scholarly journals Standard reference sequences for submission of HLA genotyping for the 18th International HLA and Immunogenetics Workshop

HLA ◽  
2021 ◽  
Author(s):  
Benedict M. Matern ◽  
Steven J. Mack ◽  
Kazutoyo Osoegawa ◽  
Martin Maiers ◽  
Matthias Niemann ◽  
...  
Keyword(s):  
Hla Genotyping ◽  
Reference Sequences

Molecular Evidence for Nosocomial Transmission of Human Immunodeficiency Virus from a Surgeon to One of His Patients

1998 ◽  
Vol 72 (5) ◽  
pp. 4537-4540 ◽  
Author(s):  
Alain Blanchard ◽  
Stéphane Ferris ◽  
Sophie Chamaret ◽  
Denise Guétard ◽  
Luc Montagnier
Keyword(s):  
Human Immunodeficiency Virus ◽  
Viral Genome ◽  
Pcr Amplification ◽  
Nosocomial Transmission ◽  
Molecular Evidence ◽  
Immunodeficiency Virus ◽  
Reference Sequences ◽  
Hiv Type 1 ◽  
Viral Sequences

ABSTRACT We have investigated the molecular evidence in favor of the transmission of human immunodeficiency virus (HIV) from an HIV-infected surgeon to one of his patients. After PCR amplification, theenv and gag sequences from the viral genome were cloned and sequenced. Phylogenetic analysis revealed that the viral sequences derived from the surgeon and his patient are closely related, which strongly suggests that nosocomial transmission occurred. In addition, these viral sequences belong to group M of HIV type 1 but are divergent from the reference sequences of the known subtypes.

scholarly journals Addressing widespread misidentifications of traditional medicinal mushrooms in Sanghuangporus (Basidiomycota) through ITS barcoding and designation of reference sequences

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shan Shen ◽  
Shi-Liang Liu ◽  
Ji-Hang Jiang ◽  
Li-Wei Zhou
Keyword(s):  
Species Identification ◽  
Rolling Circle Amplification ◽  
Practical Method ◽  
Morphological Characters ◽  
Its Sequences ◽  
Commercial Development ◽  
Medicinal Mushrooms ◽  
Rolling Circle ◽  
Reference Sequences ◽  
Its Barcoding

Abstract“Sanghuang” refers to a group of important traditionally-used medicinal mushrooms belonging to the genus Sanghuangporus. In practice, species of Sanghuangporus referred to in medicinal studies and industry are now differentiated mainly by a BLAST search of GenBank with the ITS barcoding region as a query. However, inappropriately labeled ITS sequences of “Sanghuang” in GenBank restrict accurate species identification and, to some extent, the utilization of these species as medicinal resources. We examined all available 271 ITS sequences related to “Sanghuang” in GenBank including 31 newly submitted sequences from this study. Of these sequences, more than half were mislabeled so we have now corrected the corresponding species names. The mislabeled sequences mainly came from strains utilized by non-taxonomists. Based on the analyses of ITS sequences submitted by taxonomists as well as morphological characters, we separate the newly described Sanghuangporus subbaumii from S. baumii and treat S. toxicodendri as a later synonym of S. quercicola. Fourteen species of Sanghuangporus are accepted, with intraspecific distances up to 1.30% (except in S. vaninii, S. weirianus and S. zonatus) and interspecific distances above 1.30% (except between S. alpinus and S. lonicerinus, and S. baumii and S. subbaumii). To stabilize the concept of these 14 species of Sanghuangporus, their taxonomic information and reliable ITS reference sequences are provided. Moreover, ten potential diagnostic sequences are provided for Hyperbranched Rolling Circle Amplification to rapidly confirm three common commercial species, viz. S. baumii, S. sanghuang, and S. vaninii. Our results provide a practical method for ITS barcoding-based species identification of Sanghuangporus and will promote medicinal studies and commercial development from taxonomically correct material.

Incidence and impact of allele-specific anti-HLA antibodies and high-resolution HLA genotyping on assessing immunologic compatibility

2021 ◽  
Vol 82 (3) ◽  
pp. 147-154
Author(s):  
Daria Zavyalova ◽  
Joseph Abraha ◽  
Ping Rao ◽  
Gerald P. Morris
Keyword(s):  
High Resolution ◽  
Hla Antibodies ◽  
Hla Genotyping ◽  
Allele Specific

scholarly journals Genetic and Pathogenic Characterization of QX(GI-19)-Recombinant Infectious Bronchitis Viruses in South Korea

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1163
Author(s):  
So-Youn Youn ◽  
Ji-Youn Lee ◽  
You-Chan Bae ◽  
Yong-Kuk Kwon ◽  
Hye-Ryoung Kim
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Prevention ◽  
South Korea ◽  
Prevention And Control ◽  
Genetic Recombination ◽  
Detection Methods ◽  
Infectious Bronchitis ◽  
Reference Sequences ◽  
And Control

