scholarly journals Prevalence of HCV and Its Correlation with HCV Genotypes

2021 ◽  
Vol 3 (4) ◽  
pp. 133-136
Author(s):  
Pankaj Kumar Gadhia ◽  
Monika Patel ◽  
Khushboo Daryani ◽  
Salil Vaniawala
Keyword(s):  
Sanger Sequencing ◽  
Liver Inflammation ◽  
Genotype 1 ◽  
Rt Pcr ◽  
Genotype 3 ◽  
Predominant Genotype ◽  
Biological Features ◽  
Sequencing Method ◽  
Positive Results ◽  
Timely Treatment

Introduction: Hepatitis C virus is known to cause liver inflammation, which may progress to liver cirrhosis and hepatocellular carcinoma. The genomes of HCV display sequence heterogenicity, thus, are classified in different genotypes and subtypes. Genotyping aids in understanding the epidemiology, biological features of the virus and inspecting the outbreak of the viral infection. Materials and Methods: In the present study, HCV viral RNA was isolated and quantified by RT-PCR technique followed by determining its genotype by Sanger sequencing method from the blood samples of infected patients. Results: Out of 40 samples, 25 showed positive results and 15 samples showed copy number lower than detection limit (< 35 IU/ml). Of 25 patients, the predominant genotype was 3 (a, b, g, i, k) followed by genotype 1 (a, b, g) and 4(a, c). Conclusion: The results revealed that genotype 3b accounted for the highest number of cases with positive HCV viral load as compared to genotype 1 and 4. The higher prevalence of genotype 3 shows that the needful measure and timely treatment should be conducted.

scholarly journals 694. Unexpected Diversity of Rotavirus Genotypes in Pediatric Population

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S399-S399
Author(s):  
Dimitra Koukou ◽  
Panagiota Chatzichristou ◽  
Elizabeth-Barbara Tatsi ◽  
Theodota Liakopoulou ◽  
Genovepha Chronopoulou ◽  
...  
Keyword(s):  
Acute Gastroenteritis ◽  
Sanger Sequencing ◽  
Pediatric Population ◽  
Demographic Data ◽  
Viral Gastroenteritis ◽  
Rt Pcr ◽  
Predominant Genotype ◽  
Pediatric Hospitals ◽  
Emergency Units ◽  
Group A

Abstract Background Rotavirus (RV) is the leading cause of viral gastroenteritis in children. Although RV genotypes differ geographically and temporally, five are the predominant genotypes circulating worldwide. Aim of our study was to monitor possible changes in distribution of Rotavirus genotypes circulating in Greek pediatric population during the post vaccine era. Methods Demographic data and fecal samples were collected from children ≤15 years old with symptoms of acute gastroenteritis who visited emergency units of Pediatric Hospitals in Greece from September 2016 to August 2019. Samples were tested for RV Group A antigen with rapid immunochromatographic assay. Positive samples were further G and P typed employing RT-PCR, semi-nested multiplex PCR and Sanger sequencing of the VP7 and VP4 genes. Results A total of 660 children participated in the study with median age 31±29 months. Males outnumbered females (59%). Most of them lived in urban cities (85%). RV genotyping distribution was G4P[8] (41%), G1P[8] (22%), G2P[4] (14%), G9P[8] (8%), G9P[4] (5,5%), G12P[8] (2%) and G3P[8] (1,8%). Unusual and mixed genotypes were identified in 3,2% and 2,5% of the samples respectively. During 2016-2017 and 2017-2018, G4P[8] was the predominant genotype in 67% and 51% of the annual samples. However, in 2018-2019 the most common genotypes were G9P[8] and G9P[4] (33% in total) followed by G2P[4] (27%). Interestingly, the genotype G9P[4] was not detected at all in the first two years of the study. Conclusion This study indicates diversity of the predominant RV genotypes in Greek children during 2016-2019. The emergence of G9 as the most common genotype as well as the significant detection of uncommon ones highlight the importance of continuous surveillance of RV genotyping during the post vaccine period. Disclosures All Authors: No reported disclosures

Covid-19: A review of its clinical features, effects on gastrointestinal system and possibility of faecal transmission

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 623-627
Author(s):  
Kanishk K Adhit ◽  
Anjankar Ashish P ◽  
Siddhaarth K
Keyword(s):  
Clinical Presentation ◽  
Throat Swab ◽  
Respiratory Illness ◽  
Review Article ◽  
Gastrointestinal System ◽  
Rt Pcr ◽  
Significant Evidence ◽  
Stool Samples ◽  
High Possibility ◽  
Positive Results

In China, Wuhan in the province of China, COVID-19 a patient suffering from pneumonia was tested and to identify the cause, the throat swab of the patient was tested. On 7th January 2020 WHO declared the identification as COVID-19. And then it was proclaimed as a pandemic. It classically causes a respiratory illness presenting as a mild cough, fever and . However, several investigators have advocated the involvement of the gastrointestinal tract and liver in COVID-19 infection similar to other infections. Further research studies have shown results that are expanding the possibility of transmission because RT-PCR assessment has shown significant evidence for the presence of virus not only in samples but also in stool samples. Studies have shown that virus in stool samples have got positive results even after the illness has resolved, and two respiratory tests were done 24 hours after COVID-19 being tested negative. The review article the different findings of the clinical presentation of COVID-19. It sheds light on the effects of COVID-19 in the gastrointestinal system along with the reasons for the high possibility of transmission of COVID-19 through the route.

scholarly journals Advances in Hepatitis E Virus Biology and Pathogenesis

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 267
Author(s):  
Shaoli Lin ◽  
Yan-Jin Zhang
Keyword(s):  
Pregnant Women ◽  
Hepatitis E Virus ◽  
Case Fatality ◽  
Hepatitis E ◽  
Host Cells ◽  
High Rate ◽  
Rapid Progression ◽  
Genotype 1 ◽  
Genotype 3 ◽  
Zoonotic Infections

Hepatitis E virus (HEV) is one of the causative agents for liver inflammation across the world. HEV is a positive-sense single-stranded RNA virus. Human HEV strains mainly belong to four major genotypes in the genus Orthohepevirus A, family Hepeviridae. Among the four genotypes, genotype 1 and 2 are obligate human pathogens, and genotype 3 and 4 cause zoonotic infections. HEV infection with genotype 1 and 2 mainly presents as acute and self-limiting hepatitis in young adults. However, HEV infection of pregnant women with genotype 1 strains can be exacerbated to fulminant hepatitis, resulting in a high rate of case fatality. As pregnant women maintain the balance of maternal-fetal tolerance and effective immunity against invading pathogens, HEV infection with genotype 1 might dysregulate the balance and cause the adverse outcome. Furthermore, HEV infection with genotype 3 can be chronic in immunocompromised patients, with rapid progression, which has been a challenge since it was reported years ago. The virus has a complex interaction with the host cells in downregulating antiviral factors and recruiting elements to generate a conducive environment of replication. The virus-cell interactions at an early stage might determine the consequence of the infection. In this review, advances in HEV virology, viral life cycle, viral interference with the immune response, and the pathogenesis in pregnant women are discussed, and perspectives on these aspects are presented.

scholarly journals Hepatitis E Virus Occurrence in Pigs Slaughtered in Italy

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 277
Author(s):  
Eleonora Chelli ◽  
Elisabetta Suffredini ◽  
Paola De Santis ◽  
Dario De Medici ◽  
Santina Di Bella ◽  
...  
Keyword(s):  
Hepatitis E Virus ◽  
Phylogenetic Analyses ◽  
Hepatitis E ◽  
Rt Pcr ◽  
High Seroprevalence ◽  
Genotype 3 ◽  
Sporadic Cases ◽  
Wild Boar Meat ◽  
Small Clusters ◽  
Frequent Exposure

In Europe, foodborne transmission has been clearly associated to sporadic cases and small clusters of hepatitis E in humans linked to the consumption of contaminated pig liver sausages, raw venison, or undercooked wild boar meat. In Europe, zoonotic HEV-genotype 3 strains are widespread in pig farms but little information is available on the prevalence of HEV positive pigs at slaughterhouse. In the present study, the prevalence of HEV-RNA positive pigs was assessed on 585 animals from 4 abattoirs located across Italy. Twenty-one pigs (3.6%) tested positive for HEV in either feces or liver by real-time RT-PCR. In these 21 pigs, eight diaphragm muscles resulted positive for HEV-RNA. Among animals collected in one abattoir, 4 out of 91 plasma tested positive for HEV-RNA. ELISA tests for the detection of total antibodies against HEV showed a high seroprevalence (76.8%), confirming the frequent exposure of pigs to the virus. The phylogenetic analyses conducted on sequences of both ORF1 and ORF2 fragments, shows the circulation of HEV-3c and of a novel unclassified subtype. This study provides information on HEV occurrence in pigs at the slaughterhouse, confirming that muscles are rarely contaminated by HEV-RNA compared to liver, which is the most frequently positive for HEV.

scholarly journals Novel manifestations of Warburg micro syndrome type 1 caused by a new splicing variant of RAB3GAP1: a case report

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Raziyeh Khalesi ◽  
Ehsan Razmara ◽  
Golareh Asgaritarghi ◽  
Ali Reza Tavasoli ◽  
Yasser Riazalhosseini ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Cerebral White Matter ◽  
Global Developmental Delay ◽  
Spastic Diplegia ◽  
Amplification Refractory Mutation System ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
Mutation System ◽  
Warburg Micro Syndrome

