain), and G3 (buffalo strain). G1 was the dominant genotype in Edirne, and G3 was the second most common. Additionally, polymorphism in AgB1 and AgB2 gene regions was found. This study is the first to report on Echinococcus granulosus G2 (Tasmania sheep strain) in Turkey and G3 (buffalo strain) and antigen B polymorphism in Thrace. The study results will contribute to the prevention and control programs for cystic echinococcosis in Turkey and worldwide.

Molecular characterization of slc5a6a and its association with growth and body conformation in bighead carp (Hypophthalmichthys nobilis)

The slc5a6 (solute carrier family 5 member 6) gene is associated with the transport of several water-soluble vitamins and plays an important role in growth and development. Meanwhile, slc5a6a was localized in a genome-wide association analysis of head size and shape in bighead carp. In this study, characterization of slc5a6a were performed in bighead carp (Hypophthalmichthys nobilis), an important food fish in Asia. The full-length sequence of slc5a6a gene is 21,355 bp, with a cDNA of 5483 bp and open reading frame encoding 625 amino acids. Sequence comparison and phylogenetic analysis indicate that SLC5A6A is relatively conserved across vertebrates. Slc5a6a of bighead carp (Hynslc5a6a) is expressed in unfertilized eggs and embryonic stages like a maternal gene, with the highest expression in liver, followed by pituitary and muscle. In the expression of liver and pituitary of fast growing (Heavy group, HG) and slow growing (Light group, LG) individuals, HG is significantly higher than LG (P < 0.05). Three single nucleotide polymorphisms (g 0.5998 T > C, g.6104 A>G, g 0.21131 T > C) were identified in Hynslc5a6a and significantly associated with body weight (BW), body length (BL) and head length (HL). In one of the bighead carp populations, a combined triplotype CCGGCC of Hynslc5a6a was significantly better than TTAATC in the phenotype values of BW, HL and head width traits by 33.03 %, 12.26 % and 11.59 %, respectively. These results suggest that Hynslc5a6a plays an important regulation role in the growth and body conformation and dominant genotypes of this key gene are potentially applicable in marker-assisted selection in bighead carp.

Nationwide and long-term molecular epidemiologic studies of mumps viruses that circulated in Japan between 1986 and 2017.

In Japan, major mumps outbreaks still occur every 4-5 years because of low mumps vaccine coverage (30-40%) owing to the voluntary immunization program. Herein, to prepare for a regular immunization program, we aimed to reveal the nationwide and long-term molecular epidemiological trends of the mumps virus (MuV) in Japan. Additionally, we performed whole-genome sequencing (WGS) using next-generation sequencing to assess results from conventional genotyping using MuV sequences of the small-hydrophobic (SH) gene. We analyzed 1,064 SH gene sequences from mumps clinical samples and MuV isolates collected from 25 prefectures from 1986 to 2017. The results showed that six genotypes, namely B (110), F (1), G (900), H (3), J (41), and L (9) were identified, and the dominant genotypes changed every decade in Japan since the 1980s. Genotype G has been exclusively circulating since the early 2000s. Seven clades were identified for genotype G using SH sequence-based classification. To verify the results, we performed WGS on 77 representative isolates of genotype G using NGS and phylogenetically analyzed them. Five clades were identified with high bootstrap values and designated as Japanese clade (JPC)-1, -2, -3, -4, -5. JPC-1 and -3 accounted for over 80% of the total genotype G isolates (68.3 and 13.8%, respectively). Of these, JPC-2 and -5, were newly identified clades in Japan through this study. This is the first report describing the nationwide and long-term molecular epidemiology of MuV in Japan. The results provide information about Japanese domestic genotypes, which is essential for evaluating the mumps elimination progress in Japan after the forthcoming introduction of the mumps vaccine into Japan's regular immunization program. Furthermore, the study shows that WGS analysis using NGS is more accurate than results obtained from conventional SH sequence-based classification and is a powerful tool for accurate molecular epidemiology studies.

Characterization of Rotavirus Infection in Hospitalized Children under 5 with Acute Gastroenteritis 5 Years after Introducing the Rotavirus Vaccines in South Korea.

