Curate reference tree: remove recombinant/frameshifted/low-quality sequences

data/enpen/enterovirus/cva16/CHANGELOG.md

@@ -1,3 +1,7 @@
+## Unreleased
+
+The dataset was manually curated to remove recombinant, frameshifted, and other low-quality sequences, including several recombinants from Xu et al. (2025). Single recombinants were excluded, but recurring circulating recombinant forms (e.g. a 5'UTR recombinant) were kept to preserve tree diversity. Some sequences with apparent frameshifts were also kept, since they show normal evolution and tree topology.
+
 ## 2026-04-22T11:53:11Z
 
 Initial release of a Coxsackievirus A16 dataset for lineage classification!

data/enpen/enterovirus/cva16/README.md

@@ -2,11 +2,11 @@
 
 | Key                  | Value                                                                 |
 |----------------------|-----------------------------------------------------------------------|
-| authors              | [Nadia Neuner-Jehle](https://eve-lab.org/people/nadia-neuner-jehle/), [Alejandra González-Sánchez](https://www.vallhebron.com/en/professionals/alejandra-gonzalez-sanchez), [Emma B. Hodcroft](https://eve-lab.org/people/emma-hodcroft/), [ENPEN](https://escv.eu/european-non-polio-enterovirus-network-enpen/)                                                 |
-| name                 | Coxsackievirus A16                                                     |
+| authors              | [Nadia Neuner-Jehle](https://eve-lab.org/people/nadia-neuner-jehle/), [Alejandra González-Sánchez](https://www.vallhebron.com/en/professionals/alejandra-gonzalez-sanchez), [Emma B. Hodcroft](https://eve-lab.org/people/emma-hodcroft/), [ENPEN](https://escv.eu/european-non-polio-enterovirus-network-enpen/)                         |
+| name                 | Coxsackievirus A16                                                    |
 | reference            | [Static Inferred Ancestor](https://github.com/enterovirus-phylo/nextclade_a16/blob/master/resources/inferred-root.fasta)               |
-| workflow             | https://github.com/enterovirus-phylo/nextclade_a16                          |
-| path                 | `enpen/enterovirus/cva16`                                                                 |
+| workflow             | <https://github.com/enterovirus-phylo/nextclade_a16>                  |
+| path                 | `enpen/enterovirus/cva16`                                             |
 | clade definitions    | A–F                                                                   |
 
 ## Scope of this dataset
@@ -27,15 +27,15 @@ This dataset supports:
 
 ## Subgenogroups of Coxsackievirus A16
 
-Subgenogroups B1a, B1b and B1c represent the major phylogenetic divisions of CVA16 and are commonly used in virological surveillance and the literature. They are defined based on phylogenetic clustering and do not necessarily reflect antigenic differences. 
+Subgenogroups B1a, B1b and B1c represent the major phylogenetic divisions of CVA16 and are commonly used in virological surveillance and the literature. They are defined based on phylogenetic clustering and do not necessarily reflect antigenic differences.
 
 In recent years, additional recombinant forms have been identified and labeled C-F (also referred to as B2, B3, and D). These recombinant forms cluster with the prototype strain (clade A).
 
 Overall, these designations are based on phylogenetic structure and characteristic mutations, and are widely used in molecular epidemiology, similar to subgenotype systems for other enteroviruses. Unlike influenza (H1N1, H3N2) or SARS-CoV-2, there is no universally standardized global lineage nomenclature for enteroviruses; naming instead follows conventions established in published studies and surveillance practices.
 
 ## Related Enteroviruses
 
-CVA16 is closely related to other Enterovirus A (EV-A) viruses, including EV-A71, EV-A120, and CVA5. If you are not certain that your sequences contain only CVA16, we recommend using the "[Multiple Datasets](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-web/getting-started.html#multi-dataset-mode)" tab instead of "Single Dataset". We are currently working on improving multiple virus assignment. 
+CVA16 is closely related to other EV-A viruses, including EV-A71, EV-A120, and CVA5. If you are not certain that your sequences contain only CVA16, we recommend using the "[Multiple Datasets](https://docs.nextstrain.org/projects/nextclade/en/stable/user/nextclade-web/getting-started.html#multi-dataset-mode)" tab instead of "Single Dataset".
 
 This prevents Nextclade from forcing sequences to align to the CVA16 reference tree. For example, EV-A71 sequences may still align and receive a clade assignment (often near recombinant forms).
 
@@ -46,6 +46,7 @@ If you are unsure how to proceed, please contact us. We are happy to assist.
 ## Reference types
 
 This dataset includes several reference points used in analyses:
+
 - *Static Inferred Ancestor:* Reconstructed ancestral sequence inferred with an outgroup, representing the likely founder of CVA16. Serves as a stable reference.
 
 - *Parent:* The nearest ancestral node of a sample in the tree, used to infer branch-specific mutations.
@@ -59,6 +60,7 @@ This dataset includes several reference points used in analyses:
 All references use the coordinate system of the G-10 sequence.
 
 ## Issues & Contact
+
 - For questions or suggestions, please [open an issue](https://github.com/enterovirus-phylo/nextclade_a16/issues) or email: eve-group[at]swisstph.ch
 
 ## What is a Nextclade dataset?