Abstract Background The present study aimed to determine the underlying genetic factors causing the possible Warburg micro syndrome (WARBM) phenotype in two Iranian patients. Case presentation A 5-year-old female and a 4.5-year-old male were referred due to microcephaly, global developmental delay, and dysmorphic features. After doing neuroimaging and clinical examinations, due to the heterogeneity of neurodevelopmental disorders, we subjected 7 family members to whole-exome sequencing. Three candidate variants were confirmed by Sanger sequencing and allele frequency of each variant was also determined in 300 healthy ethnically matched people using the tetra-primer amplification refractory mutation system-PCR and PCR-restriction fragment length polymorphism. To show the splicing effects, reverse transcription-PCR (RT-PCR) and RT-qPCR were performed, followed by Sanger sequencing. A novel homozygous variant—NM_012233.2: c.151-5 T > G; p.(Gly51IlefsTer15)—in the RAB3GAP1 gene was identified as the most likely disease-causing variant. RT-PCR/RT-qPCR showed that this variant can activate a cryptic site of splicing in intron 3, changing the splicing and gene expression processes. We also identified some novel manifestations in association with WARBM type 1 to touch upon abnormal philtrum, prominent antitragus, downturned corners of the mouth, malaligned teeth, scrotal hypoplasia, low anterior hairline, hypertrichosis of upper back, spastic diplegia to quadriplegia, and cerebral white matter signal changes. Conclusions Due to the common phenotypes between WARBMs and Martsolf syndrome (MIM: 212720), we suggest using the “RABopathies” term that can in turn cover a broad range of manifestations. This study can per se increase the genotype-phenotype spectrum of WARBM type 1.

scholarly journals Rapid, sensitive, full genome sequencing of Severe Acute Respiratory Syndrome Virus Coronavirus 2 (SARS-CoV-2)

2020 ◽  
Author(s):  
Clinton R Paden ◽  
Ying Tao ◽  
Krista Queen ◽  
Jing Zhang ◽  
Yan Li ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Sanger Sequencing ◽  
Respiratory Syndrome Virus ◽  
Full Genome ◽  
Miseq Sequencing ◽  
Genomic Information ◽  
Rt Pcr ◽  
Full Genome Sequencing ◽  
High Quality ◽  
Global Pandemic

AbstractSARS-CoV-2 recently emerged, resulting a global pandemic. Rapid genomic information is critical to understanding transmission and pathogenesis. Here, we describe validated protocols for generating high-quality full-length genomes from primary samples. The first employs multiplex RT-PCR followed by MinION or MiSeq sequencing. The second uses singleplex, nested RT-PCR and Sanger sequencing.

scholarly journals High-throughput immunoassays for SARS-CoV-2, considerable differences in performance when comparing three methods

2020 ◽  
Author(s):  
Oskar Ekelund ◽  
Kim Ekblom ◽  
Sofia Somajo ◽  
Johanna Pattison-Granberg ◽  
Karl Olsson ◽  
...  
Keyword(s):  
High Throughput ◽  
Rapid Test ◽  
Performance Criteria ◽  
Clinical Use ◽  
Rt Pcr ◽  
Regulatory Authorities ◽  
Flow Test ◽  
Lateral Flow Test ◽  
High Level ◽  
Positive Results

Background: The recently launched high-throughput assays for the detection of antibodies against SARS-CoV-2 may change the managing strategies for the COVID-19 pandemic. This study aimed at investigating the performance of three high-throughput assays and one rapid lateral flow test relative to the recommended criteria defined by regulatory authorities. Methods: A total of 133 samples, including 100 pre-pandemic samples, 20 samples from SARS-CoV-2 RT-PCR positive individuals, and 13 potentially cross-reactive samples were analysed with SARS-CoV-2 IgG (Abbott), Elecsys Anti-SARS-CoV-2 (Roche), LIAISON SARS-CoV-2 S1/S2 IgG (DiaSorin) and 2019-nCOV IgG/IgM Rapid Test (Dynamiker Biotechnology Co). Results: All assays performed with a high level of specificity; however, only Abbott reached 100% (95% CI 96.3-100). The pre-pandemic samples analysed with Roche, DiaSorin and Dynamiker Biotechnology resulted in two to three false-positive results per method (specificity 96.9-98.0%). Sensitivity differed more between the assays, Roche exhibiting the highest sensitivity (100%, CI 83.9-100). The corresponding figures for Abbott, DiaSorin and Dynamiker Biotechnology were 85.0%, 77.8% and 75.0%, respectively. Conclusions: The results of the evaluated SARS-CoV-2 assays vary considerably as well as their ability to fulfil the performance criteria proposed by regulatory authorities. Introduction into clinical use in low-prevalent settings, should therefore, be made with caution.

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