Mixed Genotype Research Articles

Burden and Associated Genotype Patterns of High-Risk Human Papilloma Virus Infection and Cervical Cytology Abnormalities among Women in Central India.

Background The epidemiology of human papilloma virus (HPV) infection and the pattern of HPV genotype distribution are much-needed parameters to assess the risk of cervical cancer among females. However, due to less availability of data on HPV burden and its genotypes from various geographical regions in India makes cervical cancer screening modalities and vaccination strategies difficult to implement. Objective The present study was conducted to identify the various genotypes particularly high-risk HPV types in premalignant or malignant cervical lesions. Methods The study was a hospital-based cross-sectional study wherein 295 symptomatic women were screened by Pap smear and multiplex real-time PCR was performed for HPV genotypes identification in women with abnormal cervical cytology. Results Out of 295 women, 237 (80.3%), 45 (15.3%), and 13 (4.4%) women had normal Pap smear, squamous cell carcinoma and precancerous cytology, respectively. Among these 58 women having abnormal cervical cytology, HPV was detected in 48 (81.0%) participants. Most common HPV genotypes in our study were HPV 16 (n = 29; 60.4%) followed by mixed infections; i.e., more than one type of HPV was detected (n = 10, 20.8%). HPV 18 was detected only in 6.25%, whereas other high-risk HPV genotypes were found to be 12.5%. Conclusion HPV positivity was >80% in women having abnormal Pap smear. The prevalence of HPV 18 was found to be much less in Central India, compared to other parts of country. HPV 16 was the most common genotype followed by mixed HPV genotype infections. It is evident from our study that symptomatic women even if having normal Pap smear should be screened for HPV and followed up with periodic Pap smears for detecting any change in cervical cytology, thus preventing cervical cancer in women.

Kidney Transplantation From Hepatitis-C Viraemic Donors:Considerations for Practice in the United Kingdom.

Background: Donor hepatitis-C (HCV) infection has historically represented a barrier to kidney transplantation (KT). However, direct-acting antiviral (DAA) medications have revolutionised treatment of chronic HCV infection. Recent American studies have demonstrated that DAA regimes can be used safely peri-operatively in KT to mitigate HCV transmission risk. Methods: To formulate this narrative review, a comprehensive literature search was performed to analyse results of existing clinical trials examining KT from HCV-positive donors to HCV-negative recipients with peri-operative DAA regimes. Results: 13 studies were reviewed (11 single centre, four retrospective). Outcomes for 315 recipients were available across these studies. A sustained virological response at 12 weeks (SVR12) of 100% was achieved in 11 studies. One study employed an ultra-short DAA regime and achieved an SVR12 of 98%, while another achieved SVR12 of 96% due to treatment of a missed mixed genotype. Conclusion: HCV+ KT is safe and may allow increased utilisation of organs for transplantation from HCV+ donors, who often have other favourable characteristics for successful donation. Findings from US clinical trials can be applied to the United Kingdom transplant framework to improve organ utilisation as suggested by the NHSBT vision strategy “Organ Donation and Transplantation 2030: meeting the need”.

Distribution of HCV genotypes and HCV RNA viral load in hepatitis infected patients of Kolar region, Karnataka, India.

Decisions and disease progression prediction, understanding the distribution of the hepatitis C virus (HCV) genotype and its association with viral load is significant for treatment. Therefore, it is of interest to document the distribution pattern of HCV genotypes and their association with viral load among HCV infected patients in Kolar, Karnataka. Seventy-four HCV-positive patients and not on antiviral therapy were enrolled from R.L. Jalappa hospital in Kolar, Karnataka. Blood samples were taken and demographics were recorded. HCV RNA was isolated after plasma was separated. qPCR was performed to measure the viral load, and RT-PCR was performed to determine the genotype. Genotype 3 was the prevalent (n=11, 40.7%) followed by genotype 4 (n=8, 29.6%), 2 (n=6, 22.2%), 1 (n= 13.7%), and mix (n=1, 13.7%). The median viral load of genotype 3 was a 2,87,835 IU/mL (IQR 10, 780-3, 71, 66) , genotype 2 was 81,030 IU/mL (IQR 66,495-95,565), genotype 4 was 43, 410 IU/mL (IQR 38, 355-48, 465) belongs to viral load less than 8,00,000 IU/mL. The median viral load genotype 3 was a 1, 05, 19, 500 IU/mL (IQR 49, 37, 250-2, 36, 71, 500), genotype 2 was 2,55,99,000 IU/mL (IQR 2,00,10,000-32,725,500), genotype 4 was 1,67,40,000 IU/mL (IQR 1,45,50,000-17,493,000) belonging to viral load more than 8,00,000 IU/mL category. A correlation between genotype and viral load was observed (p =1.5x10-12), of which genotype 3 showed a high viral load. Thus, HCV genotypes 1 2, 3, 4, and mixed genotype was observed in the patients studied. HCV genotype was associated with viral load in patient plasma. This data finds use in the treatment and prevention of hepatitis C in Kolar, Karnataka.

Pan-Genotypic Direct-Acting Antiviral Agents for Undetermined or Mixed-Genotype Hepatitis C Infection: A Real-World Multi-Center Effectiveness Analysis.

Although the pan-genotypic direct-acting antiviral regimen was approved for treating chronic hepatitis C infection regardless of the hepatitis C virus (HCV) genotype, real-world data on its effectiveness against mixed-genotype or genotype-undetermined HCV infection are scarce. We evaluated the real-world safety and efficacy of two pan-genotypic regimens (Glecaprevir/Pibrentasvir and Sofosbuvir/Velpatasvir) for HCV-infected patients with mixed or undetermined HCV genotypes from the five hospitals in the Changhua Christian Care System that commenced treatment between August 2018 and December 2020. This retrospective study evaluated the efficacy and safety of pan-genotypic direct-acting antiviral (DAA) treatment in adults with HCV infection. The primary endpoint was the sustained virological response (SVR) observed 12 weeks after completing the treatment. Altogether, 2446 HCV-infected patients received the pan-genotypic DAA regimen, 37 (1.5%) patients had mixed-genotype HCV infections and 110 (4.5%) patients had undetermined HCV genotypes. The mean age was 63 years and 55.8% of our participants were males. Nine (6.1%) patients had end-stage renal disease and three (2%) had co-existing hepatomas. We lost one patient to follow-up during treatment and one more patient after treatment. A total of four patients died. However, none of these losses were due to treatment-related side effects. The rates of SVR12 for mixed-genotype and genotype-undetermined infections were 97.1% and 96.2%, respectively, by per-protocol analyses, and 91.9% and 92.7% respectively, by intention-to-treat population analyses. Laboratory adverse events with grades ≥3 included anemia (2.5%), thrombocytopenia (2.5%), and jaundice (0.7%). Pan-genotypic DAAs are effective and well-tolerated for mixed-genotype or genotype-undetermined HCV infection real-world settings.

Screening for phenotypic outliers identifies an unusually low concentration of a \u03b2-lactoglobulin B protein isoform in bovine milk caused by a synonymous SNP

BackgroundMilk samples from 10,641 dairy cattle were screened by a mass spectrometry method for extreme concentrations of the A or B isoforms of the whey protein, β-lactoglobulin (BLG), to identify causative genetic variation driving changes in BLG concentration.ResultsA cohort of cows, from a single sire family, was identified that produced milk containing a low concentration of the BLG B protein isoform. A genome-wide association study (GWAS) of BLG B protein isoform concentration in milk from AB heterozygous cows, detected a group of highly significant single nucleotide polymorphisms (SNPs) within or close to the BLG gene. Among these was a synonymous G/A variation at position + 78 bp in exon 1 of the BLG gene (chr11:103256256G > A). The effect of the A allele of this SNP (which we named B’) on BLG expression was evaluated in a luciferase reporter assay in transfected CHO-K1 and MCF-7 cells. In both cell types, the presence of the B’ allele in a plasmid containing the bovine BLG gene from -922 to + 898 bp (relative to the transcription initiation site) resulted in a 60% relative reduction in mRNA expression, compared to the plasmid containing the wild-type B sequence allele. Examination of a mammary RNAseq dataset (n = 391) identified 14 heterozygous carriers of the B’ allele which were homozygous for the BLG B protein isoform (BB’). The level of expression of the BLG B’ allele was 41.9 ± 1.0% of that of the wild-type BLG B allele. Milk samples from three cows, homozygous for the A allele at chr11:103,256,256 (B’B’), were analysed (HPLC) and showed BLG concentrations of 1.04, 1.26 and 1.83 g/L relative to a mean of 4.84 g/L in milk from 16 herd contemporaries of mixed (A and B) BLG genotypes. The mechanism by which B’ downregulates milk BLG concentration remains to be determined.ConclusionsHigh-throughput screening and identification of outliers, enabled the discovery of a synonymous G > A mutation in exon 1 of the B allele of the BLG gene (B’), which reduced the milk concentration of β-lactoglobulin B protein isoform, by more than 50%. Milk from cows carrying the B’ allele is expected to have improved processing characteristics, particularly for cheese-making.

