Dominant Genotype Research Articles

Genetic diversity of porcine PRLR gene and its relationship to litter size in Large White pigs

Improving the litter performance of sows is one of the main challenges in the current pig industry. In this study, single nucleotide polymorphisms (SNPs) of the PRLR gene were performed, in order to test whether they are associated with the reproductive performance of Large White pigs. In total, we discovered nine SNP loci (g. C260G, g. C362T, g. C527G, g. A540G, g. A584G, g. A673T, g. A745G, g. C765T and g. A934G) in exon 10 of PRLR. The result showed that genotypes CC and CT at the g. C362T locus and genotype AG at g. A584G could significantly increase the litter size of different strains of Large White pigs (p < 0.05). In addition, the genotype CC at the g. C765T locus and the genotype AA at g. A934G could also increase the litter size (TNB could be increased by 1.5 piglets per year; while NBA could be increased by 0.98 piglets per year, p < 0.01). Furthermore, the haplotype combinations of H2H7 and H4H4 were the dominant combinations and contributed to larger litter sizes in the Large White pigs. In conclusion, there were dominant genotypes in the related SNP loci in the PRLR gene that were beneficial to improving the litter traits of sows. These findings will provide a reference for screening the molecular markers of a high reproductive performance in sows, and are helpful for genetic breeding and the reproductive improvement of pigs. Key words: sow, prolactin, polymorphism, reproduction, association analysis.

Colonization of Extramammary Sites with Mastitis-Associated S. aureus Strains in Dairy Goats.

Staphylococcus aureus (S. aureus), a major mastitis pathogen in dairy goats, is classified as a contagious pathogen. Although previous research has shown that extramammary body sites can be colonized with S. aureus, it is unknown whether these sites are reservoirs for intramammary infections. The aim of this research was to determine whether extramammary sites can be colonized with mastitis-associated S. aureus strains in dairy goats. Milk samples were collected from 207 primiparous goats and from 120 of these goats, extramammary site samples (hock, groin, nares, vulva and udder) were collected from a large commercial dairy goat herd in the Netherlands during four sampling visits. Extramammary site swabs and milk samples were (selectively) cultured and S. aureus isolates were spa genotyped. The prevalence of colonization of the extramammary sites at goat level was 51.7% and the prevalence of S. aureus intramammary infections was 7.2%. The nares were colonized most frequently (45%), while the groin area was colonized the least (2.5%). Six spa genotypes were identified in this herd and there was no significant difference in the distribution of spa genotypes between the milk or the extramammary sites (p = 0.141). Both in the extramammary sites and in the milk, spa genotypes t544 (82.3% and 53.3%) and t1236 (22.6% and 33.3%) were the dominant genotypes. These results show that in goats, extramammary sites, particularly the nares, are frequently colonized with mastitis-associated S. aureus strains. Extramammary sites may, thus, be a source of S. aureus intramammary infections that are not targeted by the intervention measures aimed at preventing transmission from infected udder glands.

Changes in the Epidemiological Features of Influenza After the COVID-19 Pandemic in China, the United States, and Australia: Updated Surveillance Data for Influenza Activity.

There has been a global decrease in seasonal influenza activity since the onset of the COVID-19 pandemic. We aimed to describe influenza activity during the 2021/2022 season and compare it to the trends from 2012 to 2023. We also explored the influence of social and public health prevention measures during the COVID-19 pandemic on influenza activity. We obtained influenza data from January 1, 2012, to February 5, 2023, from publicly available platforms for China, the United States, and Australia. Mitigation measures were evaluated per the stringency index, a composite index with 9 measures. A general additive model was used to assess the stringency index and the influenza positivity rate correlation, and the deviance explained was calculated. We used over 200,000 influenza surveillance data. Influenza activity remained low in the United States and Australia during the 2021/2022 season. However, it increased in the United States with a positive rate of 26.2% in the 49th week of 2022. During the 2021/2022 season, influenza activity significantly increased compared with the previous year in southern and northern China, with peak positivity rates of 28.1% and 35.1% in the second week of 2022, respectively. After the COVID-19 pandemic, the dominant influenza virus genotype in China was type B/Victoria, during the 2021/2022 season, and accounted for >98% (24,541/24,908 in the South and 20,543/20,634 in the North) of all cases. Influenza virus type B/Yamagata was not detected in all these areas after the COVID-19 pandemic. Several measures individually significantly influence local influenza activity, except for influenza type B in Australia. When combined with all the measures, the deviance explained values for influenza A and B were 87.4% (P<.05 for measures of close public transport and restrictions on international travel) and 77.6% in southern China and 83.4% (P<.05 for measures of school closing and close public transport) and 81.4% in northern China, respectively. In the United States, the association was relatively stronger, with deviance-explained values of 98.6% for influenza A and 99.1% (P<.05 for measures of restrictions on international travel and public information campaign) for influenza B. There were no discernible effects on influenza B activity in Australia between 2020 and 2022 due to the incredibly low positive rate of influenza B. Additionally, the deviance explained values were 95.8% (P<.05 for measures of restrictions on gathering size and restrictions on international travel) for influenza A and 72.7% for influenza B. Influenza activity has increased gradually since 2021. Mitigation measures for COVID-19 showed correlations with influenza activity, mainly driven by the early stage of the pandemic. During late 2021 and 2022, the influence of mitigation management for COVID-19 seemingly decreased gradually, as the activity of influenza increased compared to the 2020/2021 season.

