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PubMed1996

Human immunodeficiency virus type 1 neutralizing antibody serotyping using serum pools and an infectivity reduction assay.

Classification of human immunodeficiency virus type 1 (HIV-1) by neutralization serotype may be important for the design of active and passive immunization strategies. Neutralizing antibody serotyping is hindered by the lack of standard reagents and assay format, and by the weak activity of many individual sera. To facilitate cross-clade neutralization analysis, we used an infectivity reduction assay (IRA) and selected clade-specific serum (or plasma) pools from subjects infected with clade B and E HIV-1, respectively. Several serum pools were utilized; some were selected for strong neutralizing activity against intraclade viruses and others were derived from conveniently available samples. Against a panel of 51 clade B and E viruses, serum pools displayed strong neutralization of most intraclade viruses and significantly diminished cross-clade neutralization. Results were confirmed against a blinded panel of 20 viruses. The data indicate that the phylogenetic classification of virus subtypes B and E corresponds to two distinct neutralization serotypes. This approach to neutralizing antibody serotyping may be useful in defining the antigenic relationship among viruses from other clades.

Enzyme-Linked Immunosorbent Assay↗
PubMed1996

Beet soil-borne virus RNA 3--a further example of the heterogeneity of the gene content of furovirus genomes and of triple gene block-carrying RNAs.

The complete nucleotide sequence of RNA 3 of the Ahlum isolate of beet soil-borne virus (BSBV) was determined from cDNAs obtained with immunocaptured virus particles and denatured preparations of dsRNA. BSBV RNA 3 is unique among the plant virus RNAs studied so far in containing apparently only the coding sequences of a triple gene block (TGB). The derived amino acid sequences of the three putative TGB-encoded proteins showed the highest level of sequence similarities with those of the corresponding proteins of potato mop top furovirus (PMTV) followed by those of peanut clump furovirus and barley stripe mosaic hordeivirus. Progressively fewer similarities were found with the TGB-encoded proteins of beet necrotic yellow vein virus (uncertain classification), potato X potexvirus, and potato M carlavirus. The 3'-terminal 78 nucleotides of BSBV RNA 3 can be folded into a tRNA-like structure and a high degree of sequence similarity exists between the 122 3'-terminal nucleotides of BSBV RNA 3 and PMTV RNA 2. In other regions, however, no pronounced sequence similarities were found between the two RNAs, and PMTV RNA 2 contains an additional putative gene for a cysteine-rich protein downstream of the TGB. The two viruses are unrelated serologically. BSBV RNA 3 adds a further variant to the heterogeneity of the gene content of furovirus genomes and of triple gene block-carrying RNAs.

Amino Acid Sequence↗
PubMed1982

Principles of rational classification and nomenclature of human influenza A viruses.

To eliminate possible mistakes in the new nomenclature of influenza A viruses, approved by the WHO influenza experts Committee on February 1980, it is suggested to introduce the following changes: reestablish the independent position of subtypes of human influenza A viruses with hemagglutinins HSw1, HO and H1 and neuraminidase N1; use as a principle method for differentiation of various subtypes the hemagglutination inhibition (HI) test instead of the double immunodiffusion test (DIDT); to strengthen the leading role of the host in the classification of influenza A viruses by presenting human influenza viruses separately from the animal and avian viruses; it is advisable to change the present classification of influenza viruses by dividing the family of orthomyxoviridae into two species - Influenza A virus and Influenza B virus and promoting the existing influenza A virus subtypes into the rank of a serotype and the main antigenic variants within each type - into subtypes.

Animals↗
PubMed1995

Genetic diversity and phylogenetic classification of viral hemorrhagic septicemia virus (VHSV).

The present study was undertaken to determine the genetic diversity of viral hemorrhagic septicemia virus (VHSV) and to gain insight into the molecular epidemiology of this fish rhabdovirus. The sequences of the nonstructural (NV) protein and the transmembrane (G) protein of sequential North American and European isolates of VHSV were determined and used to compute phylogenetic trees. According to the percentage of nucleotide or amino acid similarities, North American and European isolates formed 2 clearly distant genetic groups. While North American isolates clustered into a highly homogeneous genetic group, European isolates exhibited a higher genetic variability. Subgrouping based on this variability could be correlated with both the geographic origin and the serological classification.

Amino Acid Sequence↗
PubMedDate not supplied

Mucocutaneous findings in pediatric AIDS related to degree of immunosuppression.