Development of rapid in vitro colorimetric enzymatic activity assay to differentiate macrocyclic lactone susceptible and resistant Dirofilaria immitis isolates

The filarial parasite Dirofilaria immitis causes dirofilariosis, a potentially fatal pulmonary condition in canids and felines. Dirofilariosis can be prevented by treatment with a prophylactic macrocyclic lactone (ML) regimen. Unfortunately, ML-resistant D. immitis isolates, genetically distinct from the wildtype population, have been confirmed via molecular markers. DNA-based tests for ML-resistance are costly and time-consuming. There lacks a simple and reliable in vitro biological test to differentiate D. immitis infections resulting from inadequate adherence to recommended prophylaxis regimens from those caused by truly resistant D. immitis isolates. The goal of the current study was to develop a minimally invasive rapid diagnostic in vitro biological assay to differentiate ML-susceptible from ML-resistant D. immitis isolates. The in vitro assay was developed based on the concept that MLs act on the microfilariae (mf) by paralyzing the excretory pore muscle, inhibiting the release of molecules, including enzymes, that regulate host immunity. The basis of the in vitro diagnostic assay is to assess the effects of ivermectin (IVM) exposure on the secretion of enzymes by the D. immitis mf at a concentration that distinguishes the ML-susceptible from ML-resistant isolates. The metabolic enzyme, triosephosphate isomerase (TPI), was chosen due to high abundance in the D. immitis secretome. In this study, the in vitro TPI enzymatic assay was optimized and tested in eight laboratory-maintained isolates. The ML-susceptible Missouri, Berkeley, and Georgia II isolate; the putative ML-susceptible Georgia III, and Big Head; and the ML-resistant JYD-34, Metairie, and WildCat. We observed mixed results, Missouri and Berkeley had statistically significant decreases in TPI activity following 24-hour in vitro IVM exposure. The three resistant isolates, JYD-34, Metairie, and WildCat showed no change in TPI activity following IVM exposure. The susceptible, or putative susceptible Georgia II, Georgia III, and Big Head isolates had a phenotypic response consistent with ML-resistance based on the in vitro assay. However, increasing genotypic evidence has presented a mixed genotype for the three isolates, indicating they may be partially selected for ML-resistance. The measurement of changes in enzymatic activity and the in vitro TPI enzymatic activity assay consequently does not appear to be a reliable detection method for ML-resistance but may be useful for identifying fully susceptible isolates.

Whole genome analysis of rotavirus strains circulating in Benin before vaccine introduction, 2016–2018

Species A rotaviruses (RVA) still play a major role in causing acute diarrhea in children under five years old worldwide. Currently, an 11-gene classification system is used to designate the full genotypic constellations of circulating strains. Viral proteins and non-structural proteins in the order VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 are represented by the genotypes Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx, respectively. In Benin, ROTAVAC® vaccine was introduced into the Expanded Programme on Immunization in December 2019. To monitor circulating RVA strains for changes that may affect vaccine performance, in-depth analysis of strains prior to vaccine introduction are needed. Here we report, the whole-gene characterization (11 ORFs) for 72 randomly selected RVA strains of common and unusual genotypes collected in Benin from the 2016 to 2018 seasons. The sequenced strains were 15 G1P[8], 20 G2P[4], 5 G9P[8], 14 G12P[8], 9 G3P[6], 2 G1P[6], 3 G2P[6], 2 G9P[4], 1 G12P[6], and 1 G1G9P[8]/P[4]. The study strains exhibited two genetic constellations designed as Wa-like G1/G9/G12-P[6]/P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1 and DS-1-like G2/G3/G12-P[4]/P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Genotype G9P[4] strains possessed a DS-1-like genetic constellation with an E6 NSP4 gene, G9-P[4]-I2-R2-C2-M2-A2-N2-T2-E6-H2. The mixed genotype showed both Wa-like and DS-1-like profiles with a T6 NSP3 gene G1/G9P[8]/[4]-I1/I2-R1/R2-C1/C2-M1/M2-A1/A2-N1/N2-T1/T6-E1/E6-H1/H2. At the allelic level, the analysis of the Benin strains, reference strains (with known alleles), vaccine strains (with known alleles) identified 2–13 and 1–17 alleles for DS-1-like and Wa-like strains, respectively. Most of the study strains clustered into previously defined alleles, but we defined 3 new alleles for the VP7 (G3 = 1 new allele and G12 = 2 new alleles) and VP4 (P[4] = 1 new allele and P[6] = 2 new alleles) genes which formed the basis of the VP7 and VP4 gene clusters, respectively. For the remaining 9 genes, 0-6 new alleles were identified for both Wa-like and DS-1-like strains. This analysis of whole genome sequences of RVA strains circulating in Benin described genetic point mutations and reassortment events as well as novel alleles. Further detailed studies on these new alleles are needed and these data can also provide a baseline for studies on RVA in the post-vaccination period.

