genotype distribution
Recently Published Documents





2022 ◽  
Vol 19 (1) ◽  
Awoke Derbie ◽  
Daniel Mekonnen ◽  
Endalkachew Nibret ◽  
Melanie Maier ◽  
Yimtubezinash Woldeamanuel ◽  

Abstract Background Cervical cancer is caused by infection with high-risk human papillomaviruses (HR-HPVs). It is one of the leading causes of cancer-related deaths in Ethiopia and globally. To develop efficient vaccination and HPV-based cervical cancer screening approaches, data on genotype distribution of HPVs is crucial. Hence, the study was aimed to review HPV genotype distribution in Ethiopia. Methods Research articles were systematically searched using comprehensive search strings from PubMed/Medline and SCOPUS. Besides, Google Scholar was searched manually for grey literature. The last search was conducted on 18 August 2021. The first two authors independently appraised the studies for scientific quality and extracted the data using Excel sheet. The pooled HPV genotype distribution was presented with descriptive statistics. Results We have included ten studies that were reported from different parts of the country during 2005 and 2019. These studies included 3633 women presented with different kinds of cervical abnormalities, from whom 29 different HPV genotypes with a sum of 1926 sequences were reported. The proportion of high-risk, possible/probable high-risk and low-risk HPVs were at 1493 (77.5%), 182 (9.4%) and 195 (10.1%), respectively. Of the reported genotypes, the top five were HPV 16 (37.3%; 95% CI 35.2.1–39.5%), HPV 52 (6.8%; 95% CI 5.8–8.0%), HPV 35 (4.8%; 95% CI 3.9–5.8%), HPV 18 (4.4%; 95% CI 3.5–5.3%) and HPV 56 (3.9%: 95% CI 3.1–4.9%). Some of other HR-HPV groups include HPV 31 (3.8%), HPV 45 (3.5%), HPV 58 (3.1%), HPV 59(2.3%), and HPV 68 (2.3%). Among the high-risk types, the combined prevalence of HPV 16/18 was at 53.7% (95% CI 51.2–56.3%). HPV 11 (2.7%: 95% CI 2.1–3.5%), HPV 42 (2.1%: 95% CI 1.5–2.8%) and HPV 6 (2.1%: 95% CI 1.4–2.7%) were the most common low-risk HPV types. Conclusions We noted that the proportion of HR-HPV types was higher and HPV 16 in particular, but also HPV 52, HPV 35 and HPV 18, warrant special attention in Ethiopian’s vaccination and HPV based cervical screening program. Additional data from other parts of the country where there is no previous HPV genotype report are needed to better map the national HPV genotypes distribution of Ethiopia.

2022 ◽  
Yunyun Fang ◽  
Jingjing Zhang ◽  
Linlin Ji ◽  
Chaoyu Zhu ◽  
Yuanyuan Xiao ◽  

Abstract Objective: To investigate the relationship between glucagon-like peptide-1 receptor (GLP1R) gene polymorphisms and susceptibility to early-onset type 2 diabetes (EOD).Methods: Samples from 316 type 2 diabetes (T2DM) patients with EOD (n = 137) and late-onset T2DM (n = 179) and 145 non-diabetic individuals were analyzed. Multiplex PCR combined with resequencing HI-Reseq technology was used to detect single nucleotide polymorphisms (SNPs) of the GLP1R gene, and the allele frequency, genotype distribution, and clinical parameters were analyzed between each diabetes subgroup and the control group.Results: Sixteen SNPs were identified in the exonic region of the GLP1R gene according to the minor allele frequency (MAF > 0.05) in the participants. Among these, the GLP1R rs3765467 (G→A) mutation was statistically associated with EOD. Compared with that of the GG carriers, carriers of genotype AA at rs3765467 had a decreased risk of EOD after adjusting for sex and body mass index. In the dominant model, the frequencies of the rs3765467 AA+GA genotype were significantly decreased in the EOD group, and carriers of genotype AA+GA at rs3765467 had a decreased risk of EOD after adjusting for sex and body mass index. Moreover, fasting c peptide levels were significantly higher in GA+AA genotype carriers than that in GG genotype carriers.Conclusion: The GLP1R rs3765467 polymorphism was significantly associated with the age at T2DM diagnosis, and thus may be used as a marker to screen and detect individuals at risk of developing EOD.The name of the clinical trials registry: Exploration of early warning indicators for diabetic chronic complications. The approval number is 2016-004.The approval date is June 12, 2016.

Narcisa Muresu ◽  
Giovanni Sotgiu ◽  
Silvia Marras ◽  
Davide Gentili ◽  
Illari Sechi ◽  

The assessment of human papillomavirus (HPV) genotype dynamics could support the adoption of more tailored preventive actions against cervical cancer. The aim of the study was to describe the prevalence of HPV infection, HPV genotype distribution, and the epidemiological characteristics of women with ASC-US cytology since the introduction of HPV-DNA testing in Sardinia (Italy), (March 2016–December 2020). Specimens were tested by RT-PCR for 14 high-risk HPV genotypes. A total of 1186 patients were enrolled, with a median (IQR) age of 41 (38–48) years. Of these women, 48.1% were positive for at least one HPV genotype; 311 (26.2%) women were vaccinated with a median (IQR) age of 38 (30/47) years. The percentage of prevalence of HPV-16, -31, -66, -56, and -51 was 36.3%, 18.7%, 11.9%, 11.4% and 10.7%, respectively. The highest prevalence of infection was found in women aged <41 years, and single women. Moreover, women aged >41 years (OR: 0.51, 95% CI: 0.31–0.86; p-value: 0.01), having parity (OR: 0.57, 95% CI: 0.34–0.96, p-value: 0.04), and higher educational level (OR: 0.39, 95% CI: 0.18–0.87; p-value: 0.02) were associated with a lower CIN2+ risk. We did not find a significant difference in terms of prevalence of HPV-16 infection between vaccinated and non-vaccinated (18.3% vs. 17.1%; p-value < 0.001). Our results support the adoption of nonavalent HPV-vaccine to prevent the most prevalent infections caused by HPV-16 and -31 genotypes and underscore the need of surveillance to implement tailored vaccination programs and preventive strategies.

PLoS ONE ◽  
2022 ◽  
Vol 17 (1) ◽  
pp. e0260897
Marissa J. M. Traets ◽  
Roel H. T. Nijhuis ◽  
Servaas A. Morré ◽  
Sander Ouburg ◽  
Jasper A. Remijn ◽  

Background Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can manifest with varying disease severity and mortality. Genetic predisposition influences the clinical course of infectious diseases. We investigated whether genetic polymorphisms in candidate genes ACE2, TIRAP, and factor X are associated with clinical outcomes in COVID-19. Methods We conducted a single-centre retrospective cohort study. All patients who visited the emergency department with SARS-CoV-2 infection proven by polymerase chain reaction were included. Single nucleotide polymorphisms in ACE2 (rs2285666), TIRAP (rs8177374) and factor X (rs3211783) were assessed. The outcomes were mortality, respiratory failure and venous thromboembolism. Respiratory failure was defined as the necessity of >5 litres/minute oxygen, high flow nasal oxygen suppletion or mechanical ventilation. Results Between March and April 2020, 116 patients (35% female, median age 65 [inter quartile range 55–75] years) were included and treated according to the then applicable guidelines. Sixteen patients (14%) died, 44 patients (38%) had respiratory failure of whom 23 required endotracheal intubation for mechanical ventilation, and 20 patients (17%) developed venous thromboembolism. The percentage of TIRAP polymorphism carriers in the survivor group was 28% as compared to 0% in the non-survivor group (p = 0.01, Bonferroni corrected p = 0.02). Genotype distribution of ACE2 and factor X did not differ between survivors and non-survivors. Conclusion This study shows that carriage of TIRAP polymorphism rs8177374 could be associated with a significantly lower mortality in COVID-19. This TIRAP polymorphism may be an important predictor in the outcome of COVID-19.

2022 ◽  
Vol 19 (1) ◽  
Xiangpeng Wang ◽  
Yuan Song ◽  
Xiaofei Wei ◽  
Guanyu Wang ◽  
Ruili Sun ◽  