Infectious bronchitis viruses (IBVs) are evolving continuously via genetic drift and genetic recombination, making disease prevention and control difficult. In this study, we undertook genetic and pathogenic characterization of recombinant IBVs isolated from chickens in South Korea between 2003 and 2019. Phylogenetic analysis showed that 46 IBV isolates belonged to GI-19, which includes nephropathogenic IBVs. Ten isolates formed a new cluster, the genomic sequences of which were different from those of reference sequences. Recombination events in the S1 gene were identified, with putative parental strains identified as QX-like, KM91-like, and GI-15. Recombination detection methods identified three patterns (rGI-19-I, rGI-19-II, and rGI-19-III). To better understand the pathogenicity of recombinant IBVs, we compared the pathogenicity of GI-19 with that of the rGI-19s. The results suggest that rGI-19s may be more likely to cause trachea infections than GI-19, whereas rGI-19s were less pathogenic in the kidney. Additionally, the pathogenicity of rGI-19s varied according to the genotype of the major parent. These results indicate that genetic recombination between heterologous strains belonging to different genotypes has occurred, resulting in the emergence of new recombinant IBVs in South Korea.

scholarly journals Nothing in (sponge) biology makes sense – except when based on holotypes

2015 ◽  
Vol 96 (2) ◽  
pp. 305-311 ◽  
Author(s):  
Dirk Erpenbeck ◽  
Merrick Ekins ◽  
Nicole Enghuber ◽  
John N.A. Hooper ◽  
Helmut Lehnert ◽  
...  
Keyword(s):  
New Species ◽  
Reference Material ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Plasticity ◽  
Morphological Characters ◽  
Molecular Techniques ◽  
Reference Sequences ◽  
Species Descriptions ◽  
Preservation History

Sponge species are infamously difficult to identify for non-experts due to their high morphological plasticity and the paucity of informative morphological characters. The use of molecular techniques certainly helps with species identification, but unfortunately it requires prior reference sequences. Holotypes constitute the best reference material for species identification, however their usage in molecular systematics and taxonomy is scarce and frequently not even attempted, mostly due to their antiquity and preservation history. Here we provide case studies in which we demonstrate the importance of using holotype material to answer phylogenetic and taxonomic questions. We also demonstrate the possibility of sequencing DNA fragments out of century-old holotypes. Furthermore we propose the deposition of DNA sequences in conjunction with new species descriptions.

Challenges for the standardized reporting of NGS HLA genotyping: Surveying gaps between clinical and research laboratories

2021 ◽  
Author(s):  
Kazutoyo Osoegawa ◽  
Gonzalo Montero-Martín ◽  
Kalyan C. Mallempati ◽  
Miranda Bauer ◽  
Robert P. Milius ◽  
...  
Keyword(s):  
Hla Genotyping ◽  
Standardized Reporting

scholarly journals HLA-B*15:01 is associated with asymptomatic SARS-CoV-2 infection

2021 ◽  
Author(s):  
Danillo G Augusto ◽  
Tasneem Yusufali ◽  
Noah D Peyser ◽  
Xochitl Butcher ◽  
Gregory M Marcus ◽  
...  
Keyword(s):  
Critical Role ◽  
Human Leukocyte ◽  
Asymptomatic Infection ◽  
Baseline Survey ◽  
Symptomatic Infection ◽  
Symptomatic Disease ◽  
Leukocyte Antigen ◽  
Hla Genotyping ◽  
Asymptomatic Individuals ◽  
Test Result

Background. Evidence has shown that a large proportion of SARS-CoV-2 infected individuals do not experience symptomatic disease. Owing to its critical role in immune response, we hypothesized that variation in the human leukocyte antigen (HLA) loci may underly asymptomatic infection. Methods. We enrolled 29,947 individuals registered in the National Marrow Donor Program for whom high-resolution HLA genotyping data were available in a smartphone-based study designed to track COVID-19 symptoms and outcomes. Among 21,893 individuals who completed the baseline survey, our discovery (N=640) and replication (N=788) cohorts were comprised of self-identified White subjects who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci (HLA-A, -B, -C, -DRB1, -DQB1) with asymptomatic vs. symptomatic infection. Results. HLA-B*15:01 was significantly increased in asymptomatic individuals in the discovery cohort compared to symptomatic (OR = 2.45; 95%CI 1.38-4.24, p = 0.0016, pcorr = 0.048), and we reproduced this association in the replication cohort (OR= 2.32; 95%CI = 1.10-4.43, p = 0.017). We found robust association of HLA-B*15:01 in the combined dataset (OR=2.40 95% CI = 1.54-3.64; p = 5.67 x10-5) and observed that homozygosity of this allele increases more than eight times the chance of remaining asymptomatic after SARS-CoV-2 infection (OR = 8.58, 95%CI = 1.74-34.43, p = 0.003). Finally, we demonstrated the association of HLA-B*15:01 with asymptomatic SARS-Cov-2 infection is enhanced by the presence of HLA-DRB1*04:01 Conclusion. HLA-B*15:01 is strongly associated with asymptomatic infection with SARS-CoV-2 and is likely to be involved in the mechanism underlying early viral clearance.

scholarly journals HLA genotyping in pediatric celiac disease patients

2014 ◽  
Vol 14 (3) ◽  
pp. 171 ◽  
Author(s):  
Biljana Stanković ◽  
Nedeljko Radlović ◽  
Zoran Leković ◽  
Dragana Ristić ◽  
Vladimir Radlović ◽  
...  
Keyword(s):  
Celiac Disease ◽  
Hla Genotyping
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