Pattern and Prevalence of Hepatitis B virus genotypes in Among Discordant Partners Enugu, Southeastern Nigeria

Hepatitis B virus (HBV) continues to cause significant global health problems despite the presence of a potential vaccine and other clinical approaches. This study was designed to investigate the pattern and spread of HBV genotypes among discordant and concordant partners of hepatitis B virus infection in Enugu State, Nigeria. The study involved a cross-sectional study consisting of 150 subjects (120 discordant and concordant partners of hepatitis B, and 30 controls). HBsAg was screened using a rapid ELISA diagnostic strip and re-screened to reaffirm the result using Ichroma Fluorescence Immunoassay (FIA) analyser. Multiplex nested polymerase chain reaction using type specific primers was used to identify the HBV genotypes. Statistical analysis was performed using Graph Pad Prism. HBV genotype E (75%), A (10%) and a mixed genotype of A and E (mixed infection (15%) were gotten with genotype E being the most predominant. This study has established the high prevalence of genotype E as the most predominant HBV genotype in circulation in Enugu, southeastern Nigeria.

Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories.

SummaryDevelopmental progression and cellular diversity are largely driven by transcription factors (TFs); yet, characterizing their loss-of-function phenotypes remains challenging and often disconnected from their underlying molecular mechanisms. Here, we combine single-cell regulatory genomics with loss-of-function mutants to jointly assess both cellular and molecular phenotypes. Performing sci-ATAC-seq at eight overlapping time points during Drosophila mesoderm development could reconstruct the developmental trajectories of all major muscle types and reveal the TFs and enhancers involved. To systematically assess mutant phenotypes, we developed a single-nucleus genotyping strategy to process embryo pools of mixed genotypes. Applying this to four TF mutants could identify and quantify their characterized phenotypes de novo and discover new ones, while simultaneously revealing their regulatory input and mode of action. Our approach is a general framework to dissect the functional input of TFs in a systematic, unbiased manner, identifying both cellular and molecular phenotypes at a scale and resolution that has not been feasible before.

First report of Flavescence dorée phytoplasma identification and characterization in three species of leafhoppers

Phytoplasma strains were sporadically found in specimens of Hishimonus hamatus, Japananus hyalinus and Graphocephala fennahi caught during an entomological survey conducted in Southern Switzerland on the edges and woods surrounding cultivated vineyards in 2017. The subsequent molecular characterization of the pathogens allowed to identify them as strains strictly associated to Flavescence dorée, a serious European grapevine disease, transmitted from vine to vine by the leafhopper Scaphoideus titanus. In particular, M12 and M50 genotypes were found in H. hamatus and J. hyalinus, respectively, while G. fennahi harboured mixed phytoplasma genotypes with at least two different Flavescence dorée isolates. The potential importance of these findings in the frame of the Flavescence dorée epidemics in Europe is discussed.

The impact of genetic variations in sofosbuvir metabolizing enzymes and innate immunity mediators on treatment outcome in HCV-infected patients

Hepatitis C virus (HCV) is the leading cause of liver diseases worldwide. At present, combinations of different classes of direct-acting antiviral agents (DAAs) are used as treatment options for HCV, in which sofosbuvir (SOF) is the common DAA among different therapeutic regimes. In Egypt, SOF plus daclatasvir (DCV) is the widely used anti-HCV treatment protocol. Herein, we aimed to assess the association between 3 single-nucleotide polymorphisms (SNPs) at the genes coding for 2 SOF metabolizing enzymes: histidine triad nucleotide-binding protein 1 (HINT1) rs4696/rs7728773 and nucleoside diphosphate kinase 1 (NME1) rs3760468, together with the most potent anti-HCV innate molecule, i.e., interferon lambda 3 (IFNL3) rs12979860 and the response to SOF/DCV in Egyptian patients chronically infected with genotype 4 (GT4). SNPs were genotyped using real-time PCR in DNA from patients who achieved sustained virological response (SVR) at 12 weeks post-SOF/DCV treatment (i.e., responders; n = 188), patients who failed to achieve SVR12 (i.e., non-responders; n = 109), and healthy controls (n = 62). Our results demonstrated that patients bearing HINT1 rs7728773 CT/TT (odds ratio 2.119, 95% CI 1.263–3.559, p = 0.005) and IFNL3 rs12979860 CC (odds ratio 3.995, 95% CI 2.126–7.740, p = 0.0001) were more likely to achieve SVR12. However, neither HINT1 rs4696 nor NME1 rs3760468 seems to contribute to the responsiveness to SOF/DCV. Binary regression analysis defined 5 predictor factors independently associated with SVR12: age, bilirubin, hemoglobin, early stages of fibrosis, and combined HINT1 rs7728773 and IFNL3 rs12979860 favorable and mixed genotypes (odds ratio 3.134, 95% CI 1.518–6.47, p = 0.002), and that was confirmed by the combined ROC curve for the 5 predictor factors (AUC = 0.91, 95% CI 0.869–0.95, P = 0.0001). In conclusion, these data suggest that the two SNPs have the potential in predicting the response rate to SOF/DCV treatment in patients infected with HCV GT4. This study is the first to investigate the pharmacogenetics of SOF metabolizing enzyme and introduce HINT1 rs7728773 as a novel SNP that predicts the treatment efficacy.