We herein characterized rotavirus infection in hospitalized children under 5 years of age with gastroenteritis after introducing rotavirus vaccines in South Korea from 20 February 2012, to 31 March 2013. Enzyme-linked fluorescent immunoassay was performed to detect rotavirus antigens. G and P genotyping was performed using nested multiplex PCR. For the failed PCR samples, sequencing was conducted. We performed a test-negative case-control study to estimate vaccine effectiveness. Vaccine effectiveness was measured using a multivariate logistic regression model. Rotavirus was detected in 16 (13.2%) of the 121 patients, with a seasonal peak in April 2012. The dominant genotypes detected were G3P[8] (33.3%) and G4P[6] (26.7%), and vaccine effectiveness against rotavirus hospitalization was 84.9% [95% CI: 23.2-97.0] in the complete vaccinated group. A higher prevalence of rotavirus infection was observed among children with siblings than those without siblings (p &lt; 0.001). Also, the presence of siblings was significantly associated with a history of nonvaccination (p &lt; 0.001). In conclusion, the prevalence of rotavirus followed a decreasing trend, and there was no evidence of emergences of nonvaccine-type strains. Vaccine effectiveness against rotavirus hospitalization was 84.9%. Although children with siblings were more susceptible to rotavirus infection, they were less likely to receive vaccination against rotavirus.

Association analysis of PLIN2 gene polymorphisms and lambing performance in Qianbei Ma goats.

Qianbei Ma goats are one of the three most valued local goat breeds in Guizhou, China; furthermore, it has lower litter size performance. The purpose of this study was to explore the correlation between SNP (single-nucleotide polymorphisms) of PLIN2 gene and lambing performance. The bioinformatics analysis, DNA sequencing, RT-qPCR and correlation analysis methods were used to analyse the evolutionary relationship of PLIN2 protein in 13 species, to detect the expression pattern of PLIN2 gene in the gonad axis of Qianbei sheep, to explore the dominant genotype of PLIN2 related to lambing traits and to screen molecular markers related to lambing performance to guide the breeding of Qianbei Ma goats. Results showed that the Qianbei Ma goat PLIN2 protein had the closest genetic relationship with sheep and the furthest from mice, there were significant or extremely significant differences in the expression levels of the PLIN2 gene in the gonadal axis of the mothers of single- and multi-lamb groups. Compared with the reference sequence, four SNPs were found, which were g.1006 C → A and g.1171 A → G in the first and second intron regions of the PLIN2 gene, g.8514 C → T in the exon 8 region and g.9122 A → T in the 3'UTR. The correlation analysis showed that g.1006 C → A, g.8514 C → T and g.9122 A → T had significant indigenous effects on the lambing performance of Qianbei Ma goats (p < .05). The number of third births for diploid H2H5 was significantly higher than that of diploid H1H2, and the number of first to third births for diploid H2H5 was large and stable. The results showed that PLIN2 gene could be used as a candidate gene related to lambing traits of Qianbei Ma goat.

Association between DNA Repair Gene Pathway Polymorphisms and Risk of Radiation Pneumonitis: A Systematic Review and Meta-Analysis

<h3>Purpose/Objective(s)</h3> Radiation pneumonitis is a dose-limiting toxicity of radiotherapy. Genetic variation in this pathway affects post-radiotherapy DNA repair and subsequently the level of toxicity. Previous studies published within this area in lung cancer treatment have been inconsistent. Our meta-analysis therefore aimed at examining the effect of SNPs on radiation pneumonitis of lung cancer patients receiving radiotherapy. <h3>Materials/Methods</h3> We performed a systematic review of relevant studies published on or before 12 October 2021 on PubMed, Scopus, Embase, and Web of Science databases. Studies with genotyping data of lung cancer patients receiving radiotherapy were included. Conference abstracts, reviews, non-English articles, studies in which radiotherapy was used as a neoadjuvant therapy were excluded. Quality assessment was performed using the Newcastle-Ottawa Scale (NOS) by two independent reviewers. We calculated the pooled odds ratios and the 95% confidence intervals to evaluate the association between each DNA repair gene pathway polymorphism and all-grade radiation pneumonitis. The allelic, dominant, recessive, homozygous and heterozygous genotype models were used to assess the association. <h3>Results</h3> 706 studies were initially obtained after database searching and de-duplication. 15 studies (2964 patients) were included in the systematic review. The median follow-up time ranged from 3 months to 39.5 months. Under the allelic model, the G allele for NEIL1 gene was significantly associated with a reduced odds of developing radiation pneumonitis compared to the C allele for rs7402844 (OR 0.70, 95% CI: 0.49, 0.99, P = 0.04, I-square = 0%, total number of patients: 341). Similarly, the T allele for APE1 gene was significantly associated with a reduced odds of developing radiation pneumonitis compared to the G allele for rs1130409 (OR 0.59, 95% CI: 0.43, 0.81, P = 0.001, I-square = 0%, total number of patients: 432). Other SNPs were found to have no significant associations with all-grade radiation pneumonitis. <h3>Conclusion</h3> This systematic review and meta-analysis showed that two SNPs in the DNA repair gene pathway are significantly associated with the risks of developing radiation pneumonitis in lung cancer patients. Further cohort studies assessing a combination of DNA repair gene polymorphisms with a greater sample size are needed.