The normal value of the absolute CD4-positive T-lymphocyte count is relatively high in normal infants and declines steadily until 6 years of age, whereas the CD4 percentage of the total lymphocyte count is constant. The immunologic categories according to the 1994 revised pediatric human immunodeficiency virus (HIV) classification, based on CD4-positive percentage of the total lymphocyte count, is classified into three categories: no evidence of suppression (> or =25%), moderate suppression (15-24%), and severe suppression (1-14%). Our objective was to determine the prevalence of mucocutaneous findings in pediatric acquired immunodeficiency syndrome (AIDS) related to the degree of immunosuppression. We prospectively examined 120 children less than 13 years of age who were born to HIV-seropositive women and developed definite HIV infection. The prevalence of mucocutaneous findings in those children who had severe, moderate, and no evidence of immunosuppression were 62%, 43%, and 20%, respectively. The mucocutaneous findings in patients in the moderate and severe suppression groups were significantly more common than in patients without evidence of immunosuppression (p < 0.001). In the moderate immunosuppression group, 11% had two mucocutaneous findings while 21% in the severe immunosuppression group had two or more mucocutaneous findings. The most common mucocutaneous finding was oral candidiasis (33%), which had a mean corresponding CD4 percentage of the total lymphocyte count of 11.3%. Herpes zoster was found in 6% of the patients (mean CD4 percentage of the total lymphocyte count = 13.5%). Chronic herpes simplex virus (HSV) stomatitis was found in 3% of the patients (mean CD4 percentage of the total lymphocyte count = 3%). Mucocutaneous manifestations are common in pediatric AIDS. The majority of these findings have an infectious etiology. The prevalence increases as the CD4-positive percentage of the total lymphocyte count decreases. More than one mucocutaneous finding can be found at the same time in patients with moderate or severe immunosuppression.

Acquired Immunodeficiency Syndrome↗
PubMed2025

Epstein-Barr Virus Sequence Variations Among the Understudied Nasopharyngeal Carcinoma Patients of Diverse Ancestries in Southeast Asia.

Epstein-Barr virus (EBV) is associated with cancers, including lymphomas and nasopharyngeal carcinoma (NPC). To date, risk variants for NPC were mainly identified from Chinese populations, which dominated the world's total number of cases. Although Southeast Asia (SEA) countries have among the world's top yet intriguingly diverse NPC age-standardized incidence rates across subpopulations, data on EBV from SEA remains scarce. In this study, we examined 83 NPC patients of different ancestries for the presence of risk haplotypes associated with the Southern Chinese NPC and generated and analyzed 67 EBV sequences (from tissue, patient-derived xenografts and lymphoblastoid cell lines of 60 NPC patients) together with 838 published EBV genomes. Our study revealed that NPC patients of non-Chinese ancestry had fewer risk variants and haplotypes that are associated with Southern Chinese NPC and clustered distinctly from lymphomas, Southern Chinese NPC, and non-cancer controls. The distribution of non-synonymous variants was similar among NPC patients of Chinese ancestry, irrespective of geographical location. Meanwhile, non-synonymous variants in genes related to packaging, latency, and structural proteins such as BPLF1, LF3, and LMP1 varied across different ancestries. Our findings suggest possibilities of EBV adaptation to host genetics for NPC pathogenesis and warrant further research for the understudied NPC subpopulations.

Adult↗
PubMed2025

Enrichment of G-to-U Substitution in SARS-CoV-2 Functional Regions and Its Compensation via Concurrent Mutations.