Relationship of Genetic Polymorphism For CYP19 Gen of Exon 3 With Quantity and Milk Composition in Domestic Female Goats

This study was carried out to investigate the effect of the genetic polymorphism of the third exon for CYP19 gene on the quantity and composition of milk in local female goats. Blood samples were collected from female goats in the fields of some breeder in Babil Governorate/Al-Qasim City. Milk composition were examined in the Public Health Laboratory at Al-Qasim Green University/College of Veterinary Medicine, the genetic bundle of the third axon of the CYP19 gene was isolated, which was 140 bp in size, and its genotyping was determined according to the different nucleotide sequences and their association with the quantity and milk composition in the samples which tested in the Bayolat Laboratory in Al-Diwaniyah Governorate. The proportions of the distribution of the genotypes of the CYP19 gene in a sample of local female goats TT, GG and TG were 33.34%, 26.66 and 40%, respectively. The results showed prevalence of the TG genotype for CYP19 gene in the Iraqi local goats on the pure genotypes TT and GG, which was a highly significant superior (P<0.01) in the percentages of fat, protein, lactose and CFPP, as well as the significant superiority of the mixed genotype significantly on the pure genotype in the percentages of solid non-fat and density. It could be concluded from the current study that the selection of females with TG genotype as source for future generations to obtain a generation selected for the desired traits.

Genotyping of Toxoplasma gondii Strains from Goats in Jahrom District, Southern Iran.

Toxoplasma gondii is transmitted congenitally or acquired by consumption of food and water contaminated with cysts or oocysts. This study aimed at genotyping T. gondii strains from slaughtered goats in Jahrom. A total of 561 specimens (heart, diaphragm, and tongue) from 187 slaughtered goats were collected from Jahrom slaughterhouse. After DNA extraction, the T. gondii strains were genotyped by the nested PCR-RFLP based on GRA6 and 3', and 5' ends of the SAG2 gene. T. gondii infection was present in 18.2% of cases. Among the examined organs, the diaphragm was more disposed to the infection (10.2%). Furthermore, infection rates of the heart and tongue were 8.6% and 3.7%, respectively. Concurrent infection in the heart and diaphragm, tongue and diaphragm, and heart and tongue were 3.2%, 0.5%, and 0.5%, respectively. In genotyping experiments, genotype I was the most frequent genotype of T. gondii (58.8%), followed by type II (23.5%), type III (11.8%), and a combination of type I and II (5.9%). The results of this study showed the presence of different genotypes of T. gondii in goats including three major and mixed genotypes. These results can be useful in toxoplasmosis control and prevention.

S3639 Two’s a Crowd: Case Report of Hepatitis C Genotype Mixed Pattern

Introduction: We present a clinical case of an unusual laboratory abnormality, mixed pattern Hepatitis C genotype. The incidence of “mixed genotype HCV infections has been assessed across numerous geographical regions with estimates between 1.2% and 25.3% reported” (McNaughton et al, 2017, p. 524). This case highlights the importance of accurate identification of HCV genotype, subtype,and resistance-associated substitutions. Case Description/Methods: A 30-year-old male presented with a chief complaint of postprandial nausea/vomiting occurring daily for 3 weeks as well as episodes of heartburn and unintentional weight loss. He had a past history of substance abuse: intranasal and IV drug use of both heroin and cocaine. He tested positive for hepatitis C. There was remote use of alcohol (Cessation of use > 1 year),as well as a history of bipolar/depression, suicidal ideations, and self-mutilation. On physical examination BMI was 30.6. There were multiple body piercings. The liver was not palpable. Laboratory: Hepatitis C genotype-1B/3(method used: RT-PCR and reverse hybridization of the 5' UTR and core region of the HCV genome performed by Quest Diagnostics).Viral load-199,000 , Alk. Phos-86, AST-75, ALT-186, Tbil-0.5, PLT-238,000. Negative for HIV. Urine toxicology-positive for benzodiazepine& cocaine. Ultrasound elastography revealed F1 fibrosis. He was lost to care due to incarceration. Discussion: This case report highlights the unusual existence of mixed HCV genotype and the importance of accurate determination of viral genotypes and subtypes for determination of treatment with DAA. In this situation there tends to be a major and a minor genotype presumably because one is more replicatively fit. This may make selection of the appropriate DAA difficult and may explain some treatment failures.