Abstract Background Human papillomavirus (HPV) infection can cause cervical and other cancers, including vulva, vagina, penis, anus, or oropharynx. However, in China's northern Henan Province, data on the prevalence and genotype distribution of HPV among women attending gynecology clinics is limited. This study aimed to investigate the current prevalence and genotype distribution of HPV among women attending gynecology clinics in northern Henan Province. Methods This study included 15,616 women aged 16–81 years old who visited the Xinxiang central hospital's gynecology department between January 2018 and December 2019. HPV DNA was detected by a conventional PCR method followed by HPV type-specific hybridization, which was designed to detect 17 high-risk HPV (HR-HPV) genotypes and 20 low-risk HPV (LR-HPV) genotypes. HPV prevalence and corresponding 95% confidence intervals (95% CI) were calculated using SPSS 18.0. Results The overall HPV prevalence was 19.7% among women in northern Henan Province. Single, double, and multiple HPV infections accounted for 13.7%, 4.3%, and 1.8% of the total cases. Most infections were caused by HR-HPV (71.8%), and single genotype HPV infection (13.7%) was the most common pattern. The most common HR-HPV genotype was HPV16 (4.3%), followed by HPV52 (3.5%) and HPV58 (2.0%). The most common LR-HPV genotype was HPV6 (1.4%), followed by HPV61 (1.1%) and HPV81 (1.1%). Conclusions HPV infection is high among women attending gynecology clinics in northern Henan Province. The highest prevalence was found in women less than 20 years old. In northern Henan Province, the 9-valent HPV vaccine is strongly recommended for regular immunization.

2022 ◽  
Vol 25 (8) ◽  
pp. 847-854
M. V. Smolnikova ◽  
S. Yu. Tereshchenko

Lectins, being the main proteins of the lectin pathway activating the complement system, are encoded by polymorphic genes, wherein point mutations cause the protein conformation and expression to change, which turns out to have an effect on the functionality and ability to respond to the pathogen. In the current study, largescale data on the population genotype distribution of the genes for H-ficolin FCN3 rs28357092 and mannose-binding lectin-associated serine protease MASP2 rs72550870 among the indigenous peoples of the Russian Arctic regions (Nenets, Dolgans and Nganasans, a mixed population and Russians: a total sample was about 1000 newborns) have been obtained for the first time. Genotyping was carried out using RT-PCR. The frequency of the homozygous variant del/del FCN3 rs28357092 associated with the total absence of the most powerful activator of the lectin complement pathway, N-ficolin, was revealed; 0 % in the Nenets, 0.8 % in the Dolgans and Nganasans, and 3.5 % among the Russians ( p < 0.01). Analysis of the prevalence of the MASP2 genotypes has shown the predominance of the homozygous variant AA in all studied populations, which agrees with the available world data. The heterozygous genotype AG rs72550870 associated with a reduced level of protease was found to occur rarely in the Nenets, Dolgans and Nganasans compared to newborns of Caucasoid origin from Krasnoyarsk: 0.5 % versus 3.3 %, respectively. Moreover, among 323 examined Nenets, one AG carrier was identified, whereas in Russians, 16 out of 242 examined newborns were found to be AG carriers ( p < 0.001). A homozygous variant (GG) in total absence of protease with impaired binding of both MBL and ficolins was not detected in any of the 980 examined newborns. An additional analysis of infectious morbidity in Arctic populations allows one to find phenotypic characteristics related to a high functional activity of the lectin pathway of complement activation as an most important factor for the first-line of anti-infectious defense, including such new viral diseases as COVID-19.

2021 ◽  
Shirley A. Onyango ◽  
Kevin O. Ochwedo ◽  
Maxwell G. Machani ◽  
Collince J. Omondi ◽  
Isaiah Debrah ◽  

Abstract BackgroundEvolutionary pressures lead to the selection of efficient malaria vectors either resistant or susceptible to Plasmodiumparasites.These forcesmay elevate the introduction of new species genotypes that adapt to new breeding habitats which could have serious implications on malaria transmission.Thioester-containing protein 1 (TEP1) of Anopheles gambiaeplays an important role in innate immune defenses against parasites. This study aims to characterize the distribution pattern of TEP1 polymorphisms determining vector competence and subsequently malaria transmission in western Kenya. MethodsAnopheles gambiaeadult and larvae were collected using pyrethrum spray catches (PSC) and plastic dippers respectivelyfrom Homa Bay, Kakamega, Bungoma, and Kisumu countiesbetween 2017 and 2020.Collected adults and larvae reared to the adult stage were morphologically identified and then identified to sibling species by PCR.TEP1 alleles were determined using restriction fragment length polymorphisms-polymerase chain reaction (RFLP-PCR) and to validate the TEP1 genotyping results, a representative sample of alleles was sequenced.ResultsTwo TEP1 alleles (TEP1*S1 and TEP1*R2)and three corresponding genotypes (*S1/S1, *R2/S1, and *R2/R2)were identified. TEP1*S1 and TEP1*R2 with their corresponding genotypes, homozygous *S1/S1 and heterozygous *R2/S1 were widely distributed across all sites with allele frequencies of approximately 80% and 20%, respectively bothin An. gambiaeand An. arabiensis. There was no significant difference detected among the population and between the two mosquito species in TEP1 allele frequency and genotype frequency. The overall low levels in population structure (FST= 0.019) across all sites corresponded to an effective migration index (Nm= 12.571) and lowNei’s genetic distance values (<0.500) among the subpopulation.The comparative fixation index values revealed minimal genetic differentiation between speciesand high levels of gene flow among populations.ConclusionThere is a low genetic diversity and population structure in western Kenya. TEP1* R2 and TEP1*S1 were the most common alleles in both species which may have been maintained through generations in time, However, the TEP1*R2 allele was in low frequencies and may be used to estimatemalaria prevalence. Continued surveillance of the distribution of TEP1 is essential for monitoring the population dynamics of local vectors and their implications on malaria transmission and hence designing targeted vector interventions.

