The ongoing pandemic spread of a new human coronavirus, SARS-CoV-2, which is associated with severe pneumonia/disease (COVID-19), has resulted in the generation of tens of thousands of virus genome sequences. The rate of genome generation is unprecedented, yet there is currently no coherent nor accepted scheme for naming the expanding phylogenetic diversity of SARS-CoV-2. Here, we present a rational and dynamic virus nomenclature that uses a phylogenetic framework to identify those lineages that contribute most to active spread. Our system is made tractable by constraining the number and depth of hierarchical lineage labels and by flagging and delabelling virus lineages that become unobserved and hence are probably inactive. By focusing on active virus lineages and those spreading to new locations, this nomenclature will assist in tracking and understanding the patterns and determinants of the global spread of SARS-CoV-2.

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A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology.

https://aasldpubs.onlinelibrary.wiley.com/doi/epdf/10.1002/hep.20819

Consensus proposals for a unified system of nomenclature of hepatitis C virus genotypes.

HIV-1 sequences were analyzed to estimate the timing of the ancestral sequence of the main group of HIV-1, the strains responsible for the AIDS pandemic. Using parallel supercomputers and assuming a constant rate of evolution, we applied maximum-likelihood phylogenetic methods to unprecedented amounts of data for this calculation. We validated our approach by correctly estimating the timing of two historically documented points. Using a comprehensive full-length envelope sequence alignment, we estimated the date of the last common ancestor of the main group of HIV-1 to be 1931 (1915-41). Analysis of a gag gene alignment, subregions of envelope including additional sequences, and a method that relaxed the assumption of a strict molecular clock also supported these results.

/pdf/timing-the-ancestor-of-the-hiv-1-pandemic-strains-2eqamt350z.pdf

Timing the ancestor of the HIV-1 pandemic strains.

Broadly neutralizing monoclonal antibodies (MAbs) are potentially important tools in human immunodeficiency virus type 1 (HIV-1) vaccine design. A few rare MAbs have been intensively studied, but we still have a limited appreciation of their neutralization breadth. Using a pseudovirus assay, we evaluated MAbs from clade B-infected donors and a clade B HIV + plasma against 93 viruses from diverse backgrounds. Anti-gp120 MAbs exhibited greater activity against clade B than non-B viruses, whereas anti-gp41 MAbs exhibited broad interclade activity. Unexpectedly, MAb 4E10 (directed against the C terminus of the gp41 ectodomain) neutralized all 90 viruses with moderate potency. MAb 2F5 (directed against an epitope adjacent to that of 4E10) neutralized 67% of isolates, but none from clade C. Anti-gp120 MAb b12 (directed against an epitope overlapping the CD4 binding site) neutralized 50% of viruses, including some from almost every clade. 2G12 (directed against a high-mannose epitope on gp120) neutralized 41% of the viruses, but none from clades C or E. MAbs to the gp120 V3 loop, including 447-52D, neutralized a subset of clade B viruses (up to 45%) but infrequently neutralized other clades (≤7%). MAbs b6 (directed against the CD4 binding site) and X5 (directed against a CD4-induced epitope of gp120) neutralized only sensitive primary clade B viruses. The HIV + plasma neutralized 70% of the viruses, including some from all major clades. Further analysis revealed five neutralizing immunotypes that were somewhat associated with clades. As well as the significance for vaccine design, our data have implications for passive-immunization studies in countries where clade C viruses are common, given that only MAbs b12 and 4E10 were effective against viruses from this clade.

Comprehensive Cross-Clade Neutralization Analysis of a Panel of Anti-Human Immunodeficiency Virus Type 1 Monoclonal Antibodies

Objective
To estimate the global and regional distribution of HIV-1 subtypes and recombinants between 2000 and 2007.

/pdf/global-trends-in-molecular-epidemiology-of-hiv-1-during-2000-1oors0ouxz.pdf

Global trends in molecular epidemiology of HIV-1 during 2000–2007

A clear and consistent genetic classification of human immunodeficiency virus-type 1 (HIV-1) strains continues to be of great utility in epidemiological tracking of the AIDS pandemic and in vaccine design. It also provides a foundation for detecting any biological differences that may have evolved

HIV-1 Nomenclature Proposal

1 Dept. of Zoology, Univ. of Oxford, Oxford, UK 2 Dept. of Microbiology, Univ. of Washington, Seattle, WA 3 Division of AIDS, NIH, Bethesda, MD 4 Henry M. Jackson Foundation, Rockville, MD 5 Group T-10, Los Alamos National Lab., Los Alamos, NM 6 Santa Fe Institute, Santa Fe, NM 7 Depts. of Medicine and Microbiology, Univ. of Alabama at Birmingham, Birmingham, AL 8 Dept. of Clinical Virology, Swedish Inst. for Infectious Disease Control,Solna, Sweden 9 Dept. of Policy, Strategy and Research, UNAIDS, Geneva, Switzerland 10 Laboratoire Retrovirus, IRD, Montpellier, France 11 HIV/AIDS and Retrovirology Branch, CDC. Atlanta, GA 12 Dept. of Infectious Disease Epidemiology, National Public Health Inst., Helsinki, Finland 13 Institute of Genetics, Univ. of Nottingham, Nottingham, UK 14 Dept. of Medicine, Northwestern Univ. Medical School, Chicago, IL

RK Funkhouser

Papers

HIV-1 Nomenclature Proposal

HIV-1 nomenclature proposal: a reference guide to HIV-1 classification.