RETRACTED: A complex evolutionary relationship between HHV-6A and HHV-6B
Authors: Mario Clerici
Uberto Pozzoli
Manuela Sironi
Diego Forni
Rachele Cagliani
Journal: Virus Evolution (2019)
Discipline: MICROBIOLOGY
Keywords: HHV-6; Human betaherpesvirus; population structure; recombination; viral evolution.
Affiliations: Bioinformatics, Scientific Institute IRCCS E. Medea, Bosisio Parini, Lecco, Italy, Department of Physiopathology and Transplantation, University of Milan, Milan, Italy, IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy

Abstract:  Human betaherpesviruses 6A and 6B (HHV-6A and HHV-6B) are highly prevalent in human populations. The genomes of these viruses can be stably integrated at the telomeres of human chromosomes and be vertically transmitted (inherited chromosomally integrated HHV-6, iciHHV6). We reconstructed the population structure of HHV-6 and we show that HHV-6A genomes diverged less than HHV-6B genomes from the ancestral common HHV-6A/B population. Analysis of ancestry proportions indicated that HHV-6A exogenous viruses and iciHHV-6A derived most of their genomes from distinct ancestral sources. Conversely, exogenous viral and iciHHV-6B populations were similar in terms of ancestry components, with no evident geographic structuring. Most HHV-6B genomes sampled to date derive from viral populations that experienced considerable drift. However, a population of HHV-6 exogenous viruses, currently classified as HHV-6B and sampled in New York state, formed a separate cluster (NY cluster) and harbored a considerable portion of HHV-6A-like ancestry. Recombination detection methods identified these viruses as interspecies recombinants, but phylogenetic reconstruction indicated that the recombination signals are due to shared ancestry. In analogy to iciHHV-6A, NY cluster viruses have high nucleotide diversity and constant population size. We propose that HHV-6A sequences and the NY cluster population diverged from an ancestral HHV-6A-like population. A relatively recent bottleneck of the NY (or a related) population with subsequent expansion originated most HHV-6B genomes currently sampled. Our findings indicate that the distinction between HHV-6A and -6B is not as clear-cut as previously thought. More generally, epidemiological and clinical surveys would benefit from taking HHV-6 genetic diversity into account. 

Retracted: Yes

PubPeer comments:
 2019 retraction. https: academic.oup.com ve article 5 2 vez054 5638896 The authors of u201cA complex evolutionary relationship between HHV-6A and HHV-6Bu201d (doi: 10.1093 ve vez043) have requested retraction of their paper. All authors agree with this action. Virus Evolution is retracting the paper because its findings are unreliable due to honest experimental error. Specifically, analyses and conclusions were based on the retrieval of genome sequences from GenBank that were erroneous (accession numbers: KY239023.1, KY274487.1u2013KY274525.1, KY290171.1u2013KY290221.1, KY315520.1u2013KY315558.1). These genomes have been since corrected on GenBank (accession numbers: KY239023.2, KY274487.2u2013KY274525.2, KY290171.2u2013KY290221.2, KY315520.2u2013KY315558.2). Raw read data for the genome assemblies are available on SRA (accession numbers: SRR8717229, SRR8745772u2013SRR8745811, SRR8749118u2013SRR8749151, SRR8749387u2013SRR8749420, SRR8757190u2013SRR8757227, SRR9736967u2013SRR9737010). Since this mistake affects a significant portion of the paperu2019s results the journal has decided that a retraction, rather than a correction, is the most appropriate course of action. Virus Evolution apologises for any inconvenience caused by this retraction, and thanks the authors for their rapid action and open communication in dealing with this matter. ,