FUNCTIONAL ROLE OF THE TP53 GENE SINGLE NUCLEOTIDE POLYMORPHISM P72R (C&gt;G) IN PATIENTS WITH TYPE 2 DIABETES MELLITUS OF THE EAST UKRAINIAN POPULATION

Recently, the role of stress-regulatory pathways in the development and progression of type 2 diabetes mellitus (T2DM) and associated cardiovascular diseases has been widely investigated. The aim of the study was to assess the relationship of polymorphic variants P72R (C&gt;G) of the TP53 gene with the functional and metabolic characteristics of type 2 diabetic patients in the East Ukrainian population. Materials and methods. 50 T2DM patients (female/male: 21/29) aged 53.34±1.43 yrs., with diabetes duration of 6.25±0.89 yrs., HbA1c level of 7.12±0.21%, body mass index of 31.19±0.93 kg/m2, with waist-to-hip ratio of 0.96±0.01, with the presence of coronary heart disease in 38 cases, hypertension in 46 cases, and their combination in 37 cases. Characteristics of carbohydrate/lipid metabolism, parameters of insulin resistance, chronic inflammation, and a number of adipokines were determined in the subjects. Genotyping for single nucleotide polymorphism P72R (C&gt;G) TP53 was performed by the method of polymerase chain reaction with appropriate primers and BstUI endonuclease. Testing of null hypotheses was carried out using the t, F and c2 criteria at the significance level of P≤0.05. Results. There was a noticeable tendency (P=0.05) to increase in frequency of the recessive allele G, mainly in men, which requires further extended studies. In addition, carriers of the minor genotype are characterized by a significantly younger age of T2DM manifestation. Under the statistically similar parameters that characterize the degree of obesity and glucose metabolism compensation, the connection of the G-allele with insulin resistance, both hepatic (HOMA-IR) and associated with adipose tissue (HOMA-IR/adiponectin, adiponectin/leptin) was observed. Carriers of the recessive allele are also characterized by an increased atherogenic coefficient relative to the dominant CC genotype, a significant decrease in the levels of adiponectin (total and high molecular weight) and omentin, and an increase in the levels of leptin and vaspin in the circulation. According to the recessive model, the presence of the G-allele is accompanied by a weak but probable increase in the levels of highly sensitive C-reactive protein (CC vs. CG+GG: 1.92±0.42 mg/l vs. 4.62±0.94 mg/l, P &lt;0.05). The above suggests that the G-allele may be a predictor of a greater risk of cardiovascular disease development in patients with T2DM. Conclusions. It has been proven that the P72R polymorphism of the TP53 gene is functional for the East Ukrainian population, because against the background of a comparable degree of obesity and glucose metabolism compensation, carriers of the minor G-allele are characterized by a greater degree of insulin resistance and a proatherogenic shift in the hormonal activity of adipose tissue. A tendency to increase in frequency of the G-allele in men with type 2 diabetes was revealed, and it was determined that carriers of the minor genotype are characterized by a significantly younger age of diabetes manifestation. The obtained results substantiate the need for further research to assess the role of this polymorphism in the Ukrainian population.

Association of variations in the CAT and prognosis in lung cancer patients with platinum-based chemotherapy.

PURPOSE: To explore the relationship between ATM, ATR and CAT polymorphisms and prognosis of lung cancer patients received platinum-based chemotherapy. METHODS: 404 patients with lung cancer who received platinum-chemotherapy were enrolled and DNA typing was performed. Cox regression analysis and stratification analyses was performed to assess relationships between OS and PFS with SNPs genotypes. The prognosis of lung adenocarcinomaand squamous cell carcinomapatients was analyzed with The Cancer Genome Atlas (TCGA) database according to the grouping of CAT expression. RESULTS: CAT rs769217 was significantly related to PFS of patients with lung cancer who received platinum-chemotherapy. In the Additive model, rs769217 was associated with PFS (HR = 0.747, 95% CI = 0.581-0.960, p = 0.023). In the Dominant model, CT and TT genotypes led to lung cancer progression 0.738 times more than CC genotype. In stratification analyses of association between CAT rs769217 polymorphisms and PFS, the HR of patients at stage IV in additive model was 0.73, and HR was 0.745 (p = 0.034) in dominant model. For OS analyses, HR was 0.672 in the older lung cancer patients (>55 years old) in additive model. Meanwhile, in the Dominant model, it was found that the older patients with CT and TT genotypes had better prognosis, and the risk of death after receiving platinum-based chemotherapy was 0.692 times that of patients with CC genotype (p = 0.037). TCGA data shows that LUAD patients with high CAT expression have longer OS (p = 0.020). CONCLUSION: CAT rs769217 is significantly related to PSF of platinum-based chemotherapy in lung cancer patients and may be a biomarker for predicting the prognosis of lung cancer patients with platinum-based chemotherapy.