Genetic and Cross Neutralization Analyses of Coxsackievirus A16 Circulating in Taiwan from 1998 to 2021 Suggest Dominant Genotype B1 can Serve as Vaccine Candidate.

Coxsackievirus A16 (CVA16) is well known for causing hand-foot-and-mouth disease (HFMD) and outbreaks were frequently reported in Taiwan in the past twenty years. The epidemiology and genetic variations of CVA16 in Taiwan from 1998 to 2021 were analyzed in this study. CVA16 infections usually occurred in early summer and early winter, and showed increased incidence in 1998, 2000–2003, 2005, 2007–2008, and 2010 in Taiwan. Little or no CVA16 was detected from 2017 to 2021. CVA16 infection was prevalent in patients between 1 to 3 years old. A total of 69 isolates were sequenced. Phylogenetic analysis based on the VP1 region showed that CVA16 subgenotype B1 was dominantly isolated in Taiwan from 1998 to 2019, and B2 was identified only from isolates collected in 1999 and 2000. There was a high frequency of synonymous mutations in the amino acid sequences of the VP1 region among CVA16 isolates, with the exception of position 145 which showed positive selection. The recombination analysis of the whole genome of CVA16 isolates indicated that the 5′-untranslated region and the non-structural protein region of CVA16 subgenotype B1 were recombined with Coxsackievirus A4 (CVA4) and enterovirus A71 (EVA71) genotype A, respectively. The recombination pattern of subgenotype B2 was similar to B1, however, the 3D region was similar to EVA71 genotype B. Cross-neutralization among CVA16 showed that mouse antisera from various subgenotypes viruses can cross-neutralize different genotype with high neutralizing antibody titers. These results suggest that the dominant CVA16 genotype B1 can serve as a vaccine candidate for CVA16.

Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa.

Salmonella enterica serovar Typhi (S. Typhi) is either widely distributed or proximally transmitted via fecally-contaminated food or water to cause typhoid fever. In Samoa, where endemic typhoid fever has persisted over decades despite water quality and sanitation improvements, the local patterns of S. Typhi circulation remain unclear. From April 2018-June 2020, epidemiologic data and GPS coordinates were collected during household investigations of 260 acute cases of typhoid fever, and 27 asymptomatic shedders of S. Typhi were detected among household contacts. Spatial and temporal distributions of cases were examined using Average Nearest Neighbor and space-time hotspot analyses. In rural regions, infections occurred in sporadic, focal clusters contrasting with persistent, less clustered cases in the Apia Urban Area. Restrictions to population movement during nationwide lockdowns in 2019–2020 were associated with marked reductions of cases. Phylogenetic analyses of isolates with whole genome sequences (n = 186) revealed one dominant genotype 3.5.4 (n = 181/186) that contains three Samoa-exclusive sub-lineages: 3.5.4.1, 3.5.4.2, and 3.5.4.3. Variables of patient sex, age, and geographic region were examined by phylogenetic groupings, and significant differences (p<0.05) associated genetically-similar isolates in urban areas with working ages (20–49 year olds), and in rural areas with age groups typically at home (<5, 50+). Isolates from asymptomatic shedders were among all three sub-lineages. Whole genome sequencing provided evidence of bacterial genetic similarity, which corroborated 10/12 putative epidemiologic linkages among cases and asymptomatic shedders, as well as 3/3 repeat positives (presumed relapses), with a median of one single nucleotide polymorphism difference. These findings highlight various patterns of typhoid transmission in Samoa that differ between urban and rural regions as well as genomic subtypes. Asymptomatic shedders, detectable only through household investigations, are likely an important reservoir and mobile agent of infection. This study advances a “Samoan S. Typhi framework” that supports current and future typhoid surveillance and control efforts in Samoa.

Association between vitamin D receptor gene TaqI (731236) polymorphisms and breast cancer risk in Iraqi women

Breast cancer BC is the most frequent cancer among women worldwide. Vitamin D inhibits cell proliferation through the vitamin D receptor (VDR), which may have an impact on the risk of BC. This studywas designed to association between VDR (Taq1 T/C)(rs 731236) single nucleotide polymorphism SNP with risk of BC in Iraqi women together with serum levels 25-hydroxyvitamin D [25-(OH) D] and CA 15-3. A case -control study women was carried out at Department of Biochemistry, College of Medicine, University of Baghdad, during the period from in the period from to October 2019 to January 2021. It included 95 women with period BC that had not received any chemotherapy. The phenotyping included the measurements of serum CA 15-3 and 25-(OH) D by using ELISA Kits. The genotyping analysis comprised of VDR- Taq1 (T/C) [rs731236] by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis. The mean (±SD) value of serum CA15-3 and 25-(OH)D levels were significantly increase (p &lt; 0.05), in BC women than in control. The risk of BC was significantly increased with VDR Taq 1 SNP (T/C) (rs 731236) in heterozygous and dominant genotypes in women with BC. The TC carriers (OR=1.904, 95% C.I= 1.055, 3.43, X2=4.612, p= 0.03) and dominant TC+CC (OR=1.895, 95%C.I=1.664, 3.37, X2 = 4.75, P= 0.02). Homozygous CC carriers (OR=1.798, 95%C.I = 0.382, 8.457, X2= 0.565, p= 0.45) did not observe significant difference, and border line allele frequency C allele carriers (OR=1.888, 95%C.I=0.941..3.789, X2=3.239, p= 0.07) when compared with wild TT genotype. The significant association between VDR Taq 1 SNP (T/C) (rs 731236) and plasma V D levels among BC women (p= 0.04). In Conclusion the VDR Taq 1 SNP (T/C) (rs 731236) variant could be regarded genetic risk factor for BC development. Vitamin D receptor gene-Taq1 polymorphism was associated with plasma VD.

Differentiation of ‘Candidatus Liberibacter asiaticus’ in Saudi Arabia based on tandem repeat variability in genomic locus

Citrus greening, or huanglongbing, is a destructive disease threatening many citrus worldwide, and drastically altering the global dynamics of the citrus industry. The disease is caused by one of several unculturable bacterial species belonging to ‘Candidatus Liberibacter’. The recent availability of complete genome sequences of ‘Candidatus Liberibacter asiaticus’ (CLas) has facilitated comprehensive assessments of genomic variability using a range of approaches, including short tandem repeat analysis. The objective of this study was to evaluate the genetic diversity of CLas populations in Saudi Arabia based on tandem repeat number (TRN) within the CLIBASIA_01645 locus, predicted to encode the bacteriophage C1 repressor protein. Results indicated that the genotype richness of the Saudi Arabian CLas isolates was conserved by 27% based on the TRN locus. Four different genotypes TRN2, TRN3, TRN4, and TRN5 were identified. However, the TRN2 and TRN5 were the most dominant genotypes. All four of the TRN genotypes were associated with CLas-positive mandarin (Citrus reticulata) or sweet orange (C. sinensis) citrus trees. The diversity (H = 0.69) and evenness (H'=0.914) were overall relatively high, with the northern region of Saudi Arabia harboring the highest diversity (0.7) and evenness score (0.9–1.0). Phylogenetic analysis of the CLas-bacteriophage C1 repressor protein of the Saudi Arabian isolates indicated CLas was more closely related to ‘Candidatus Liberibacter africanus’ than to ‘Candidatus Liberibacter americanus’.

