Common Genotypes Research Articles

MOLECULAR EPIDEMIOLOGY OF ALPHA THALASSEMIA MUTATIONS IN DUHOK CITY, KURDISTAN REGION OF IRAQ: A 9-YEAR RETROSPECTIVE STUDY

ABSTRACT Background: Alpha thalassemia demonstrates high prevalence in Iraq, particularly among consanguineous Kurdish subgroups. However, data remains limited regarding the molecular epidemiology of causative alpha globin mutations in this population. This study aimed to elucidate the mutational spectrum and temporal distribution of alpha thalassemia alleles among native inhabitants of Duhok City in northern Iraq. Methods: In this retrospective cross-sectional study, positive alpha globin genetic testing records of 1,295 Duhok natives at a specialized northern Iraqi laboratory from 2014-2022 were analyzed to determine mutant genotype and allele frequencies. Results: The five most common mutant genotypes detected were -α3.7/-α3.7 (5.5%), -α3.7/αα (19.1%), -αMED/αα (3.2%), -α3.7/-αMED (2.6%) and ααIVS1-5nt/αα (1.5%). The -α3.7 deletion was predominant affecting 43.8% of alleles. A steady 9-year upward annual detection trajectory was observed. Conclusions: Population-specific molecular analysis may provide seminal evidence to shape thalassemia screening and prevention policies targeting the high-risk marginalized Kurdish community in northern Iraq.

Mutations in tumor suppressor genes Vhl and Rassf1a cause DNA damage, chromosomal instability and induce gene expression changes characteristic of clear cell renal cell carcinoma.

RASSF1A is frequently biallelically inactivated in clear cell renal cell carcinoma (ccRCC) due to loss of chromosome 3p and promoter hypermethylation. Here we investigated the cellular and molecular consequences of single and combined deletion of the Rassf1a and Vhl tumor suppressor genes to model the common ccRCC genotype of combined loss of function of RASSF1A and VHL. In mouse embryonic fibroblasts and in primary kidney epithelial cells, double deletion of Rassf1a and Vhl caused chromosomal segregation defects and increased formation of micronuclei, demonstrating that pVHL and RASSF1A function to maintain genomic integrity. Combined Rassf1a and Vhl deletion in kidney epithelial cells in vivo increased proliferation and caused mild tubular disorganization, but did not lead to the development of kidney tumors. Single cell RNA-sequencing unexpectedly revealed that Rassf1a or Vhl deletion both induce the expression of an overlapping set of genes in a sub-population of proximal tubule cells. Many of these genes are also upregulated in the Vhl/Trp53/Rb1 deficient mouse model of ccRCC. In other subsets of proximal tubule cells, combined Vhl/Rassf1a deletion induced the expression of additional genes that were not upregulated in each of the single knockouts. The expression of the human homologues of Rassf1a-regulated genes correlate negatively with RASSF1 expression levels in human ccRCC. Our results suggest that the loss of RASSF1A function establishes a ccRCC-characteristic gene expression pattern.

Genetic diversity of hepatitis delta virus in Afghanistan: insights from complete genome analysis

BackgroundA significant gap exists in the comprehensive genomic characterization of hepatitis delta virus in Afghanistan. Therefore, the primary aim of this investigation is to elucidate the molecular profile of the complete genome of HDV circulated among general population of Afghanistan.MethodsFour serologically positive samples for anti-delta antibody were confirmed via real-time polymerase chain reaction and subjected to entire genome amplification using two sets of primers to generate partially overlapping segments, which were subsequently sequenced. Phylogenetic and evolutionary divergence analysis were conducted using the MEGA7 software package.ResultsUltimately, the whole genomes of four HDV isolates from Afghanistan were assigned to genotype I. The amino acid composition of the hepatitis delta antigen and its functional motifs were consistent with genotype I. However, the subtype-specific amino acid signature revealed potential differences in subtypes.ConclusionGenotype I is the most common HDV genotype in analyzed samples, with potential subtype heterogeneity and no significant functional impact from HDAg variations.

