diff --git a/config/description.md b/config/description.md index 7cdae654..e92c684b 100644 --- a/config/description.md +++ b/config/description.md @@ -1,11 +1,12 @@ We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Please note that although data generators have generously shared data in an open fashion, that does not mean there should be free license to publish on this data. Data generators should be cited where possible and collaborations should be sought in some circumstances. Please try to avoid scooping someone else's work. Reach out if uncertain. -We maintain two views of MPXV evolution: +We maintain three views of MPXV evolution: -The first is [`monkeypox/hmpxv1`](https://nextstrain.org/monkeypox/hmpxv1), which focuses on recent viruses transmitting from human-to-human and includes viruses belonging to the hMPXV1 clade as denoted by [Happi et al](https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853). Here, we conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 × 10-5 subs per site per year). +The first is [`mpox/mpxv-IIb-B.1`] (https://nextstrain.org/mpox/mpxv-IIb-B.1), which focuses on lineage B.1 of the global outbreak that started in 2022 and includes as many sequences as possible. Here, we conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 × 10-5 subs per site per year). -The second is [`monkeypox/mpxv`](https://nextstrain.org/monkeypox/mpxv), which focuses on broader viral diversity and includes viruses from the animal reservoir and previous human outbreaks, encompassing clades I, IIa and IIb as described in [Happi et al](https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853) with and recently endorsed by a [WHO convened consultation](https://worldhealthorganization.cmail20.com/t/ViewEmail/d/422BD62D623B6A3D2540EF23F30FEDED/F75AF81C90108C72B4B1B1F623478121?alternativeLink=False). +The second is [`mpox/mpxv-IIb`](https://nextstrain.org/mpox/mpxv-IIb), which focuses on recent viruses transmitting from human-to-human and includes viruses belonging to clade IIb. All good quality sequences that are not lineage B.1 are included, while lineage B.1 sequences is heavily subsampled to allow non-B.1 diversity to be studied.Here, we also conduct a molecular clock analysis in which evolutionary rate is estimated from the data (with a resulting estimate of ~6 × 10-5 subs per site per year). +The third is [`mpox/mpxv`](https://nextstrain.org/monkeypox/mpxv), which focuses on broader viral diversity and includes viruses from the animal reservoir and previous human outbreaks, encompassing clades I, IIa and IIb as described in [Happi et al](https://virological.org/t/urgent-need-for-a-non-discriminatory-and-non-stigmatizing-nomenclature-for-monkeypox-virus/853) and recently endorsed by a [WHO convened consultation](https://worldhealthorganization.cmail20.com/t/ViewEmail/d/422BD62D623B6A3D2540EF23F30FEDED/F75AF81C90108C72B4B1B1F623478121?alternativeLink=False). #### Analysis Our bioinformatic processing workflow can be found at [github.com/nextstrain/monkeypox](https://github.com/nextstrain/monkeypox) and includes: