Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.

SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat posed by a new variant is essential for adapting response efforts when community transmission is detected. In this study, we compare the dynamics of two variants, Alpha and Iota, by integrating genomic surveillance data to estimate the effective reproduction number (Rt) of the variants. We use Connecticut, United States, in which Alpha and Iota co-circulated in 2021. We find that the Rt of these variants were up to 50% larger than that of other variants. We then use phylogeography to show that while both variants were introduced into Connecticut at comparable frequencies, clades that resulted from introductions of Alpha were larger than those resulting from Iota introductions. By monitoring the dynamics of individual variants throughout our study period, we demonstrate the importance of routine surveillance in the response to COVID-19

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Systematic Biology 59 (2010): 518-533, doi:10.1093/sysbio/syq037.An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g. plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level ‘supergroups’, many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Further, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduces power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88-451) and levels of missing data (17-69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g. SAR, Rhizaria, Excavata), while the proposed supergroup ‘Chromalveolata’ is rejected. Further, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxonrich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data

Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

Publisher Copyright: © 2021 O'Toole Á et al.Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we track the international dispersal of lineages B.1.1.7 and B.1.351 (variant 501Y-V2). We account for potential biases in genomic surveillance efforts by including passenger volumes from location of where the lineage was first reported, London and South Africa respectively. Using the software tool grinch (global report investigating novel coronavirus haplotypes), we track the international spread of lineages of concern with automated daily reports, Further, we have built a custom tracking website (cov-lineages.org/global_report.html) which hosts this daily report and will continue to include novel SARS-CoV-2 lineages of concern as they are detected.Peer reviewe

A Mitogenomic Re-Evaluation of the Bdelloid Phylogeny and Relationships among the Syndermata

<div><p>Molecular and morphological data regarding the relationships among the three classes of Rotifera (Bdelloidea, Seisonidea, and Monogononta) and the phylum Acanthocephala are inconclusive. In particular, Bdelloidea lacks molecular-based phylogenetic appraisal. I obtained coding sequences from the mitochondrial genomes of twelve bdelloids and two monogononts to explore the molecular phylogeny of Bdelloidea and provide insight into the relationships among lineages of Syndermata (Rotifera + Acanthocephala). With additional sequences taken from previously published mitochondrial genomes, the total dataset included nine species of bdelloids, three species of monogononts, and two species of acanthocephalans. A supermatrix of these 10–12 mitochondrial proteins consistently recovered a bdelloid phylogeny that questions the validity of a generally accepted classification scheme despite different methods of inference and various parameter adjustments. Specifically, results showed that neither the family Philodinidae nor the order Philodinida are monophyletic as currently defined. The application of a similar analytical strategy to assess syndermate relationships recovered either a tree with Bdelloidea and Monogononta as sister taxa (Eurotatoria) or Bdelloidea and Acanthocephala as sister taxa (Lemniscea). Both outgroup choice and method of inference affected the topological outcome emphasizing the need for sequences from more closely related outgroups and more sophisticated methods of analysis that can account for the complexity of the data.</p> </div

Support for alternative bdelloid roots and major bdelloid and syndermate clades from various phylogenetic analyses.

<p>Strategy indicates 1) method of inference (ML, maximum likelihood; MB, Bayesian inference in MrBayes; PB, Bayesian inference in Phylobayes; MP, maximum parsimony), 2) model of substitution (JTT, MtRev, Mixed, and WAG, empirical amino acid models; CAT, site heterogeneous model of Phylobayes with Poisson or GTR exchange profiles), 3) and other data manipulation techniques (partitioned, alignment partitioned by proteins sharing the same model of evolution; recoded, alignments Dayhoff-recoded). The bootstrap support values and posterior probabilities for bdelloid roots as well as bdelloid and syndermate major clades recovered from these analyses are provided (P, others − bdelloid root between <i>Philodina</i> and others; M, others − bdelloid root between <i>Macrotrachela</i> and others; RHM − <i>Rotaria</i>, <i>Habrotrocha</i>, <i>Macrotrachela</i> clade; HAP – <i>Habrotrocha</i>, <i>Adineta</i>, <i>Philodina</i> clade; PRA − <i>Philodina</i>, <i>Rotaria</i>, <i>Adineta</i> clade; HRA − <i>Habrotrocha</i>, <i>Rotaria</i>, <i>Adineta</i> clade; Eurotatoria, support for Bdelloidea + Monogononta; Lemniscea, support for Bdelloidea + Acanthocephala. There are two values listed for each syndermate analysis, regular type indicates results from the Syndermata + Platyhelminthes dataset and boldface indicates results from the Syndermata + Chaetognatha dataset. lnL, log-likelihoods.</p

Possible sister relationships among lineages of Syndermata and the morphological support for each.

<p>Possible sister relationships among lineages of Syndermata and the morphological support for each.</p

Results from Dayhoff-recoding alignments to reduce compositional biases.

<p>Bold type indicates significantly deviating amino acid compositions.</p

Syndermate topology tests.

<p>The two values for each entry represent the topology tests conducted with Platyhelminthes (first value) and Chaetognatha (second value) as outgroups.Relationships tested included Lemniscea (Bdelloidea+Acanthocephala), Eurotatoria (Bdelloidea+Monogononta), and Monogononta+Acanthocephala.lnL, log likelihood; AU, P-value for approximately unbiased test; SH, P-value for Shimodaira-Hasegawa test.Boldface indicates statistical significance at the alpha level of <0.05.</p

Bdelloid phylogenies.

<p>Maximum Likelihood and Bayesian phylogenies reconstructed with concatenated mitochondrial proteins and rooted with Monogononta and Acanthocephala. Left and right trees represent two predominant topologies, where the root lies between <i>Macrotrachela</i> and the rest of the bdelloids (left) or <i>Philodina</i> and the rest of the bdelloids (right). The left tree represents the topology recovered from three analyses: 1) ML + JTT, 2) MrBayes + MtRev, and 3) Phylobayes with CAT + Poisson model. Bootstrap support values and posterior probabilities for the position of the root are listed in the order given above for each analysis. The right tree represents the topology recovered from six analyses: 1) ML + MtRev, 2) ML + Partitioned data (models were assigned to each partition and partitions were generated by grouping together genes that shared the same model) 3) ML + JTT on Dayhoff-recoded data, 4) Maximum Parsimony, 5) MrBayes + WAG, and 6) Phylobayes with CAT + GTR model. Bootstrap support values and posterior probabilities for the position of the root and the RHM clade (<i>Rotaria</i>, <i>Habrotrocha</i>, and <i>Macrotrachela</i>) are listed in the order given above for each analysis. Thicker branches indicate clades strongly supported by most analyses (bootstrap support or posterior probability >90). Red taxon labels indicate members of the family Philodinidae, green taxon labels indicate the family Habrotrochidae, and black indicates the family Adinetidae. Neither Philodinidae nor the order Philodinida is monophyletic. Line represents 0.25 amino acid substitutions per site. Summaries of strategies and support value provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043554#pone-0043554-t002" target="_blank">Table 2</a>.</p