Genetic diversity, genotyping and evolutionary history of the global population of Orthotospovirus tomatomaculae genomic segments

AbstractTomato spotted wilt virus (Orthotospovirus tomatomaculae; TSWV) is a destructive pathogen that affects over 1000 plant species worldwide. To elucidate its evolutionary mechanisms, genetic diversity and emergence timeline, we examined around 100 TSWV isolates with complete genome sequences available in GenBank. This study also included the complete genome of a TSWV isolate, IRP4, which has recently been implicated in an outbreak affecting greenhouse‐grown bell peppers in Iran. Pairwise genetic divergence analysis revealed varying levels of genetic differences among TSWV RNA segments. Phylogenetic and sequence analysis determined that the global TSWV population consists of three major groups based on each of the three RNA segments (L, M, and S). Results suggested multiple introductions of the virus into different regions, indicating that the geographical origin of the isolates is not the sole factor determining their phylogenetic grouping. The large incongruences observed in the phylogeny of the TSWV segments and the analysis of genetic diversity patterns highlight extensive reassortment events in TSWV. As a result, 11 genotypes were identified within the TSWV population. The Iranian IRP4 isolate, along with nine other isolates from Europe, Asia, and South America shared a common genotype designated L3‐M1‐S1. This suggests that this potentially reassortant genotype has undergone long‐distance intercontinental movement. Similar to IRP4, the majority of TSWV isolates with the L3‐M1‐S1 genotype were also obtained from pepper, suggesting a potential role of the host plant in the evolution of this genotype. Furthermore, temporal analysis suggests that the existing population of TSWV, circulating between 1996 and 2023, originated from a common ancestor that existed 107–284 years ago. The population size of TSWV experienced a significant expansion for 10–15 years since 1980 and then remained constant until recently.

Genetic Variability and Character Association among Common Bean (Phaseolus vulgaris L.) Genotypes at Areka, Southern Ethiopia

Evaluating genetic variability among genotypes is vital for identifying superior genotypes because selecting parents who create segregating populations is critical in breeding programs. The current study was done at Areka Agricultural Research Center during the 2020/21 major cropping season, with the goal of estimating genetic diversity and character connection among 25 common bean genotypes. The experiment consisted of two replications of a 5 x 5 simple lattice design. Data were obtained on 12 quantitative parameters, and the analysis of variance revealed extremely significant variations between genotypes for all characters. It demonstrated that genotypes vary significantly. GCV and PCV were highest in plant height, number of pods per plant, biological yield, number of seeds per plant, and seed yield, while lowest in days to flowering and days to maturity. Plant height, number of pods per plant, number of seeds per plant, biological yield, and seed yield all showed significant broad-sense heritability (H2) and high predicted genetic advance as a percentage of mean GAM. This suggested the presence of additive gene activity in the inheritance of these traits. The number of major branches per plant, biological yield, days of 50% flowering, hundred seed weight, and harvest index all show a highly substantial and positive link with seed yield at both genotypic and phenotypic levels. The biological yield and harvest index both have a strong positive direct effect on seed output. As indicated, these traits could be utilized for selection to increase seed output. Based on the D2 value, 25 common bean genotypes were divided into four clusters. Clusters I and IV had the greatest inter-cluster distance (766.78), whereas clusters I and II had the smallest (53.78). Breeding programs could use genotypes from distant clusters to increase variety. Thus, the enormous genetic variation among common bean genotypes must be evaluated for use in common bean breeding efforts.

Genetic assessment of apolipoprotein E polymorphism and PRNP genotypes in rapidly progressive dementias in Pakistan

ABSTRACT Rapidly progressive dementias (RPDs) are a type of fatal dementias that cause rapid progression of neuronal dysfunction. This study aimed to assess the prevalence of APOE genotypes (ε2, ε3, ε4) and PRNP mutations (E200K, M129V) in the general population of Pakistan because of their association with RPDs, including Rapidly Progressive Alzheimer’s Disease (rpAD) and Creutzfeldt-Jakob Disease (CJD). Blood samples (n = 100) were collected from healthy Pakistani population and the stated mutations were assessed using polymerase chain reaction. In the analysis of the APOE genotype, ε3/ε3 genotype was the most common (95%), followed by ε3/ε4 (5%) and ε2 allele was completely absent. A low frequency of ε4 allele and the absence of a protective ε2 allele is associated with an increased risk of rpAD. In the case of PRNP mutations, the most common genotype was M129-Ε200 (71%) and V129-Ε200 (29%). E200K mutation was completely absent from the given population. It is noteworthy that the MM homozygous genotype was present in 71 samples, VV genotype was present in 29. Homozygosity on codon 129, as observed in most of our samples, has been associated with more efficient production of PrPSc and disease pathology. This study provides preliminary data indicating that rpAD and CJD pose a significant threat to the Pakistani population.

Prevalence of Different Dengue Serotypes in Northern India, 2021-2022: A Tertiary Care Hospital-Based Study.

Dengue fever is a substantial emerging and reemerging arboviral virus in tropical and subtropical areas that seriously threatens public health worldwide. India is experiencing rising dengue epidemics in urban and rural regions linked to all four serotypes. The objective is to examine the serotypes and genotypes of the circulating dengue virus (DENV) at a tertiary care center in eastern Uttar Pradesh, India, from 2020 to 2021. This retrospective cross-sectional observational study involved dengue patients from January 2021 to December 2022. The genetic analysis of the circulating DENV was conducted by amplifying the partial CprM (511-bp) gene using nested reverse transcriptase polymerase chain reaction (RT-PCR), followed by sequencing. Only those positive for NS1 antigen (n = 581) were included in the study. A total of 204 cases (35.1%) were seropositive, with 96 cases (37.4%) out of 257 in 2021 and 108 cases (33.3%) out of 324 in 2022. With 119 cases (58.3%), men were most affected. The nested RT-PCR for dengue revealed three DENV-1 to DENV-3, except for DENV-4. DENV-2 and DENV-3 were the most predominant serotypes, with 98 (48%) and 94 (46%) cases, respectively. Conversely, DENV-1 was the least prevalent with cases 3 (1.6%). Unfortunately, 35 (17.2%) of the 204 cases died. DENV-2 had the highest mortality rate, with 23 deaths (65.7%). In cases with DENV-3, nine (25.7%) died. This study revealed regional disparities in DENV serotype prevalence in India. If regional differences in the most common serotypes and genotypes are identified early in the season, molecular surveillance may predict major dengue outbreaks and severity.

High frequency of HPV high-risk preventable genotypes in Ecuadorian women with invasive cervical cancer.

To determine the distribution of human papillomavirus (HPV) genotypes in invasive cervical cancer samples from Ecuadorian women who attended the Cancer Institute (Sociedad de Lucha Contra el Cáncer - SOLCA). Archived formalin-fixed paraffin-embedded (FFPE) cervical cancer tissue samples collected during 2017-2021 were deparaffinized, and nucleic acid extraction and purification was performed using silica columns. The obtained nucleic acids were analyzed using INNO-LiPA® HPV Genotyping Extra II per the manufacturer's specifications. Data were retrieved from records, and HPV genotypes were determined from the FFPE samples. The study included samples from 190 women diagnosed with invasive cervical cancer, with a median age of 52.78 years. Squamous cell carcinoma accounted for 78.94% of the cases, while 21.05% had adenocarcinoma. Among the 190 samples, 80.53% tested positive for HPV DNA, while 19.47% were negative. The most common genotypes detected were HPV 16 (64.05%), 18 (16.99%), and 58 (6.54%). HPV infection frequency was higher in samples from patients with elementary level education (p < 0.05). This study provides valuable insights into the distribution of HPV genotypes in invasive cervical cancer samples from Ecuadorian women. The results indicate an elevated presence of HPV 16, HPV 18, and HPV 58, which are vaccine-preventable genotypes.

Response of Common and Tepary Bean Genotypes to Three Macrophomina phaseolina Isolates Inoculated at Different Growth Stages

Ashy stem blight caused by the fungus Macrophomina phaseolina (Tassi) Goidanich affects Phaseolus spp. in all growth stages. The identification of genotypes with durable resistance is crucial for disease management. The objectives of this research were to determine the following: the aggressiveness of three fungal isolates; the response of common (P. vulgaris L.) and tepary bean (P. acutifolius A. Gray) genotypes at vegetative and midflowering stages; and the presence or absence of SMe1Em5.110 and SS18 molecular markers. Seventeen genotypes were inoculated with the PRI21, PRI22, and PRI23M isolates at the V5 and R2 stages in the greenhouse in Lajas and Isabela. The disease severity was evaluated at 42 days postinoculation. The isolate PRI23M was more aggressive (mean score of 6.2 at V5 and 6.8 at R2) than PRI21 (5.4 and 5.3) in Isabela, whereas there were no significant differences between PRI21 (5.5 and 4.2) and PRI22 (5.0 and 4.3) in Lajas. Tepary bean PI 462025 was intermediate (3.6 to 6.5) to the three isolates, whereas BAT477 and SEA 5 common beans were intermediate to PRI21 and PRI22 and susceptible (scores &gt;6.5) to PRI23M at both growth stages. Likewise, ‘Bella’, ‘Beníquez’, and ‘Verano’ were susceptible to PRI21 and PRI23M at V5 and R2 stages in Isabela. Neither of these genotypes amplified for the two molecular markers. In contrast, NY6020-4 with the SS18 marker was intermediate to PRI21 and PRI22 at the R2 stage in Isabela and Lajas. Moreover, UPR-Mp-22 with the SMe1Em5.110 and SS18 markers was resistant (&lt;3.6) to PRI21 at the V5 stage in both locations and at R2 in Isabela. Two inoculations of M. phaseolina isolates are recommended to identify genotypes with resistance throughout the growing season.

Baseline data on distribution of human papillomavirus (HPV) genotypes in cervical samples of gynecological patients before implementation of population-based HPV vaccination program in Poland.

Free-of-charge vaccination against human papillomavirus (HPV) of 12-13-year-old teenagers was introduced on the 1st of June 2023 in Poland. Data on baseline HPV genotype cervical distribution are crucial to evaluate potential changes after full implementation of the vaccination program. We aimed at evaluating the status of HPV infection and distribution of HPV genotypes in cervical cytology of gynecological patients tested in one of the largest HPV laboratories in Poland. Data on all HPV tests performed in ALAB Laboratoria Sp. z o. o. in Poland in 2018-2021 were analyzed, focusing on tests that identified genotypes: 6, 11, 16, 18, 26, 31, 33, 35, 39, 40, 42, 44, 45, 51, 52, 53, 54, 56, 58, 59, 61, 62, 66, 67, 68, 70, 73, 81, 82, 83, 89. Distribution of HPV genotypes was assessed among HPV-positive women. Among 11.151 medical records retrieved in women with valid HPV test results, 5.681 were positive (50.9%), of whom 2.929 were infected with a single genotype (51.6%). At least one high-risk (HR) genotype was detected in 4.351 women (76.6%). Among all HPV-positive women, the most common HR genotypes were HPV-16, HPV-31 and HPV-66 (24.0%, 11.3%, 11.3%, respectively). HPV-53 was the most prevalent among non-HR types (10.5%). HPV-16 followed by HPV-31 and HPV-66 were the most frequent genotypes in the studied cohort. These results may be compared with the same methodology after full roll-out of HPV vaccination program in the future to track potential changes in HPV genotype distribution.

Study of rotavirus genotypes G and P in one Egyptian center-cross-sectional study

BackgroundRotavirus-associated gastroenteritis is a common health problem in children, different variations of rotavirus genotypes differ according to geographic locations and the practice of wide-scale vaccination. Therefore, the present study aimed to detect both the G and P genotypes of rotavirus in children ≤ 5 years old in one center in Egypt as a cross-sectional study, to correlate the genotypes with various demographic and clinical data in infected children and to evaluate the common mixed genotypes G and P in infected children.MethodThe cross-sectional study included children with acute gastroenteritis ≤ 5 years old from January 2023 till March 2024 recruited from Mansoura University Children’s Hospital, Egypt based upon laboratory diagnosis by exclusion of bacterial and protozoa pathogens. The stool samples were obtained from each child and subjected to detection of rotavirus antigen by enzyme-linked immunosorbent assay (ELISA) followed by genotypes identification of G and P genotypes by nested polymerase chain reaction (PCR).ResultA nested PCR study for rotavirus genotypes revealed that G1 was the most common genotype (24.7%) followed by G2 (21.1%), G3 (20%), G9 (20%), and G4 (14.1%). The genotyping of the P genotype revealed that P9 was the commonest genotype (24.7%), followed by P4 (21.2%), P10 (20%), P8 (17.6%) and P6 (16.5%). The commonest combined genotypes of G and P were G1P4 (85.7%), G3P8(88.2%), followed by G2P6 (77.8%) and G9P9(76.5%) and G4P9 (66.7%) followed by G4P10 (33.3%), G9P10(23.5%), G2P10(22.2%), G1P10 (14.3%), G3P10(11.8%). The distribution was significant (P = 0.001). The positive rotavirus antigen was more frequently detected in females (55.3%) than males (44.7%, Odd ratio 0.2, 95% CI 0.22–0.71, P = 0.001). There was a significant association between the summer season and positive rotavirus antigen (P = 0.001) and rural residence of the patients (Odd ratio 6,9 95%CI 3,5-13.5, P = 0.001). The significant associated clinical sign with positive rotavirus antigen was fever (Odd ratio 3,3, 95%CI 1,8-6.05, P = 0.001). The genotypes G and P were significantly associated with positive rotavirus antigen as all cases positive by antigen had been detected by nested PCR with the commonest genotypes G4 (24.7%, P = 0.001) and genotype P9 (24.7%, P = 0.001).ConclusionThe present study highlights the common genotypes of rotavirus at one center in Egypt, G1, G2, and G3 were the commonest G genotypes. As regard genotype P the commonest genotypes were P9, P4, and P10. The commonest combined genotypes were G1P4, G3P8, G2P6. There was no effect of the practice of rotavirus vaccination at limited rates at private health sections as the rotavirus is still a major pathogen of acute gastroenteritis in children. There is a need for the inclusion of rotavirus vaccination in the national program of children vaccination in Egypt.

Monte Carlo simulation for dosage optimization of the best available therapy for bloodstream infections secondary to carbapenemase-producing Klebsiella pneumoniae in critically ill patients

ObjectiveWe aimed to use Monte Carlo simulation, based on pharmacokinetic/pharmacodynamic targets, to investigate and determine the optimal dosage of the available combination therapies for carbapenem-resistant Klebsiella pneumoniae (CRKP) in critically ill patients. MethodsWe collected CRKP clinical isolates from Phramongkutklao Hospital between October 2020 and June 2022. A molecular study of resistant genes was performed using polymerase chain reaction. Broth microdilution checkerboards were used to evaluate the mono- and synergistic antibiotic activities. Monte Carlo simulation was used to determine the optimal antibiotic regimens, based on the probability of target attainment (PTA) and cumulative fraction of response. ResultsThe 54 CRKP isolates were resistant to tigecycline (100%), colistin (75.9%), amikacin (70.4%), and gentamicin (63.0%). The most common carbapenemase genotype was blaoxacillinases (OXA)-48-like (42.6%), followed by blaNew Delhi metallo beta-lactamase (NDM) (29.6%) and coexistence of blaOXA-48-like and blaNDM (22.2%). Based on the PTA, synergistic and additive activities against CRKP isolates were observed with appropriate dosages of tigecycline–colistin (67.9%), tigecycline–gentamicin (62.2%), and tigecycline–amikacin (51.4%). ConclusionsTigecycline–colistin was the best available combination therapy for critically ill patients with CRKP, especially NDM. When used in combination with tigecycline, a colistin creatinine clearance of <90 mL/min can raise the cumulative fraction of response target and less nephrotoxicity.

Characteristics of maternal antibodies transferred to foals raised through maternal equine rotavirus A vaccination

Equine rotavirus A (ERVA) can cause foal diarrhoea and the most common ERVA genotypes are G3P[12] and G14P[12]. Since the introduction of a monovalent killed G3P[12] vaccine, infection in neonates has decreased. We aimed to determine the dynamics and longevity of maternally derived anti-G3P[12] neutralizing antibodies (NAbs) in foals and what, if any, cross-reactivity exists between maternally derived NAbs against G14P[12]. Serum samples were collected from 50 mare-foal pairs before each vaccination and up to 6 months post-foaling for mares and up to 7 months of age for foals. These samples were then used for virus-neutralization antibody assays with both G3P[12] and G14P[12] viruses. We observed that vaccination of mares could increase their serum NAb titers. Pre-nursing serum samples of foals collected at birth before the first nursing contained no detectable NAbs. In contrast, post-nursing serum samples of foals showed a significant amount of NAb levels, thereby confirming that these NAbs are passed through the mare’s colostrum. Our study demonstrated that there is variation in the ratio of NAbs transferred from the serum of mares to the serum of their foals. Results also confirmed evidence of cross-reactivity between maternal antibodies in the serum of G3P[12] vaccinated dams and G14P[12]. Heterologous (G14P[12]) NAb titers were about 2- to 4-fold lower than homologous (G3P[12]) titers in colostrum, milk, and serum samples of both mares and their foals. Our data demonstrate that G3 and G14 NAbs in the serum of foals decreased steadily over time with the lowest point measured at approximately 4 months of age.

Association of multilocus sequence typing, MSH2 gene mutations, and antifungal resistance in Candida glabrata: implications for clinical outcomes in Chinese hospitals

BackgroundCandida glabrata is the second most common cause of invasive candidiasis worldwide. In this study, we determined the clinical characteristics and drug sensitivity of C. glabrata isolates and investigated the associations between MSH2 gene mutations, sequence types (ST), and drug resistance.MethodsA total of 154 C. glabrata isolates were collected from patients being treated in three hospitals in China. The antifungal sensitivity of the strains was assessed using the broth microdilution method. Multilocus sequence typing (MLST) was also performed, followed by MSH2 sequencing. The clinical features and outcomes of C. glabrata infection were analysed for a total of 49 strains, which were collected from patients with invasive Candida infection at Longhua Hospital.ResultsAll 154 isolates were found to be susceptible to amphotericin, 5-fluorocytosine, anidulafungin, caspofungin, and micafungin, whereas 11.7% were fluconazole-resistant, 18.8% were itraconazole non-wild type, and 35.7% were voriconazole non-wild type. ST7 (62.34%) was the most common ST genotype, followed by ST10 (16.88%) and ST15 (7.79%). The total azole resistance rates for all isolates, ST7, ST10, and other STs were 36.4, 42.7, 34.6, and 18.8%, respectively. The ST7 and ST10 isolates were characterised by a higher drug resistance rate than the other minor ST isolates. Moreover, 59.09% of isolates had one or more MSH2 non-synonymous mutations, with V239L being the most commonly detected mutation. The frequency of MSH2 mutations was significantly higher in azole-resistant isolates than in other isolates, whereas P6L or L87P mutations were associated with the highest azole resistance rates of up to 87.5% and 80%, respectively. Our results indicated that ST7 and ST15 are independent predictors of mortality caused by C. glabrata infection and revealed a higher 30-day mortality in patients infected with these strains than in those infected with other ST isolates.ConclusionsOur findings revealed the relationships between MLST, MSH2 gene mutations, and drug resistance in the common pathogenic fungus C. glabrata, and thereby enabled us to identify strains that are associated with higher rates of mortality. These findings will contribute to enhancing our understanding of the pathogenesis of C. glabrata infection.

Epidemiological and typing features of HPV co-infections in MSM with mpox: A hospital-based prospective study

ObjectivesRecent mpox outbreaks highlight diverse transmission modes, with sexual behavior prominent in China's IIb strain. Nevertheless, despite HPV being a common sexually transmitted pathogen, there is a paucity of research into its coexistence and genotype distribution within this patients population. MethodsWe conducted a study at the Third People's Hospital of Shenzhen from May to September 2023. We collected information on mpox patients, including their sociodemographic and clinical characteristics. Anal swabs were collected for HPV genotyping. ResultsAmong 73 MSM mpox cases, HIV positivity was 56.2 % (41/73) and HPV positivity 80.4 % (41/51). Multiple HPV infections were prevalent (56.9 %, 29/51), especially among HIV-positive (93 %, 27/29). HPV16 (29.3 %, 12/41) was the most common high-risk genotype, followed by HPV59 (26.8 %, 10/41), HPV42 (19.5 %, 8/41), HPV6 (14.6 %, 6/41), and HPV54 (14.6 %, 6/41). HPV infection was significantly associated with HIV infection (p = 0.001). Additionally, HIV infection (p = 0.001) and PCR-detected positive sites for mpox (p = 0.047) were associated with high-risk HPV infection. ConclusionsIn this study, most of the mpox patients were found to be infected with HPV, mostly with high-risk types and multiple infections. Therefore, it is strongly recommended that mpox-infected individuals intensify HPV-related screening, prevention, and treatment measures.

Northwestern Himalayan common beans: A treasure trove for breeding resistant bean cultivars for multiple foliar pathogens

Common bean (Phaseolus vulgaris. L) is attacked by a lot of important foliar diseases like anthracnose, bean common mosaic virus, angular leaf spot, bean golden yellow mosaic virus, and common bacterial blight. In the present study, we exploited anthracnose resistant germplasm of 122 common bean genotypes for the identification of broad spectrum and durable resistance for multiple foliar diseases. We utilized linked molecular markers and found some promising genotypes with 11 resistance genes. These genotypes possess significant potential as parental lines for gene pyramiding strategies, to enhance disease resistance in common beans. We also highlighted the need for new generation markers over SCAR markers to streamline genotypic screening and expedite the breeding of disease-resistant common bean varieties. Our phenotypic studies identified a few bean landraces highly resistant to the new BCMV NL-1n strain. Consequently, the genome wide association study also confirms the presence of already identified resistance genes. Additionally, our study reconfirms the presence of the recently identified bc-urgene in our material. The bean landraces of northern India contain novel regions associated with BCMV resistance on Pv03, Pv05, Pv04, Pv06, Pv07, Pv09, and Pv11. This study provides the list of bean genotypes that can be used to breed resistant cultivars and may also contain new resistance genes to a most important viral disease of common beans.

Genotype-phenotype correlation analysis of patients with thalassemia in quanzhou city, southeast of China

BackgroundThe carrying rate of thalassemia is high in Quanzhou city. However, there are few large-scale studies on the correlation analysis between genotype and phenotype of thalassemia in Quanzhou. In this study, the genotype and phenotype data of 1076 individuals with thalassemia in Quanzhou city were analyzed to provide reference data for screening and diagnosis of thalassemia in this region. Material and methodsReverse dot blot hybridization (RDB-PCR), Gap-PCR and nested PCR were used to detect the thalassemia genotype. Clinical and hematological parameters of 1076 individuals of thalassemia were collected to analyze the correlation between genotype and phenotype. ResultsAmong 2997 subjects, 1076 cases diagnosed as thalassemia gene carrier or patients, with detection rate 35.9 %, among which Southeast Asian deletion (--SEA)/αα was the most common α-thalassemia genotype (48.4 %) and one rare genotype was detected: HKαα/--SEA (0.1 %). Subjects with thalassemia alone showed the least severe symptoms of anemia with higher red blood cell count (RBC) and hemoglobin (Hb), lower red blood cell distribution width (RDW) than those with iron deficiency (ID) or iron overload (IO) (p < 0.05). The Hb, mean corpuscular volume (MCV), mean corpuscular hemoglobin (MCH) levels in gene carriers of α-thalassemia were higher than those of β-thalassemia, while RBC, RDW and serum ferritin (SF) levels were lower than the later(p < 0.05). Among individuals with --SEA/αα, the Hb, MCV, MCH, mean corpuscular hemoglobin concentration (MCHC) and SF levels of subjects≥19 years old were higher than those of ≤18 years old. For cases ≥19 years old, the RBC, Hb and SF levels in male were higher than that in female, while MCHC level was lower than female(p < 0.05). ConclusionThe difference of hematological phenotypes in patients with thalassemia is not only affected by their genotype, but also the influence of gender and age.

Unveiling the genotypic diversity of Candida albicans and Candida dubliniensis in the oral cavities of drug abusers in Ahvaz, Iran

Candida albicans is a diploid yeast that, under certain conditions, can cause oral or oropharyngeal infections, particularly in immunocompromised individuals. Recent molecular investigations have classified genotypes A, B, and C for Candida albicans, along with genotype D for Candida dubliniensis. This study aimed to identify the different genotypes of the C. albicans complex in drug abusers in Iran. Oral swabs were collected from drug abusers and cultured on CHROMagar Candida. A 21-plex PCR method was employed for the detection of isolates, and the Candida 25S rDNA gene was amplified using primer pairs CA-INT-L and CA-INT-R for ABC genotyping of C. albicans. Out of the 245 substance abusers screened, 151 individuals (61.63 %) were found to harbor the C. albicans complex. The most common genotype among patients was genotype D (39.1 %), followed by genotype A (31.12 %), genotype B (9.93 %), and genotype C (5.29 %). Additionally, 14.56 % of patients had a mixed genotype. Notably, significant differences in genotype distribution were observed in relation to age, underlying diseases, and marital status (P < 0.05). This study highlights the significance of molecular genotyping in understanding the epidemiology of C. albicans and C. dubliniensis in at-risk groups.

Familial Mediterranean fever in children from central-southern Italy: a multicentric retrospective cohort study.

Although familial Mediterranean fever (FMF) is a relevant disease in countries surrounding the Mediterranean Sea, there are still few reports from Italy. We retrospectively evaluated patients with FMF diagnosed according to the EuroFever/PRINTO classification criteria in three pediatric rheumatology referral centers in central-southern Italy. Logistic regression analysis assessed the associations between age at disease onset and symptoms. Overall, 48 patients were enrolled (28 females, 20 males), with a median age at onset of 3.3 [3.1] years, and a median follow-up period of 5.1 [10.8] years. The most common MEFV genotype was M694V/- (11 patients, 22.9%), followed by M694V/M694V (6 patients, 12.5%). At onset, recurrent fever was observed in 47 patients (97.9%), with a median time between attacks of 18 [11] days. Overall, recurrent fever was observed in all patients, abdominal pain in 44 (91.7%), and chest pain in 18 (37.5%). At the last follow-up visit, 24 patients were on colchicine (50%), 2 on biologic (4.2%), and 6 on both (12.5%). Canakinumab was the most used biologic drug, in 6 (12.5%) patients. MEFV genotype was associated with disease severity (p = 0.007) and the use of a biological drug (p = 0.01). FMF prevalence in the Abruzzo region was found highly than expected (at least 1:45,000). Differently, we found a relevant gap among FMF patients expected and observed in the Apulia and Sicily regions. FMF is a relevant issue in central-southern Italy. A large epidemiologic study should be performed to better define its prevalence in the country. Key Points • Italian children with familial Mediterranean fever tend to have an early age of onset, primarily manifesting with recurrent fever and characteristic associated symptoms. • Many MEFV gene variants are present in Italian children with familial Mediterranean fever, and these patients are most often heterozygous, exhibiting a mild to moderate phenotype. • The prevalence of familial Mediterranean fever in Italy is still unknown but recently estimated to be around 1:60,000, probably higher in central and southern Italy. • According to our cohort, the prevalence of FMF in the Abruzzo region is at least 1:45,000, higher than expected. Differently, we found lower prevalence rates of the disease in Apulia and Sicily.

An updated phylogeography and population dynamics of porcine circovirus 2 genotypes: are they reaching an equilibrium?

Porcine circovirus 2 (PCV2) emerged more than three decades ago as one of the most impactful pathogens in the swine industry. Despite being a DNA virus, one of the hallmarks of PCV2 is its high evolutionary rate, which has led to the emergence of different genotypes, each exhibiting varying degrees of evolutionary success. Current knowledge suggests the occurrence of three main waves of genotype dominance, alternating over time (i.e., PCV2a, PCV2b, and PCV2d), alongside less prevalent genotypes. However, although PCV2d is currently the most common genotype nowadays, the others continue being circulating in the pig population. The present study reconsidered the epidemiological and evolutionary patterns of PCV2 genotypes using phylodynamic analyses, benefiting from an almost 10-fold increase in ORF2 sequence availability compared to previous studies. Additionally, a phylogeographic analysis was performed to investigate viral dispersal patterns and frequency, and the selective pressures acting on the capsid protein were estimated and compared among genotypes. While successive emergence of major genotypes was confirmed, this study extends previous findings by revealing subsequent prevalence fluctuations of PCV2a and PCV2b after their initial decline. This evolutionary process may represent an example of balancing selection, specifically negative frequency-dependent selection, where a genotype fitness diminishes as it becomes more common, and vice versa. Variations in genotype- or clade-specific immunity-affected by the local prevalence of viral groups-combined with the periodic introduction of strains that have independently evolved in different regions, may have led to fluctuations in the population dynamics of major genotypes over time. These fluctuations were associated with ongoing evolution and variations in the capsid amino acid profile. These findings have profound implications for future control strategies. Although PCV2d remains the most prevalent and widespread genotype, other genotypes should not be neglected. Control strategies should thus target the entire PCV2 population, with a focus on fostering broader and more cross-protective immunity.