QX-type infectious bronchitis virus infection in roosters can seriously injure the reproductive system and cause sex hormone secretion disorder

ABSTRACT Since its discovery, QX-type avian infectious bronchitis virus (IBV) has rapidly spread worldwide and become the most prevalent dominant genotype in Asia and Europe. Currently, although the pathogenicity of QX-type IBV in the reproductive system of hens is widely and deeply understood, its pathogenicity in the reproductive system of roosters remains largely unknown. In this study, 30-week-old specific pathogen-free (SPF) roosters were used to investigate the pathogenicity of QX-type IBV in the reproductive system after infection. The results showed that QX-type IBV infection caused abnormal testicular morphology, moderate atrophy and obvious dilatation of seminiferous tubules, and produced intense inflammation and obvious pathological injuries in the ductus deferens of infected chickens. Immunohistochemistry results showed that QX-type IBV can replicate in spermatogenic cells at various stages and in the mucous layer of the ductus deferens. Further studies showed that QX-type IBV infection affects plasma levels of testosterone, luteinizing hormone, and follicle-stimulating hormone as well as causes changes in transcription levels of their receptors in the testis. Furthermore, the transcription levels of StAR, P450scc, 3βHSD and 17βHSD4 also changed during testosterone synthesis after QX-type IBV infection, indicating that the virus can directly affect steroidogenesis. Finally, we found that QX-type IBV infection leads to extensive germ cell apoptosis in the testis. Collectively, our results suggest that QX-type IBV replicates in the testis and ductus deferens, causing severe tissue damage and disruption of reproductive hormone secretion. These adverse events eventually lead to mass germ cell apoptosis in the testis, affecting the reproductive function of roosters.

CYP2D6 genetic polymorphisms in Saudi systemic lupus erythematosus patients: A cross-sectional study.

To determine the prevalence of selected single nucleotide polymorphisms (rs1080985, rs28624811, rs1065852, rs28371725, and rs1135840) in cytochrome P450 2D6 (CYP2D6) gene among Saudi systemic lupus erythematosus (SLE) patients and to investigate the association between the genetic variants and clinical features of SLE. This cross-sectional study was carried out on adult Saudi patients at King Khalid University Hospital, Riyadh, Saudi Arabia. Patients with confirmed SLE based on the 2012 Systemic Lupus International Collaborating Clinics classification criteria were included in the study. Peripheral blood was collected for genomic deoxyribonucleic acid extraction and TaqMan® technologies were used for target genotyping. For statistical analysis, differences in genotype frequencies were determined using the Chi-square test, and the association between the variant genotypes and SLE features was evaluated using logistical regression models. There were 107 participants included in this study. Overall, the most predominant (23.4%) recessive genotype was AA in rs28624811, and the least prevalent (1.9%) recessive genotype was TT in rs28371725. Moreover, the variant rs1080985 genotypes (GC or CC) were significantly associated with the presence of serositis manifestation (OR=3.15, p=0.03), even after adjusting for age and gender. However, the dominant rs28624811 genotype (GG) was associated with renal involvement (OR=2.56, p=0.03). Systemic lupus erythematosus patients carrying CYP2D6 variants might be considered at risk for certain manifestations of SLE. Further studies are needed to investigate the implication of these genetic variations in clinical outcomes and drug response.

Genetic Diversity of Norovirus in Children with Acute Gastroenteritis in Southwest Nigeria, 2015–2017

Norovirus (NoV) is a leading cause of viral gastroenteritis globally, especially in children below five years. Epidemiological studies on the diversity of NoV in middle- and low-income countries, including Nigeria, are limited. This study aimed to determine the genetic diversity of NoV in children below five years with acute gastroenteritis at three hospitals in Ogun State, Nigeria. A total of 331 fecal samples were collected from February 2015 to April 2017, while 175 were randomly selected and analyzed using RT-PCR, partial sequencing and phylogenetic analyses of both the polymerase (RdRp) and capsid (VP1) genes. NoV was detected in 5.1% (9/175; RdRp) and 2.3% (4/175; VP1) of samples, with 55.6% (5/9) co-infection with other enteric viruses. A diverse genotype distribution was identified, and GII.P4 was the dominant RdRp genotype detected (66.7%), with two genetic clusters, followed by GII.P31 (22.2%). The rare GII.P30 genotype (11.1%) was detected at a low rate for the first time in Nigeria. Based on the VP1 gene, GII.4 was the dominant genotype (75%), with two variants, Sydney 2012 and possibly New Orleans 2009, co-circulating during the study. Interestingly, both intergenotypic, GII.12(P4) and GII.4 New Orleans(P31), and intra-genotypic, GII.4 Sydney(P4) and GII.4 New Orleans(P4), putative recombinant strains were observed. This finding suggests the first likely report of GII.4 New Orleans(P31) in Nigeria. In addition, GII.12(P4) was first described in Africa and globally in this study, to the best of our knowledge. This study provided insights into the genetic diversity of NoV circulating in Nigeria, which would be useful for ongoing and future vaccine design and monitoring of emerging genotypes and recombinant strains.

A genetic Study to Darwin's tubercle trait of External ear in the Population of Salah Al –Dein and Kirkuk

A genetic study for the trait of Darwin's tubercle in two ways : first , on a sample consisted of 52 family from Tikrit city in governorate Salah AL-Dein and 125 individual from their sons and 63 family from governorate of Kirkuk and 188 individual from their sons . Secondly , adoption of pedigree analysis method for seven families from governorate of Salah El-Dein and Kirkuk , which confirmed the darwin's tubercle trait is a genetic trait and the presence of tubercle is dominant absence . The results of Presence Darwin's tubercle also revealed different forms : Nodosity tubercle , Enlargement tubercle and Projection. The present study support the truth of single gene locus hypothesis for the inheritance of this trait , in spite of it record the presence of one offspring have darwin's tubercle between two parents do not have darwin's tubercle in one family. The results of the study distribution of phenotypic for the trait showed on a sample consisted of 1415 individual from the citizens of the governorate of Salah Al-Dein (920♂: 495♀) from the original samples (1446) , an elevated percentage of the presence tubercle among the males (99.2%) than the females (98.4%) . The percentage of presence tubercle in the whole population was (98.9%) . Concering the allelic frequency for the gene of darwin's tubercle, the D allele was observed a higher frequency than the d allele in the whole population of the governorate: 0.895, 0.105 for both of them respectively . Expected frequencies of the three genotypes of darwin's tubercle trait , revealed a prevalence of the homozygous (dominant) genotype DD over the homozygous (recessive) and heterozygous genotype in the population of the governorate: 0.801, 0.188, 0.011 for DD , Dd and dd respectively.

Genotyping and antimicrobial resistance profiles of chicken originated Salmonella Enteritidis isolates.

Salmonellosis is a common foodborne zoonosis worldwide. The most common Salmonella serovar in humans is Salmonella enterica subsp. enterica serovar Enteritidis (50.3%) in the world. The main transmission route for S. Enteritidis is consumption of contaminated poultry products. Therefore, it is important to determine the diversity and spread of chicken-originated S. Enteritidis isolates in order to monitor and control salmonellosis. Pulsed-field gel electrophoresis (PFGE) and multiple locus variable number of tandem repeats analysis (MLVA) are frequently used for typing of S. Enteritidis isolates. This study aimed to determine the antimicrobial resistance (AMR) profiles and MLVA and PFGE genotypes of chicken-originated S. Enteritidis isolates. A total of 200 S. Enteritidis isolated from chicken broiler, layer, and breeder flocks from different locations in Turkey were investigated by Kirby-Bauer disk diffusion method, PFGE, and MLVA. The AMR test indicated that 57% of the S. Enteritidis isolates were susceptible to all antimicrobials, while 39% were resistant to at least one antimicrobial. The highest resistance (25%) was against ampicillin. Multi-drug resistance rate was low (21%) and mostly from broiler flocks (93%). All isolates were genotyped into 32 different PFGE genotypes (PT) and 34 different MLVA genotypes (MT). The dominant genotypes were PT6 (12.5%) and MT22 (50%). In specific sample groups, there was a correlation between genotypes, breeding type, geographic location, and isolation years of the isolates. There was no significant difference in the discrimination power of PFGE and MLVA. However, MLVA was more suitable for large sample groups and routine genotyping because it was easier, quicker, and less labor-intensive to use.

Prevalence, Characterization, and Antimicrobial Resistance of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli from Domestic Free-Range Poultry in Agogo, Ghana

Poultry has been suggested as an important source for extended-spectrum beta-lactamase (ESBL)-producing bacteria that can lead to difficult-to treat infections in humans. Therefore, this study aims to determine the frequency, the genetics, and antimicrobial resistance profiles of ESBL-producing Escherichia coli in domestic free-range poultry in Agogo, Ghana. The study was set up and piloted from January 2019 until June 2019. Between June and December 2019, fecal samples (N = 144) were collected from free-roaming chickens from domestic farms in the regions of Sukuumu, Bontodiase, and Freetown and cultured on ESBL screening agar. Strain identification and antibiotic susceptibility were performed using the VITEK 2 compact system. ESBL-producing E. coli were confirmed using the double disk synergy test. Molecular characterization of ESBL-associated genes (blaTEM, blaSHV, and blaCTX-M) were performed using conventional polymerase chain reaction (PCR) and further sequencing of obtained PCR amplicons. The result showed that 56.2% (n/N = 81/144) of collected fecal samples were positive for ESBL-producing E. coli. Majority of the isolates showed resistance to tetracycline (93.8%, n/N = 76/81) and trimethoprim-sulfamethoxazole (66.7, n/N = 54/81), whereas resistance to carbapenems was not found. The majority of ESBL-producing E. coli carried the blaCTX-M genes, with blaCTX-M-15 being the dominant (95.1%, n/N = 77/81) genotype. In this study, we report high frequencies of ESBL-producing E. coli in smallholder free-range poultry representing a potential source of infection, highlighting the need for control of antibiotic use and animal hygiene/sanitation measures, both important from a One Health perspective.

Molecular Characterization, Expression Profile, and A 21-bp Indel within the ASB9 Gene and Its Associations with Chicken Production Traits.

A growing number of studies have shown that members of the ankyrin repeat and suppressors of cytokine signaling (SOCS) box-containing protein (ASB) family are extensively involved in biological processes such as cell growth, tissue development, insulin signaling, ubiquitination, protein degradation, and skeletal muscle membrane protein formation, while the specific biological role of ankyrin-repeat and SOCS box protein 9 (ASB9) remains unclear. In this study, a 21 bp indel in the intron of ASB9 was identified for the first time in 2641 individuals from 11 different breeds and an F2 resource population, and differences were observed among individuals with different genotypes (II, ID, and DD). An association study of a cross-designed F2 resource population revealed that the 21-bp indel was significantly related to growth and carcass traits. The significantly associated growth traits were body weight (BW) at 4, 6, 8, 10, and 12 weeks of age; sternal length (SL) at 4, 8, and 12 weeks of age; body slope length (BSL) at 4, 8, and 12 weeks of age; shank girth (SG) at 4 and 12 weeks of age; tibia length (TL) at 12 weeks of age; and pelvic width (PW) at 4 weeks of age (p < 0.05). This indel was also significantly correlated with carcass traits including semievisceration weight (SEW), evisceration weight (EW), claw weight (CLW), breast muscle weight (BMW), leg weight (LeW), leg muscle weight (LMW), claw rate (CLR), and shedding weight (ShW) (p < 0.05). In commercial broilers, the II genotype was the dominant genotype and underwent extensive selection. Interestingly, the ASB9 gene was expressed at significantly higher levels in the leg muscles of Arbor Acres broilers than those of Lushi chickens, while the opposite was true for the breast muscles. In summary, the 21-bp indel in the ASB9 gene significantly influenced the expression of the ASB9 gene in muscle tissue and was associated with multiple growth and carcass traits in the F2 resource population. These findings suggested that the 21-bp indel within the ASB9 gene could be used in marker-assisted selection breeding for traits related to chicken growth.

Vaccine evaluation and genotype characterization in children infected with rotavirus in Qatar

BackgroundWe characterized and identified the genetic and antigenic variations of circulating rotavirus strains in comparison to used rotavirus vaccines.MethodsRotavirus-positive samples (n = 231) were collected and analyzed. The VP7 and VP4 genes were sequenced and analyzed against the rotavirus vaccine strains. Antigenic variations were illustrated on the three-dimensional models of surface proteins.ResultsIn all, 59.7% of the hospitalized children were vaccinated, of which only 57.2% received two doses. There were no significant differences between the vaccinated and non-vaccinated groups in terms of clinical outcome. The G3 was the dominant genotype (40%) regardless of vaccination status. Several amino acid changes were identified in the VP7 and VP4 antigenic epitopes compared to the licensed vaccines. The highest variability was seen in the G3 (6 substitutions) and P[4] (11 substitutions) genotypes in comparison to RotaTeq®. In comparison to Rotarix®, G1 strains possessed three amino acid changes in 7-1a and 7-2 epitopes while P[8] strains possessed five amino acid changes in 8-1 and 8-3 epitopes.ConclusionsThe current use of Rotarix® vaccine might not be effective in preventing the infection due to the higher numbers of G3-associated cases. The wide range of mutations in the antigenic epitopes compared to vaccine strains may compromise the vaccine’s effectiveness.ImpactThe reduced rotavirus vaccine effectiveness necessitate regular evaluation of the vaccine content to ensure optimal protection.We characterized and identified the genetic and antigenic variations of circulating rotavirus strains in comparison to the Rotarix vaccine strain that is used in Qatar.The study highlight the importance for regular monitoring of emerging rotavirus variants and their impact on vaccine effectiveness in young children.

Human papillomavirus genotype distribution among women with and without cervical cancer: Implication for vaccination and screening in Ghana.

Determining the high-risk human papillomavirus (HR-HPV) genotypes burden in women with and without cervical cancer afford a direct comparison of their relative distributions. This quest is fundamental to implementing a future population-based cervical cancer prevention strategy in Ghana. We estimated the cervical cancer risk by HPV genotypes, and the HPV vaccine-preventable proportion of cervical cancer diagnosed in Ghana. An unmatched case-control study was conducted at the two largest cervical cancer treatment centres in Ghana from 1st October 2014 to 31st May 2015. Cases were women diagnosed with cervical cancer and controls were women without cervical cancer who were seeking care at the two hospitals. Nested multiplex polymerase chain reaction (NM-PCR) was used to detect HPV infection in cervical samples. Logistic regression was used to determine the association between the risk of cervical cancer and identified HPV infection. P ≤0.05 was considered statistically significant. HPV deoxyribonucleic acid (DNA) data were analysed for 177 women with cervical cancer (cases) and 201 without cancer (controls). Cervical cancer was diagnosed at older ages compared to the age at which controls were recruited (median ages, 57 years vs 34 years; p < 0.001). Most women with cervical cancer were more likely to be single with no formal education, unemployed and less likely to live in metropolitan areas compared to women without cervical cancer (all p-value <0.001). HPV DNA was detected in more women with cervical cancer compared to those without cervical cancer (84.8% vs 45.8%). HR-HPV genotypes 16, 18, 45, 35 and 52 were the most common among women with cervical cancer, while 66, 52, 35, 43 and 31 were frequently detected in those without cancer. HPV 66 and 35 were the most dominant non-vaccine genotypes; HPV 66 was more prevalent among women with cervical cancer and HPV 35 in those without cervical cancer. Cervical cancer risk was associated with a positive HPV test (Adjusted OR (AOR): 5.78; 95% CI: 2.92-11.42), infection with any of the HR-HPV genotypes (AOR: 5.56; 95% CI: 3.27-13.16) or multiple HPV infections (AOR: 9.57 95% CI 4.06-22.56). Women with cervical cancer in Ghana have HPV infection with multiple genotypes, including some non-vaccine genotypes, with an estimated cervical cancer risk of about six- to ten-fold in the presence of a positive HPV test. HPV DNA tests and multivalent vaccine targeted at HPV 16, 18, 45 and 35 genotypes will be essential in Ghana's cervical cancer control programme. Large population-based studies are required in countries where cervical cancer is most prevalent to determine non-vaccine HPV genotypes which should be considered for the next-generation HPV vaccines.

Epidemiological characteristics of human adenovirus 2, 3 and 7 genetypes in hospitalized children with respiratory infection in a hospital of pediatric in Hebei Province from 2018 to 2020

Objective: To investigate the epidemiological characteristics of human adenovirus (HADV) 2, 3 and 7 in hospitalized children with respiratory infection. Methods: A total of 25 686 children with respiratory infection hospitalized at Children's Hospital of Hebei Province from January 2018 to December 2020 were retrospectively included.Deep sputum or nasopharyngeal aspirates of those children were collected. Then thirteen common respiratory pathogens were detected by multiplex PCR. 510 HADV positive specimens were randomly selected via random number and classified for type 2, 3 and 7 using a multiplex real-time quantitative PCR. SPSS 21.0 software was used to perform all of the statistical analyses. Enumeration data were expressed by frequency and percentage. χ2 test was used for comparison between groups. Results: The HADV-positive rate was 7.99% (2 052/25 686). Children at age 3-<6 years had the highest HADV-positive rate (11.44%). The HADV-positive rate in 2019 was highest (10.64%). Among the 510 HADV-positive specimens, the proportion of type 3 was the highest (31.16%), followed by type 7 (21.37%) and type 2 (11.18%). The rate of type 2 in 2019 was significantly lower than that in 2018 and 2020 (χ2=8.954 and 16.354; P=0.003 and <0.01), while the rate of type 3 was significantly higher than that in 2018 and 2020 (χ2=5.248 and 4.811; P=0.022 and 0.028). The rate of type 2, type 3 and type 7 were lowest in winter, spring and autumn, respectively. The rate of type 2 increased significantly in autumn and the rate of type 3 and type 7 increased significantly in winter.The co-detection rate of HADV with other respiratory pathogens was 43.33%(221/510). Among, the co-detection rate of type 3 was highest (47.32%), and the co-detection rate of type 2, 3 and 7 was significantly higher than the alone detection rate (χ2=20.438, P<0.01; χ2=42.105, P<0.01; χ2=27.573, P<0.01).The proportion of severe pneumonia in children with type 7 positive (15.89%) was higher than that in children with non-type 7 positive (8.23%) (χ2=5.260, P=0.022). Conclusion: HADV is one of the important pathogens of children with respiratory infection in Children's Hospital of Hebei Province. The susceptible population of HADV is preschool children aged 3 to 6 years. HADV often co-detects with other respiratory pathogens. Type 3 and 7 is likely to be the dominant genotypes in this region, and type 7 may be one of the risk factors of severe pneumonia in children.