Mireia Valles-Colomer ◽  
Rodrigo Bacigalupe ◽  
Sara Vieira-Silva ◽  
Shinya Suzuki ◽  
Youssef Darzi ◽  

AbstractAlthough the composition and functional potential of the human gut microbiota evolve over the lifespan, kinship has been identified as a key covariate of microbial community diversification. However, to date, sharing of microbiota features within families has mostly been assessed between parents and their direct offspring. Here we investigate the potential transmission and persistence of familial microbiome patterns and microbial genotypes in a family cohort (n = 102) spanning 3 to 5 generations over the same female bloodline. We observe microbiome community composition associated with kinship, with seven low abundant genera displaying familial distribution patterns. While kinship and current cohabitation emerge as closely entangled variables, our explorative analyses of microbial genotype distribution and transmission estimates point at the latter as a key covariate of strain dissemination. Highest potential transmission rates are estimated between sisters and mother–daughter pairs, decreasing with increasing daughter’s age and being higher among cohabiting pairs than those living apart. Although rare, we detect potential transmission events spanning three and four generations, primarily involving species of the genera Alistipes and Bacteroides. Overall, while our analyses confirm the existence of family-bound microbiome community profiles, transmission or co-acquisition of bacterial strains appears to be strongly linked to cohabitation.

2021 ◽  
Marzieh Rahbaran ◽  
Maryam Hassani Doabsari ◽  
Farshad Sharifi ◽  
Mahdi Afshari ◽  
Mandana Hasanzad

Abstract Background: Prostate cancer (PC) is one of the most common cancers among men. Genetic predisposition is emerging as a risk factor for PC development. The Androgen receptor (AR) gene is associated with the development and prognosis of PC. Understanding the AR mutations is very important in the precision treatment of PC-resistant patients to androgen deprivation therapy. In this study, we investigate any association between common AR mutations with the risk of PC.Methods and results: In this case-control study, blood samples were collected from 121 radical prostatectomy (RP) patients who were pathologically diagnosed with PC and 120 benign prostate hyperplasia (BPH) subjects as a control group. The targeted area of the AR gene was amplified by PCR and confirmed by the Sanger sequencing method. The target area of the AR gene screened for 124 alterations in intron 7, 44 mutations in exon 8, and 52 variants in the 3'UTR region. rs113528927 DelIns AC>ACACACCAC had the most frequent mutant alleles between case and control groups, but this genotype distribution among the two recruited groups was not significant. Only one mutation, c.2644C>A, was observed in exon 8 in BPH subjects, and six alterations were detected in 3'UTR.Conclusions: For the first time in the Iranian population, AR common mutations were screened in PC patients, and our results indicate no relationship with the risk of PC, which means that other potential molecular risk factors may be engaged for PC in our population.

Mathematics ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 96
Nicholas Bessonov ◽  
Gennady Bocharov ◽  
Vitaly Volpert

The paper is devoted to a nonlocal reaction-diffusion equation describing the development of viral infection in tissue, taking into account virus distribution in the space of genotypes, the antiviral immune response, and natural genotype-dependent virus death. It is shown that infection propagates as a reaction-diffusion wave. In some particular cases, the 2D problem can be reduced to a 1D problem by separation of variables, allowing for proof of wave existence and stability. In general, this reduction provides an approximation of the 2D problem by a 1D problem. The analysis of the reduced problem allows us to determine how viral load and virulence depend on genotype distribution, the strength of the immune response, and the level of immunity.

Sign in / Sign up

Export Citation Format

Share Document