We surveyed single nucleotide variant (SNV) patterns from 5&#x2009;903&#x2009;647 complete SARS-CoV-2 genomes. Among 10&#x2009;012 SNVs, APOBEC-mediated C-to-U (C&#x2009;>&#x2009;U) deamination was the most prevalent, followed by G&#x2009;>&#x2009;U and other RNA editing-related substitutions including (A&#x2009;>&#x2009;G, U&#x2009;>&#x2009;C, G&#x2009;>&#x2009;A). However, C&#x2009;>&#x2009;U mutations were less frequent in functional regions, for example, S protein, intrinsic disordered regions, and nonsynonymous mutations, where G&#x2009;>&#x2009;U were over-represented. Notably, G-loss substitutions rarely appeared together. Instead, G-gain mutations tended to more frequently co-occur with others, with a marked preference in the S protein, suggesting a compensatory mechanism for G loss in G&#x2009;>&#x2009;U mutations. The temporal patterns revealed C&#x2009;>&#x2009;U frequency declined until late 2021 then resurged in early 2022. Conversely, G&#x2009;>&#x2009;U steadily decreased, with a pronounced drop in January 2022, coinciding with reduced COVID-19 severity. Vaccinated individuals exhibited a slightly but significantly higher C&#x2009;>&#x2009;U frequency and a notably lower G&#x2009;>&#x2009;U frequency compared to the unvaccinated group. Additionally, cancer patients had higher G&#x2009;>&#x2009;U frequency than general patients during the same period. Interestingly, none of the C&#x2009;>&#x2009;U SNVs were uniquely identified in 2724 environmental samples. These findings suggest novel functional roles of G&#x2009;>&#x2009;U in COVID-19 symptoms, potentially linked to oxidative stress and reactive oxygen species, while C&#x2009;>&#x2009;U remains the dominant substitution, likely driven by host immune-mediated RNA editing.

SARS-CoV-2↗
PubMed2003

Nucleotide sequence and phylogenetic classification of candidate human papilloma virus type 92.

From a basal cell carcinoma (BCC) the complete genome of candidate human papillomavirus (HPV) type 92 was characterized. Phylogenetically, the candidate HPV 92 was relatively distantly related to other cutaneous HPV types within the B1 group. By quantitative real time PCR, 94 viral copies were present per cell in the BCC and another BCC contained 1 viral copy per cell. Lower copy numbers were found in two solar keratoses (1 copy per 33 cells and 1 copy per 60 cells) and two squamous cell carcinomas (1 copy per 436 cells and 1 copy per 1143 cells). The high viral load of HPV 92 in two BCCs differs from the low amount of HPV DNA reported from nonmelanoma skin cancers.

Basal Cell Carcinoma↗
PubMed2003

Serological reactivity of baculovirus-expressed Ebola virus VP35 and nucleoproteins.

Ebola virus (EBOV) is a member of the family Filoviridae and is classified as a biosafety level 4 virus. This classification makes the preparation of antigen and performance of diagnostic assays time-consuming and complicated. The objective of this study was to evaluate the value of EBOV immunoassays based on recombinant nucleoprotein (r-NP) and recombinant VP35 (r-VP35) using large serum panels of African origin and from primates. Furthermore, we investigated whether the results obtained with EBOV r-VP35 enzyme-linked immunosorbent assay (ELISA) could improve on the findings obtained with the EBOV r-NP ELISA. The full-length EBOV NP and VP35 of the EBOV subtype Zaire were expressed as histidine-tagged recombinant proteins in the baculovirus expression system. The antigenic reactivity and specificity of these recombinant proteins were determined by Western blotting and ELISA using EBOV specific monoclonal antibodies. The results obtained with the r-NP and r-VP35 ELISAs were compared with the results obtained in an indirect immunofluorescence assay based on native EBOV subtype Zaire. EBOV specific monoclonal antibodies reacted specifically with the respective proteins in both Western blot and ELISA. Five hundred and twenty six samples from humans and primates were tested with r-NP and r-VP35 ELISAs. Monkey serum samples positive for EBOV subtype Reston and Zaire were both positive in the EBOV r-NP ELISA, whereas only the EBOV Zaire infected monkeys were positive in the r-VP35 ELISA. The sensitivity and specificity values of the EBOV recombinants' ELISAs compared to those of the immunofluorescence assay were 92% and 99% for r-NP and 44% and 100% for r-VP35. r-NP ELISA proved to be a sensitive and specific assay for EBOV diagnosis and for epidemiological studies for both EBOV subtypes Reston and Zaire. The use of r-VP35 in an ELISA format has no additional value for EBOV serodiagnosis.

Adolescent↗
PubMed2026

Community-driven updates for comprehensive long-read metagenomics and enhanced binning in nf-core/mag v5.