Biased Genotype Distributions of Candida albicans Strains Associated with 649 Clinical Vulvovaginal Candidiasis in China.

Vulvovaginal candidiasis (VVC), which is most frequently caused by Candida albicans, is a common problem worldwide. Despite the fact that extensive epidemiological studies have been performed, the cause of recurrent VVC (RVVC) remains uncertain. The aims of this work were to compare the genotypes of C. albicans strains causing different conditions of VVC, and explore the relationship between the drug resistance and genotype of C. albicans strains. In our study, we collected 649 independent strains from VVC patients in China. Isolates were tested for in vitro susceptibility to fluconazole, itraconazole, voriconazole, amphotericin B and caspofungin in accordance with the Clinical Laboratory Standards Institute (CLSI) document M27-A3. Genotyping was performed using PCR targeting specific CAI locus marker. C. albicans is the main pathogen of VVC, but the proportion of non-candida albicans (NAC) infection is also increasing, and we also found increased cases of mixed infection. Some C. albicans are resistant to multiple drugs. The strains with the genotypes including 16-16, 18-18 and 22-22 was likely to be the dominant genotype of uncomplicated VVC (p < 0.05). The genotypes of complicated VVC are mainly distributed in 30-45, 33-45, 32-46 and 39-45. Strains of 30-45, 32-45, 30-47 and 30-46 genotypes showed resistance to fluconazole, itraconazole, voriconazole and amphotericin B respectively. Our work suggests that the dominant genotypes with higher repeat number of C. albicans strains were more prevalent in patients with RVVC and drug-resistant strains, however, strains with uncomplicated VVC were more likely to distribute in homozygous. Identification of specific genotypes that correlate with different conditions of VVC and drug resistant is also of diagnostic and therapeutic significance.

Comparative evaluation of XPD and XPG gene polymorphism in oral squamous cell carcinoma and tobacco chewers: An observational study.

The study indicated that XPD and XPG gene polymorphism is associated with the development of oral potentially malignant disorders (OPMDs) and oral squamous cell carcinoma. Xeroderma pigmentosa (XP) is a part of the complex DNA repair system. Xeroderma pigmentosum group G (XPG) and xeroderma pigmentosum group D (XPD) gene function in the nucleotide excision repair (NER) pathway. XPG and/or XPD gene alterations can cause defective DNA repair efficiency which ultimately leads to genomic instability and carcinogenesis. Thus, this study helps in early detection of OPMDs among individuals who have not yet developed any oral lesions and also helps in the management of oral squamous cell carcinoma as if XP gene polymorphism is known. The aim of the study was to evaluate the expression of XPD and XPG gene polymorphism in oral squamous cell carcinoma cases. The study also had the objective to evaluate and compare the expression of XPG and XPD gene polymorphism in oral squamous cell carcinoma (OSCC) cases, tobacco chewers without any oral lesions, and normal healthy individuals without any habit. A total of 150 subjects were included in the study and genotyped for the expression of XPD (AC) and XPG (GC) gene polymorphism using polymerase chain reaction (PCR) and agarose gel electrophoresis method. XPD genotype for the study shows that most of the cases of OSCC show heterozygous (AC) genotype (64%), whereas in tobacco chewers without any oral lesions wild (AA) genotype (54%) is more common than other types. XPG genotype for the study shows that wild (GG) type is the most dominant genotype both in OSCC cases (78%) and tobacco chewers without any oral lesion (56%). The study shows the association of XPD and XPG gene polymorphism with the risk of developing OPMDs and oral cancer.

Is the Physiological Composition of the Vaginal Microbiome Altered in High-Risk HPV Infection of the Uterine Cervix?

