Oropouche blog post

static-site/content/blog/2024-06-18-oropouche-analysis-and-resources.md

@@ -0,0 +1,69 @@
+---
+author: "Miguel Paredes, James Hadfield, John Anderson, Jover Lee, Trevor Bedford"
+date: "2024-10-18"
+title: "Phylogenetic analysis of Oropuche Virus"
+sidebarTitle: "Oropouche Phylogenetic Analysis and Resources"
+---
+
+# Phylogenetic analysis
+
+[Oropouche virus](https://www.sciencedirect.com/science/article/pii/S016817022400011X#sec0003) is a segmented, negative-sense, single-stranded RNA virus from the Orthobunyavirus genus. It is the causative agent of Oropouche fever: an often self-limited, non-specific disease characterized by headache, arthralgia, myalgia, nausea, vomiting, chills, and/or photophobia. Oropouche virus is maintained primarily through an enzootic cycle between pale-throated sloths (Bradypus tridactylus), non-human primates and other wild mammals via transmission through Culicoides paraensis midges, with urbanization contributing to the rise of human cases acquired through the same arthropod vector (**Fig. 1**).
+
+
+[![fig1](img/oropouche_host_view.png)](https://nextstrain.org/oropouche/L?c=host)
+**Figure 1.  Time-resolved phylogeny for the L segment highlighting the host the sequence was acquired from.** 98% of sequences in our sample are human, so we have very limited information into the host reservoir dynamics.
+
+Since its original description in 1955 in Trinidad and Tobago, Oropouche virus has caused multiple local outbreaks throughout Latin America, primarily in Amazonian states of Brazil (**Fig. 2**).
+
+[![fig2](img/oropouche_country_map.png)](https://nextstrain.org/oropouche/L?p=grid)
+**Figure 2. Geographic spread of Oropouche virus in the Americas.**
+
+Since late 2023, however, there has been a documented increase in local cases not only in Brazil but also in Cuba, Bolivia, Colombia, Peru, as well as travel-associated cases not only throughout the Americas but in Europe as well. [In 2024 alone](https://www.paho.org/en/documents/epidemiological-update-oropouche-americas-region-6-september-2024), there have been more than 9,800 confirmed cases, including two deaths. We find the majority of cases in 2023-2024 nested within the diversity of the viruses sampled in Brazil, suggesting Brazil as a main source (**Fig. 3**). Alternatively, we also see [evidence of a separate, ongoing lineage in Peru.](https://nextstrain.org/staging/oropouche/L?f_country=Peru) 
+
+
+[![fig3](img/oropouche_recent_seqs.png)](https://nextstrain.org/oropouche/L?dmin=1986-01-01&p=full)
+**Figure 3. L segment tree shows the 2023-2024 sequences from Brazil clustering together.** Sequences from Cuba, Colombia and Ecuador nest within the diversity of this Brazilian clade. Concurrently, we also see an ongoing lineage in Peru that is separate from the Brazilian clade. 
+
+Oropouche virus has a segmented genome made up of the L (Large), M (Medium), and S (Small) segments; phylogenetic trees for these segments are constructed independently: 
+- [https://nextstrain.org/oropouche/L](https://nextstrain.org/oropouche/L) 
+- [https://nextstrain.org/oropouche/M](https://nextstrain.org/oropouche/M) 
+- [https://nextstrain.org/oropouche/S](https://nextstrain.org/oropouche/S)
+
+The segmented nature of Oropouche virus allows for genetic reassortment events. Similarly to [Gutierrez et al.](https://pmc.ncbi.nlm.nih.gov/articles/PMC7022353/), all three phylogenies display topographical differences, suggesting the presence of reassortment events on the genome. For example, while the phylogenies of the L and M segments show more robust clustering of the sequences from Brazil throughout time, the S segment phylogeny shows the Brazil sequences scattered throughout the tree  (**Fig. 4**). If we focus on the most recent sequences from 2022-2024, however, we do find more robust clustering of the sequences from Brazil, similar to the results presented by [Naveca et al](https://www.nature.com/articles/s41591-024-03300-3). 
+
+
+[![fig4](img/oropouche_s_and_m_segment.png)](https://nextstrain.org/oropouche/M:oropouche/S)
+**Figure 4. Comparison of the M (top) and S (bottom) segment trees shows distinct topographical differences, suggesting the presence of reassortment events.**
+
+
+We can track the co-evolution of the Oropouche segments via tanglegrams. For example, if we focus on the L and M segments (**Fig. 5**), we can see evidence of at least two recombination events.
+
+
+[![fig5](img/oropouche_tanglegram.png)](https://nextstrain.org/oropouche/L:oropouche/M)
+**Figure 5. Tanglegram of L and M segments.**
+
+# Nextstrain resources
+
+## Curated sequences and metadata
+
+We curate sequence data and metadata from NCBI as the starting point for our analyses. Curated sequences and metadata are available as flat files at:
+
+L segment
+
+- [data.nextstrain.org/files/workflows/oropouche/L/sequences.fasta.zst](data.nextstrain.org/files/workflows/oropouche/L/sequences.fasta.zst)
+- [data.nextstrain.org/files/workflows/oropouche/L/metadata.tsv.zst](data.nextstrain.org/files/workflows/oropouche/L/metadata.tsv.zst)
+
+M segment
+
+- [data.nextstrain.org/files/workflows/oropouche/M/sequences.fasta.zst](data.nextstrain.org/files/workflows/oropouche/M/sequences.fasta.zst)
+- [data.nextstrain.org/files/workflows/oropouche/M/metadata.tsv.zst](data.nextstrain.org/files/workflows/oropouche/M/metadata.tsv.zst)
+
+S segment
+
+- [data.nextstrain.org/files/workflows/oropouche/S/sequences.fasta.zst](data.nextstrain.org/files/workflows/oropouche/S/sequences.fasta.zst)
+- [data.nextstrain.org/files/workflows/oropouche/S/metadata.tsv.zst](data.nextstrain.org/files/workflows/oropouche/S/metadata.tsv.zst
+)
+
+# Acknowledgements
+
+We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequences and metadata for sharing their work. Many of the recent sequences come from various publications and preprints, such as [Naveca et al.](https://www.nature.com/articles/s41591-024-03300-3), [Scachetti et al.](https://www.medrxiv.org/content/10.1101/2024.07.27.24310296v1.full), [Iani et al.](https://www.medrxiv.org/content/10.1101/2024.08.02.24311415v2.full), among others.