SUMMARY: nf-core/mag is a reproducible Nextflow pipeline for best-practice metagenomic de novo assembly and binning within the nf-core framework. Here we present a major update that adds support for long-read-only assembly and bin refinement, includes five new binning tools, expands taxonomic classification to viruses and eukaryotes, and improves bin quality evaluation with new tools and latest databases. Through sustained community-driven development spanning seven years and four primary curator teams, nf-core/mag remains actively developed as an open source workflow for metagenomic analysis, benefiting from contributions from across the broader metagenomics, nf-core, and Nextflow ecosystem. AVAILABILITY AND IMPLEMENTATION: The source code of nf-core/mag v5 is available on GitHub (https://github.com/nf-core/mag) under the open source MIT license, with v5.5.0 source code archived on Zenodo (https://zenodo.org/records/21735731). Documentation is viewable on the nf-core website (https://nf-co.re/mag).

Metagenomics↗
PubMed2026

Uncovering viral protein acquisition events and human-specific folds with pairwise comparisons of predicted protein structures.

Pairwise sequence comparisons are at the center of molecular evolutionary analyses. However, viral pairwise comparisons are challenging because extreme mutation rates and evolutionary pressure cause genomes to diverge rapidly, limiting detectable sequence similarity to fewer than 3% of virus pairs. To overcome these limitations, we compared viruses based on structural similarity, using predicted protein structures from ColabFold and Foldseek to define protein fold clusters. We represented each virus genome by its protein structural content. Pairwise similarities between viruses were then quantified using the Jaccard index based on the presence or absence of protein fold clusters. Using a recently established viral protein fold database, we compared all pairs of eukaryotic viruses in RefSeq. This approach increased the proportion of comparable viral genome pairs from 2.4% to 16.5%. Using this protein-fold representation of viruses, we were able to accurately predict viral families with an average sensitivity of 85.9%. Investigation of viral families showing limited sensitivity with this approach uncovered a laterally transferred structural cluster (Rep/NS1) broadly shared across diverse viral families and found in the avian lineage of adenoviruses. Sequence homology suggests that this Rep was acquired from Parvoviridae, but the protein is mutant in the ATPase active site, indicating possible exaptation toward a purely DNA-binding function. In Gammapapillomaviruses, several E4 clusters were associated with human tropism. In summary, by representing viruses with structural protein clusters, we can classify highly divergent viruses, trace lateral gene transfer, and uncover features associated with viral host range.

Humans↗
PubMed1994

The entire nucleotide sequence and classification of a hepatitis C virus isolate of a novel genotype from an Indonesian patient with chronic liver disease.

Three hepatitis C virus (HCV) isolates were obtained from patients with chronic liver diseases in Indonesia which were not classifiable into any of the genotypes I/1a, II/1b, III/2a, IV/2b or V/3a reported previously. The entire nucleotide sequence was determined for one HCV isolate (HC-G9); the remaining two isolates were of the same genotype based on a > 95% similarity within their partial sequences spanning 2927 nucleotides (nt). The HC-G9 genome consisted of 9440 nt including the 5' untranslated region of 341 nt, an open reading frame of 9033 nt coding for a polyprotein of 3011 amino acids and the 3' untranslated region of 66 nt (U stretch of 17 to 47 nt at the extreme 3' terminus excluded). It differed by 20 to 33% in nucleotide sequence from any of 14 HCV genomes of genotypes I/1a to IV/2b whose full-length sequences are known. By the unweighted pair-group method with arithmetic mean, HC-G9 was on a major branch (group 1) of the phylogenetic tree of HCV to which genotypes I/1a and II/1b belong. It is proposed, therefore, that the novel genotype for HC-G9 should be called 1c. A method was developed to identify genotype 1c by PCR with a primer deduced from the core gene that was specific to it. Since genotype 1c was detected in seven (15%) of 48 HCV RNA samples from Indonesian patients with chronic liver disease, but not in any of 1097 from other districts of the world, it appears to have evolved and remained in Indonesia. In addition to its epidemiological importance, the association of genotype 1c HCV with the severity of liver disease and its response to interferons deserve to be evaluated.

Amino Acid Sequence↗
PubMed2025

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.

Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ~80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

metagenome-assembled genomes↗
PubMed1984

Classification of Inoue-Melnick virus into three antigenic types.

Antigenic analysis of Inoue-Melnick virus, formerly called SMON virus, showed that isolates from patients with subacute myelo-optico-neuropathy (SMON) in Japan, thus far tested, belonged to a single antigenic type (type 1). However, Inoue-Melnick virus isolates obtained so far in the United States chiefly from patients with multiple sclerosis could be classified into three types: type 1, type 2, and an intermediate type. At the present state of knowledge, the virus has not been proven to be the causative agent of disease, hence its provisional designation as IMV.

Antigens, Viral↗