Background: Cervical cancer is the fourth most common malignancy and fourth leading cause of cancer death in women worldwide. More than 99.7% of cases are caused by human papillomavirus (HPV), while HPV types 16 and 18 cause over 70% of all cervical cancer cases. In this preliminary study, we aimed to investigate the presence of HPV infection and diversity of bacteria associated with bacterial vaginosis. Methods: Cervical swabs (n = 21) taken from women aged 21–47 years, in seventeen cases, with different degrees of cervical abnormality, and from four healthy women, were tested for the presence of HPV DNA, as well as the bacterial strains associated with bacterial vaginosis, using the real-time PCR method. Results: HPV16 was the dominant genotype in 53% (9/17) of patients with confirmed precancerous lesions (ASCUS, LSIL, and HSIL). In specimens with confirmed cytological abnormalities and hrHPV infection, we detected a wide diversity of microbes, while the most common species were Gardnerella vaginalis, Atopobium vaginae, Prevotella bivia, Ureaplasma parvum, Ureaplasma urealyticum, Leptotrichia amnionii, Bacteroides ureolyticus, and Sneathia sanguinegens. The presence of pathogens did not differ, depending on the degree of precancerous lesions or HPV type. Conclusion: In our work, HPV16 dominated in patients with cervical precancerous lesions. We also suggest an increased bacterial diversity of the vaginal microbiome in patients with cervical lesions, for which the HPV virus is largely responsible.

Detection of Porcine Circovirus Type 2a and Pasteurella multocida Capsular Serotype D in Growing Pigs Suffering from Respiratory Disease.

Simple SummaryBacterial and viral respiratory diseases are a major health problem in pig farms. Most often multiple infectious agents are involved in the development of clinical cases of respiratory diseases. It is necessary to conduct laboratory etiological tests on suspected cases. In January 2021, a 70-day-old pig herd in a pig farm in Hebei Province, China, had been suffering from respiratory problems. On the basis of this preliminary clinical diagnosis, this study carried out comprehensive laboratory detection including nucleic acid detection and sequencing, the isolation and identification of the pathogen, genetic evolution analysis, and genotype or serotype identification, as well as an analysis of the bacterial morphology characteristics and pathogenicity. The results showed that the co-infection of PCV2a and P. multocida capsular serotypes D was likely responsible for the disease. This study could provide important etiological information for effective control and treatment of the disease in pig farms.In order to diagnose a respiratory disease in a pig farm, the lungs, spleen, and lymph nodes of three dead pigs were collected for pathogen detection by PCR and isolation on the basis of preliminary clinical diagnosis. The virus isolate was identified by gene sequence analysis and Immunoperoxidase monolayer assay (IPMA). The bacterial isolate was identified by biochemical tests, 16S rDNA sequence analysis, and species- and serotype-specific PCR, and the pathogenicity was analyzed. Porcine circovirus type 2a (PCV2a) genotype from the lungs, spleen, and lymph nodes and Pasteurella (P.) multocida capsular serotypes D from the lungs were found. The PCV2a isolates could specifically bound the anti-PCV2-Cap polyclonal antibody. The 16S rDNA sequence of P. multocida isolates had 99.9% identity with that of the strain from cattle, and the isolate was highly pathogenic to mice. The results showed that the co-infection of PCV2a and P. Multocida capsular serotypes D should be responsible for the disease. The uncommon PCV2a is still prevalent in some pig farms besides the dominant PCV2d genotype. This study could provide important etiological information for effective control and treatment of the disease in pig farms.

Genetic Variations miR-10aA>T, miR-30cA>G, miR-181aT>C, and miR-499bA>G and the Risk of Recurrent Pregnancy Loss in Korean Women

This study investigated the genetic association between recurrent pregnancy loss (RPL) and microRNA (miRNA) polymorphisms in miR-10aA>T, miR-30cA>G, miR-181aT>C, and miR-499bA>G in Korean women. Blood samples were collected from 381 RPL patients and 281 control participants, and genotyping of miR-10aA>T, miR-30cA>G, miR-181aT>C, and miR-499bA>G was carried out by TaqMan miRNA RT-Real Time polymerase chain reaction (PCR). Four polymorphisms were identified, including miR-10aA>T, miR-30cA>G, miR-181aT>C, and miR-499bA>G. MiR-10a dominant model (AA vs. AT + TT) and miR-499bGG genotypes were associated with increased RPL risk (adjusted odds ratio [AOR] = 1.520, 95% confidence interval [CI] = 1.038–2.227, p = 0.032; AOR = 2.956, 95% CI = 1.168–7.482, p = 0.022, respectively). Additionally, both miR-499 dominant (AA vs. AG + GG) and recessive (AA + AG vs. GG) models were significantly associated with increased RPL risk (AOR = 1.465, 95% CI = 1.062–2.020, p = 0.020; AOR = 2.677, 95% CI = 1.066–6.725, p = 0.036, respectively). We further propose that miR-10aA>T, miR-30cA>G, and miR-499bA>G polymorphisms effects could contribute to RPL and should be considered during RPL patient evaluation.

