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trvrb committed Sep 28, 2019
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# Rapid spread of a reassortant A/H3N2 virus during the 2017-2018 influenza season
# Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

#### Barney I. Potter<sup>1</sup>, Rebecca Garten<sup>2</sup>, James Hadfield<sup>1</sup>, John Huddleston<sup>1,3</sup>, John Barnes<sup>2</sup>, Thomas Rowe<sup>2</sup>, Lizheng Guo<sup>2</sup>, Xiyan Xu<sup>2</sup>, Richard A. Neher.<sup>4,5</sup>, Trevor Bedford<sup>1</sup>, and David E. Wentworth<sup>2</sup>

<sup>1</sup>Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA, <sup>2</sup>Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA, <sup>3</sup>Molecular and Cellular Biology program, University of Washington, Seattle, WA, USA, <sup>4</sup>Biozentrum, University of Basel, Switzerland, <sup>5</sup>SIB Swiss Institute of Bioinformatics, Basel, Switzerland

## Abstract
The 2017-2018 North American influenza season caused more hospitalizations and deaths than any year since the 2009 H1N1 pandemic.
The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the viruss North American diversity falling into the A2 clade.
The majority of recorded influenza infections were caused by A(H3N2) viruses, with most of the virus's North American diversity falling into the A2 clade.
Within A2, we observe a subclade which we call A2/re that rose to comprise almost 70\% of A(H3N2) viruses circulating in North America by early 2018.
Unlike most fast-growing clades, however, A2/re contains no amino acid substitutions in the hemagglutinin (HA) segment.
Moreover, HI assays did not suggest substantial antigenic differences between A2/re viruses and viruses sampled during the 2016-2017 season.
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## Analyses
For this analysis, we manage software requirements using [conda](https://conda.readthedocs.io/en/latest/), a package manager that supports independent environments.
For the bulk of this analysis, we use tools from the [Nextstrain](nextstrain.org) pipeline.
For the bulk of this analysis, we use tools from the [Nextstrain](nextstrain.org) platform.

### Install requirements
1. Install Conda and ensure that the installation was successful.
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git clone https://github.com/nextstrain/augur.git
git clone https://github.com/auspice.git
```
4.
Download sequence data from [GISAID Epiflu](https://www.gisaid.org/) database according to instructions [here](https://github.com/nextstrain/fauna/blob/master/builds/FLU.md#upload-documents-to-vdb).
4. Download sequence data from [GISAID Epiflu](https://www.gisaid.org/) database according to instructions [here](https://github.com/nextstrain/fauna/blob/master/builds/FLU.md#upload-documents-to-vdb).
Sequences were prepared for processing using the [fauna](https://github.com/nextstrain/fauna/blob/master/builds/FLU.md#upload-documents-to-vdb) pipeline.
A full list of accessions used in this analysis after being processed by fauna can be found [here](data/analysis_references.tsv)

All phylogenetic analyses were performed on the [`all-segments` branch of augur](https://github.com/nextstrain/augur/tree/all_segments).
## Citation

[Potter BI, Garten R, Hadfield J, Huddleston J, Barnes J, Rowe T, Guo L, Xu X, Neher RA, Bedford T, Wentworth D 2019. Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season. bioRxiv: 543322..](https://doi.org/10.1101/543322)

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