The genomic characterization of Salmonella Paratyphi A from an outbreak of enteric fever in Vadodara, India.

Salmonella enterica Typhi (S. Typhi) and Paratyphi A (S. Paratyphi A) are the causative agents of enteric fever, a systemic human disease with a burden of 300 000 cases per year in India. The majority of enteric fever cases are associated with S. Typhi, resulting in a paucity of data regarding S. Paratyphi A, specifically with respect to genomic surveillance and antimicrobial resistance (AMR). Here, we exploited whole-genome sequencing (WGS) to identify S. Paratyphi A genotypes and AMR determinants associated with an outbreak of S. Paratyphi A in Vadodara, India, from December 2018 to December 2019. In total 117 S. Paratyphi A were isolated and genome sequenced, most were genotype 2.4.2 (72.6 % of all cases), which is the globally dominant genotype. The remainder were genotype 2.3 (25.6 %), while only two isolates belonged to genotype 2.4.1. A single base-pair mutation in gyrA, associated with reduced susceptibility to fluoroquinolones, was present in all of the outbreak isolates; with 74.35 % of isolates having a S83F substitution and the remainder having an S83Y substitution. Our surveillance study suggests that S. Paratyphi A is an emergent pathogen in South Asia, which may become increasingly relevant with the introduction of Vi conjugate vaccines.

Prevalence and molecular characterization of Enterocytozoon bieneusi and a new Enterocytozoon sp. in pet hairless guinea pigs (Cavia porcellus) from China.

Enterocytozoon bieneusi, the most common microsporidian species, has been detected in humans and a variety of animals worldwide. However, limited information is available on the prevalence and molecular characterization of this parasite in guinea pigs. In this study, we conducted the first investigation of E. bieneusi infection in hairless guinea pigs recently introduced into China as new exotic pets. A total of 324 fecal samples were collected from hairless guinea pigs from a pet market and four breeding facilities in China. Sequence alignment of the internal transcribed spacer (ITS) revealed an infection rate of 14.2% (46/324) and two known ITS genotypes, S7 and PGP. Genotype S7 was the dominant genotype in these animals (42/46, 91.3%). Due to significant ITS sequence divergence, four and two PGP isolates from hairless and regular guinea pigs, respectively were further identified by PCR and phylogenetic analysis based on the small subunit (SSU) rRNA gene, as well as phylogenetic analysis of the ITS locus using E. hepatopenaei and two related genera Enterospora and Nucleospora as the outgroup. Three out of the six PGP isolates were successfully sequenced and generated the same sequences. Phylogenetic analysis of SSU rRNA and ITS loci revealed that PGP isolates formed a separate clade that was distinct and far away from E. bieneusi, suggesting that they represent a new species of Enterocytozoon. These findings indicate the dominance of zoonotic E. bieneusi genotype S7 in hairless guinea pigs and the existence of a cryptic Enterocytozoon species in guinea pigs.

Identification and Characterization of Hepatitis B Virus Immune Escape Mutants in Kenya