Epidemiological investigation of infectious diseases in geese on mainland China during 2018-2021.

Geese play an important role in agricultural economics, with China producing the vast majority of goose meat consumed worldwide annually. The variations in the avian viruses and co-infections result in substantial economic losses to the goose industry in China. To understand the evolutionary characteristics and co-infections of viruses, a broad epidemiological investigation of epizootic viruses of goose was carried out in nine provinces of China during 2018-2021. Here, the results indicated that, among the 1970 clinical samples, 50.81% (1001/1970) were positive for goose astrovirus (GAstV), 18.22% (359/1970) for avian orthoreovirus, 12.74% (251/1970) for goose parvovirus, 11.02% (217/1970) for H9N2 subtype avian influenza virus, 4.01% (79/1970) for Newcastle disease virus, and 2.08% (41/1970) for fowl adenovirus. Among the six viruses, co-infections comprised a large proportion (66.37%) in the field, of which the dual infection was more common. Additionally, phylogenetic analysis of GAstVs indicated that Chinese GAstVs had formed two distinct groups, that is, GAstV-1 and GAstV-2. GAstV-2 sub-genotype II-c had arisen as the dominant genotype in the whole country. Notably, all the H9N2-AIV isolated strains harboured the mammalian adaptation markers I155T, H183N, and Q226L (H3 numbering) in the HA gene, which promotes preferential binding to human-like α2-6-linked sialic acid receptors. And beyond that, we determined that the goose-origin Muscovy Duck Reovirus isolates, showing 51.7%-96% similarities to that of other waterfowl-origin orthoreovirus isolates in sequence homology analysis of the representative part of σC, are a new variant of waterfowl-origin orthoreovirus. These data provide valuable information about the prevalence of infectious diseases in geese on mainland China.

High diversity and clonality are hallmarks of Fusarium circinatum in South Africa

AbstractPitch canker on plantation‐grown Pinus species, caused by the fungal pathogen Fusarium circinatum, first appeared in the western and southern Cape regions of South Africa. However, outbreaks have subsequently been reported from the major plantation growing regions of KwaZulu‐Natal and Limpopo in the eastern, summer rainfall regions of the country. It is more than 10 years since the last detailed population genetics studies on F. circinatum in the region were conducted. To shed light on the population biology of F. circinatum in this region of South Africa, we used microsatellite markers and mating‐type assays to study a collection of 296 isolates from different nurseries and plantation sites. Our results showed that populations in the region are highly diverse, but strongly interconnected, with various genotypes shared across nursery and plantation collection sites. In contrast to nursery populations, those associated with pitch canker outbreaks were characterized by the presence of relatively small numbers of dominant genotypes that were generally widespread across the region. Opposite mating‐type individuals occurred in most of the isolate collections, but multilocus linkage disequilibrium analyses pointed towards clonality being the main reproductive mode of F. circinatum in the region. Most of the pathogen's genetic variation could probably have resulted from multiple different introductions into the country and more specifically, into the summer rainfall region. Because the spread and establishment of invasive pathogens are typically driven by aggressive clones, the results of this study provide important considerations for current and future Pinus disease management strategies.

Norovirus Infection in Young Nicaraguan Children Induces Durable and Genotype-Specific Antibody Immunity.

There are significant challenges to the development of a pediatric norovirus vaccine, mainly due to the antigenic diversity among strains infecting young children. Characterizing human norovirus serotypes and understanding norovirus immunity in naïve children would provide key information for designing rational vaccine platforms. In this study, 26 Nicaraguan children experiencing their first norovirus acute gastroenteritis (AGE) episode during the first 18 months of life were investigated. We used a surrogate neutralization assay that measured antibodies blocking the binding of 13 different norovirus virus-like particles (VLPs) to histo-blood group antigens (HBGAs) in pre- and post-infection sera. To assess for asymptomatic norovirus infections, stools from asymptomatic children were collected monthly, screened for norovirus by RT-qPCR and genotyped by sequencing. Seroconversion of an HBGA-blocking antibody matched the infecting genotype in 25 (96%) of the 26 children. A subset of 13 (50%) and 4 (15%) of the 26 children experienced monotypic GII and GI seroconversion, respectively, strongly suggesting a type-specific response in naïve children, and 9 (35%) showed multitypic seroconversion. The most frequent pairing in multitypic seroconversion (8/12) were GII.4 Sydney and GII.12 noroviruses, both co-circulating at the time. Blocking antibody titers to these two genotypes did not correlate with each other, suggesting multiple exposure rather than cross-reactivity between genotypes. In addition, GII titers remained consistent for at least 19 months post-infection, demonstrating durable immunity. In conclusion, the first natural norovirus gastroenteritis episodes in these young children were dominated by a limited number of genotypes and induced responses of antibodies blocking binding of norovirus VLPs in a genotype-specific manner, suggesting that an effective pediatric norovirus vaccine likely needs to be multivalent and include globally dominant genotypes. The duration of protection from natural infections provides optimism for pediatric norovirus vaccines administered early in life.

Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa.

ABSTRACTFor decades, the remote island nation of Samoa (population ~200,000) has faced endemic typhoid fever despite improvements in water quality, sanitation, and economic development. We recently described the epidemiology of typhoid fever in Samoa from 2008 to 2019 by person, place, and time; however, the local Salmonella enterica serovar Typhi (S. Typhi) population structure, evolutionary origins, and genomic features remained unknown. Herein, we report whole genome sequence analyses of 306 S. Typhi isolates from Samoa collected between 1983 and 2020. Phylogenetics revealed a dominant population of rare genotypes 3.5.4 and 3.5.3, together comprising 292/306 (95.4%) of Samoan versus 2/4934 (0.04%) global S. Typhi isolates. Three distinct 3.5.4 genomic sublineages were identified, and their defining polymorphisms were determined. These dominant Samoan genotypes, which likely emerged in the 1970s, share ancestry with other 3.5 clade isolates from South America, Southeast Asia, and Oceania. Additionally, a 106-kb pHCM2 phenotypically cryptic plasmid, detected in a 1992 Samoan S. Typhi isolate, was identified in 106/306 (34.6%) of Samoan isolates; this is more than double the observed proportion of pHCM2-containing isolates in the global collection. In stark contrast with global S. Typhi trends, resistance-conferring polymorphisms were detected in only 15/306 (4.9%) of Samoan S. Typhi, indicating overwhelming susceptibility to antibiotics that are no longer effective in most of South and Southeast Asia. This country-level genomic framework can help local health authorities in their ongoing typhoid surveillance and control efforts, as well as fill a critical knowledge gap in S. Typhi genomic data from Oceania.

Association of Polymorphic Gene Variants of Xenobiotic Biotransformation Enzymes with Lung Tissue Destruction in Tuberculosis Patients

The objective: to investigate the association of polymorphic gene variants of xenobiotic biotransformation enzymes (NAT2, CYP2E1, ABCB1, GSTM1, GSTT1) and cytokines (IL1B, IL-4, IL-10, TNF) with lung tissue destruction in pulmonary tuberculosis patients.Subjects and Methods. An ethnically homogeneous population sample of unrelated individuals of Slavic nationalities (mainly Russians) living in Kursk Oblast suffering from new pulmonary tuberculosis was examined.Results. New pulmonary tuberculosis with no destructive changes in the lungs was associated with the EE genotype of the GSTM1 gene (p &lt; 0.0001) in 89.5%, while the DD genotype of the GSTM1 gene (p &lt; 0.0001) was associated with the presence of destructive changes in the lungs in 56.1% of cases; the dominant GG genotype of the TNF-α gene was associated with destructive changes in the lungs in 93.3% (p = 0.027), and the recessive GA genotype of the TNF-α gene was associated with no destructive changes in the lungs in 71.9% (p = 0.027).