Decreased Susceptibility to Dihydrofolate Reductase Inhibitors Associated With Genetic Polymorphisms in Ugandan Plasmodium falciparum Isolates.

The Plasmodium falciparum dihydrofolate reductase (PfDHFR) inhibitors pyrimethamine and cycloguanil (the active metabolite of proguanil) have important roles in malaria chemoprevention, but drug resistance challenges their efficacies. A new compound, P218, was designed to overcome resistance, but drug-susceptibility data for P falciparum field isolates are limited. We studied ex vivo PfDHFR inhibitor susceptibilities of 559 isolates from Tororo and Busia districts, Uganda, from 2016 to 2020, sequenced 383 isolates, and assessed associations between genotypes and drug-susceptibility phenotypes. Median half-maximal inhibitory concentrations (IC50s) were 42 100 nM for pyrimethamine, 1200 nM for cycloguanil, 13000 nM for proguanil, and 0.6 nM for P218. Among sequenced isolates, 3 PfDHFR mutations, 51I (100%), 59R (93.7%), and 108N (100%), were very common, as previously seen in Uganda, and another mutation, 164L (12.8%), had moderate prevalence. Increasing numbers of mutations were associated with decreasing susceptibility to pyrimethamine, cycloguanil, and P218, but not proguanil, which does not act directly against PfDHFR. Differences in P218 susceptibilities were modest, with median IC50s of 1.4 nM for parasites with mixed genotype at position 164 and 5.7 nM for pure quadruple mutant (51I/59R/108N/164L) parasites. Resistance-mediating PfDHFR mutations were common in Ugandan isolates, but P218 retained excellent activity against mutant parasites.

Gender-Specific Frequency Distribution of Hepatitis C Virus Genotypes in Punjab province, Pakistan: A Clinically Significant Descriptive Cross-Sectional Study.

Background: Hepatitis C virus (HCV) is the major cause of liver cirrhosis, chronic liver disease, and hepatocellular carcinoma. More than 10 million individuals are living with HCV infection in Pakistan. Due to unawareness, very little information is known about HCV genotype occurrence in Punjab, the largest province of Pakistan. Identification of HCV genotype is very important for HCV treatment because different genotypes of HCV respond differently to antiviral therapy.Objective: The purpose of this research was to determine the distribution frequency of different HCV genotypes in the Punjab province and to demonstrate the distribution pattern of HCV genotypes in different age groups and sexes.Materials and Methods: In this study, we performed HCV genotyping of 3692 samples collected from different sites of the Punjab province, Pakistan. Among 3692 samples, 1755 (47.5%) were males and 1937 (52.4%) were females.Results: A total of 3692 samples were subjected to HCV genotyping and 2977 (81%) patients were genotyped successfully, whereas 715 (19%) patients were found to be HCV not detected. Our study demonstrated that among typeable genotypes, 3a constituted 2582 (69.9%) patients followed by 1a (n = 280) 7.5%, 1b (n = 64) 1.7%, 2a (n = 6) 0.16%, genotype 4 (n = 10) 0.27%, 3+4 (n = 2) 0.56%, 1a+2a (n = 11) 0.29%, 1b+2a (n = 1) 0.02%, 1a+1b (n = 1) 0.02%, and 1a+1b+3 (n = 1) 0.02% patients. HCV genotype distribution was evaluated gender wise and in different age groups like 0-12, 13-18, 19-59, and >60 years. All the HCV genotypes were equally distributed among men and women. The most affected age group was 19-59 years as compared to other age groups.Conclusion: The most frequently distributed HCV genotype in Punjab was found to be genotype 3a followed by genotype 1a, and only 0.94% of infected patients had a mixed genotype infection. Genotype 1a was found to be increasing significantly in the studied population. With these results, it can be assumed that genotype 3a may be replaced by genotype 1a with the passage of time. If this happens, this situation will be challenging in terms of antiviral therapy.

Frequency Distribution of Hepatitis C Virus Genotypes with Reference to Age and Sex in Various Districts of Khyber Pakhtunkhwa, Pakistan

Background: Pakistan has the second highest prevalence of hepatitis C in the world after Egypt. Viral hepatitis is a leading cause of morbidity and mortality in Pakistan and, worryingly, reinfection rates are also on the rise. This cross-sectional study was aimed at finding the most common genotypes of hepatitis C in terms of age and sex in a Pakistani cohort. Materials and methods: The authors collected blood samples from 1,260 patients with diagnosed hepatitis C visiting a primary teaching hospital affiliated with Peshawar Medical College, Pakistan, from different districts of Khyber Pakhtunkhwa, Pakistan, between January 2017 and April 2019. Hepatitis C virus RNA was quantified by real-time polymerase chain reaction and genotyping was then performed. Results: The authors found that genotype 3a was the most prevalent type followed by 1a, mixed, and 3b, respectively. Genotypes 2a and 1b were the least prevalent in Khyber Pakhtunkhwa. The most common genotype was 3a, observed in 75.87% of cases. The most common mixed genotype was 3a+1a, observed in 39 cases (3.10%); it had a prevalence of 3.49% in females compared with 2.70% in males. Overall, the most common age group affected by hepatitis C virus was 41–50 years (31.35%), followed by the 51–60 years group (24.45%). Infection rate was comparatively low in other age groups. A significant difference was observed in the prevalence of genotype 3a and 2a among different districts. Conclusion: The authors concluded that genotype 3a was the most prevalent genotype and it was observed more frequently in the female population, with a median age of 45 years.

PREVALENCE OF DIFFERENT HEPATITIS B VIRUS GENOTYPES AND RISK FACTORS ASSOCIATED AMONG SELECTED YEMENI PATIENTS WITH CHRONIC HEPATITIS B INFECTION

Background and aims: Hepatitis B virus infection is a significant public health crisis global. Hepatitis B virus genotyping is an important tool in epidemiological studies to determine the category and extent of treatment and to predict the outcome of chronic infections, for instance hepatocellular carcinoma and cirrhosis. The study designed to determine the prevalence of hepatitis B virus genotypes among Yemeni patients with chronic hepatitis B (CHB) and to evaluate some of the associated risk factors. Methods: Fifty patients (38 males, 12 females) with chronic hepatitis B from Al-Thawra Modern General Hospital, Al-Kuwait University Hospital, and AL-Gomhoria Hospital were included. HBV DNA was first detected by conventional PCR then HBV genotypes were determined using nested and multiplex PCR. Results: Mixed HBV genotypes (A+B+C+D+E), (A+B+C+D+E+F), and (A+B+C+D) were found to be the most prevalent (60 %), it is followed by genotype D (16 %), genotype B (16%) and genotype A (8%), whereas C, E, and F genotype were not found individually among the study population. Blood transfusion was associated with mixed infection (χ2=13.06; p= 0.005). Conclusions: In assumption, this study demonstrates the general prevalence of hepatitis B virus genotypes among HBV-infected Yemeni hepatitis B patients who request medical consideration in a hospital. In mono-genotype HBV infection, genotype B and D were the most prevalent genotypes. In HBV mixed genotype infection, the A/B/C/D/E genotype was the most prevalent in the study area. In the future, based on genotype, clinical trials and treatment regimens must be individually assumed to efficiently manage chronic HBV infection. To this end, a prospective nationwide population study of HBV genotype spreading and clinical outcomes is suggested. Peer Review History: Received: 15 May 2021; Revised: 11 June; Accepted: 27 June, Available online: 15 July 2021 Academic Editor: Ahmad Najib, Universitas Muslim Indonesia, Makassar, Indonesia, ahmad.najib@umi.ac.id UJPR follows the most transparent and toughest ‘Advanced OPEN peer review’ system. The identity of the authors and, reviewers will be known to each other. This transparent process will help to eradicate any possible malicious/purposeful interference by any person (publishing staff, reviewer, editor, author, etc) during peer review. As a result of this unique system, all reviewers will get their due recognition and respect, once their names are published in the papers. We expect that, by publishing peer review reports with published papers, will be helpful to many authors for drafting their article according to the specifications. Auhors will remove any error of their article and they will improve their article(s) according to the previous reports displayed with published article(s). The main purpose of it is ‘to improve the quality of a candidate manuscript’. Our reviewers check the ‘strength and weakness of a manuscript honestly’. There will increase in the perfection, and transparency. Received file: Reviewer's Comments: Average Peer review marks at initial stage: 6.5/10 Average Peer review marks at publication stage: 7.5/10 Reviewer(s) detail: Dr. Salfarina Ramli, Department of Pharmacology and Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Teknologi MARA, 42300 Puncak Alam, Selangor, Malaysia. salfarina2892@uitm.edu.my Dr. Asia Selman Abdullah, University of Basrah, Iraq, asia_abdullah65@yahoo.com Similar Articles: EXPLOSION OF HEPATITIS B AND C VIRUSES AMONG HEMODIALYSIS PATIENTS AS A RESULT OF HEMODIALYSIS CRISIS IN YEMEN PREVALENCE AND GENOTYPING OF HEPATITIS C VIRUS IN HEMODIALYSIS PATIENTS AND EVALUATION OF HCV-CORE ANTIGEN TEST IN SCREENING PATIENTS FOR DIALYSIS IN SANA'A CITY, YEMEN PREVALENCE OF HBV AND HCV; AND THEIR ASSOCIATED RISK FACTORS AMONG PUBLIC HEALTH CENTER CLEANERS AT SELECTED PUBLIC HEALTH CENTERS IN SANA'A CITY-YEMEN

Occurrence of Giardia duodenalis in selected stations and tributary rivers of Laguna Lake, Philippines.

Fecal pollution is a major contributor to the progressive degradation of Laguna Lake, the Philippines' largest inland lake used for aquaculture, recreation, and as a source of irrigation and domestic water. Consequently, intestinal parasites may be present in this body of water, posing risks to water safety and human health. This study was able to detect the protozoan parasite, Giardia duodenalis, in three Laguna Lake stations and seven tributary rivers in a 13-month monitoring period by PCR amplification of the small subunit ribosomal RNA (SSU rRNA) gene of Giardia cysts concentrated from water samples. The pathogen was present in 37.7% of tributary samples (n = 69) and 16.7% of lake samples (n = 36). Notable frequencies of detection were observed in four tributary rivers -Bagumbayan, Taguig (66.7%); Santa Rosa, Laguna (55.6%); San Cristobal, Cabuyao, Laguna (44.4%); and Biñan, Laguna (42.9%). All test SSU rRNA gene sequences were identified as human-infective genotypes of G. duodenalis predominated by Assemblage A (94.1%). Furthermore, analysis of the glutamate dehydrogenase (gdh) gene revealed the possible presence of mixed genotypes in at least two samples. These results support the pressing need to include protozoan pathogen monitoring in Laguna Lake and its tributaries to prevent Giardia infection in humans and animals. This study also recommends microbial source tracking to identify fecal pollution sources and aid in regulation of waste discharges into the lake and its tributaries.

Cytomegalovirus Glycoprotein Polymorphisms and Increasing Viral Load in Non-Transplant Patients with Hematological Malignancies Undergoing Chemotherapy: A Prospective Observational Study.

IntroductionCytomegalovirus (CMV) predisposes to several clinical complications and is a major cause of morbidity and mortality in immunocompromised patients, including patients with hematological malignancies (HM). The present study was carried out to determine the distribution of CMV glycoprotein B, N, and O (gB, gN, and gO) genotypes and their potential effect on its viral load and on clinical outcomes in a cohort of Tunisian non-hematopoietic stem cell transplant (HSCT) patients with HM undergoing chemotherapy.MethodsCMV viral load was evaluated by real-time quantitative PCR. The gB, gN, and gO genotypes of the CMV strains were analyzed by multiplex nested PCR and sequencing.ResultsThis prospective study involved 60 clinical isolates obtained from 60 non-HSCT patients with HM undergoing chemotherapy. Mixed CMV gB, gN, and gO genotypes were the predominant glycoprotein genotypes in 31%, 41.4%, and 46.4% of patients, respectively. Mixed gB genotypes were associated with higher initial levels of CMV load (p = 0.001), increased rate of fever (0.025), and co-infection with other herpesviruses (HHVs) (p = 0.024) more frequently than in single gB genotype. Mixed gN genotypes were more associated with severe lymphopenia (ALC < 500/µL) (p = 0.01) and increased risk of death (p = 0.042) than single gN genotype. Single gO2b genotype had also a more unfavorable outcome (p = 0.009) than the other single gO genotype. Mixed gO genotypes were associated with female gender (p = 0.015), acute leukemia disease (p = 0.036), initial high level of CMV viral load (at least 1000 copies/mL) (p = 0.029), skin rash (p = 0.01) more frequently than in single gO genotype. The gO1a/gN3b linkage was associated with an increased initial viral load (p = 0.012).ConclusionInfection with mixed CMV genotypes was common and multiple gB, gN, and gO genotypes were associated with clinical manifestation and higher viral load.Supplementary InformationThe online version contains supplementary material available at 10.1007/s40121-021-00457-z.