Hepatitis B Virus (HBV) infections affect about 400 million people globally and cause about 1.4 million deaths annually. The virus displays high levels of genetic variations/mutations, some of which are immune escape mutants. The prevalence of HBV infection in Kenya is high at about 8%. This study aimed at identifying and characterizing HBV immune escape mutants in Kenya. From 547 HBV sequences available in Kenya in NCBI, and HBVdb databases in July 2021, 120 full sequences were retrieved. The S gene sequences at position 1-225, which included the “a” determinant region of the gene were analyzed using various bioinformatics tools such as Bioedit software, and Emboss Cons. The clinical significance was flagged from the search of peer-reviewed journals. Forty-six HBV-positive blood donor samples were obtained from the Kenya National Blood Transfusion Services without personal identifiers, DNA extracted, and sequenced targeting positions 1 to 520 of S genes. Mutations were similarly identified from seventeen sequences after cleaning and analysis. Out of 120 sequences that were extracted from databases and analyzed, 79 different mutations were identified. Fifteen of them were of clinical importance with an occurrence frequency of at least 5% were obtained. The majority (64.6%, n = 51), with S207N and A194V being most dominant, could result in immune escape and reduced HBsAg detection signals while 24.1% (n = 19) could result in immune escape/reduced HBsAg detection signals and high probability of hepatocellular carcinoma. Most likely to occur on the amino acids Alanine, Lysine, Serine, Asparagine, and Valine in decreasing order. The most dominant genotype was found to be Genotype A (N = 10), while four sequences were Genotype D. In contrast to the in-silico studies, the sequences from HBV samples from blood donors did not demonstrate the presence of S207N and A194V mutations and all the genotypes were type A1. Only two (13.3%) samples showed the same mutations of sK122R and sT143S for both in-silico analysis and actual sequenced samples. This study did not identify G145R mutation which is the commonest mutation within the HBsAg immunodominant “a” determinant that is associated with immune escape. The concordance of mutations in “a” determinant region of HBsAg gene among various studies is minimal. The study identified new mutations (sA194Y, sS207, sA194S, sS207I, sP46A, sA194T, sS207I, sP46R, and sT143P) that had not been published before. Four (20%) of the mutations were clinically significant. These included sS207R, sT143S, sC76F and sK122R.

First report on occurrence and genotypes of Enterocytozoon bieneusi, Cryptosporidium spp. and Cyclospora cayetanensis from diarrheal outpatients in Ningbo, Southeast China

Enterocytozoon bieneusi, Cryptosporidium spp. and Cyclospora cayetanensis are three important zoonotic pathogens which were a major cause of foodborne or waterborne intestinal diseases in humans and animals. However, very little data about occurrence and genotypes of the three parasites in Ningbo in the south wing of the Yangtze River Delta, China, which is important for a tourist city. In the present study, molecular characterization of E. bieneusi, C. cayetanensis and Cryptosporidium spp. in fecal samples from 489 diarrheal outpatients were carried out. As a result, a total of 35 (7.16%, 35/489) and three (0.61%, 3/489) samples were positive for E. bieneusi and C. cayetanensis respectively. No Cryptosporidium-positive sample or mixed-infections were detected. Four known E. bieneusi genotypes (Type IV, D, I and CHN4) and 8 novel genotypes (NBH1-NBH8) were identified with type IV was the dominant genotype (n=14), followed by genotypes D (n=5), NBH8 (n=5) and NBH7 (n=3). The remaining genotypes were found in one sample each, and these genotypes were belonged to the previously described high-potential zoonotic group 1. One novel sequence named NBC315, and the other two sequences (NBC30 and NBC370) identical with the reported sequence were detected. Therefore, the existence and importance of zoonotic potential of E. bieneusi and C. cayetanensis in diarrheal outpatients in Ningbo indicates the public health threats, and more investigations should be carried out in human populations, animals and other environmental sources from the One Health perspective.

Distribution of Genotypes of Hepatitis C Virus Studied in a Tertiary Care Hospital in Uttarakhand, India: A Retrospective Study

Introduction: With more than one million cases of Hepatitis C viral infection reported annually, it has become a major global problem. Hepatitis C Virus (HCV) is classified into 7 genotypes and 67 subtypes. Various genotypes show a wide geographical distribution worldwide. Genotypes 1 and 3 are the most common genotypes reported from India. There is minimal data available on the distribution and frequency of HCV genotypes in Uttarakhand. Aim: This three years retrospective study was undertaken to find out the distribution pattern of HCV genotypes among HCV- infected patients attending a tertiary care hospital in this Sub- Himalayan state of Uttarakhand. Materials and Methods: A total of 306 samples were tested for HCV genotyping in 3 years duration i.e., January 2018 to December 2020 at the Molecular Laboratory of Shri Guru Ram Rai Institute of Medical and Health sciences and associated Shri Mahant Indiresh Hospital, Dehradun. Genotyping was performed using HCV genotype specific Real-Time Polymerase Chain Reaction (RT-PCR) assay on Rotor-Gene Q using TRUPCR HCV Genotyping Kit (3B BlackBio Biotech India Ltd.,) as per manufacturer’s instructions. This test kit detects HCV genotypes 1, 1a, 2 (2a/ 2b), 3, 4, 5a, and 6. Results: Genotype 3 (72.7%) was the commonest genotype detected, followed by genotype 1 (13%), genotype 1a (6.25%) and genotype 4 (2.8%). Genotype 3 was the most dominant genotype in all the 3 years of the study. Two cases of genotype 5a (1.13%) and three cases of genotype 6 (1.7%) were also detected in our study. We also detected a case of mixed infection by genotype 1 and genotype 6. Conclusion: The most common genotype detected was three during the study period. Detection of genotype 5a and 6 ascertained the impact of interstate migration of people.