added consensus genomes, tree files, and overview of data analysis pi…

…pelines

README.md

@@ -1,7 +1,5 @@
 # H5N1 within-host diversity in humans and poultry in Cambodia 
 
-Using deep sequence data to characterize within-host diversity in H5N1-infected humans and poultry in Cambodia
-
 #### Louise H. Moncla<sup>1</sup>, Trevor Bedford<sup>1,2</sup>, Philippe Dussart<sup>3</sup>, Philippe Buchy<sup>4</sup>, Huachen Zhu<sup>5,6</sup>, Thomas C. Friedrich<sup>7,8</sup>, Paul F. Horwood<sup>9,10</sup>
 
 <sup>1</sup>Fred Hutchinson Cancer Research Center, Seattle, Washington, United States, <sup>2</sup>University of Washington, Seattle, Washington, United States, <sup>3</sup>Virology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia, <sup>4</sup>GlaxoSmithKline, Vaccines R&D, Singapore, Singapore,<sup>5</sup>Joint Influenza Research Centre (SUMC/HKU), Shantou University Medical College, Shantou, People's Republic of China,<sup>6</sup>State Key Laboratory of Emerging Infectious Diseases/Centre of Influenza Research, School of Public Health, The University of Hong Kong, Hong Kong, SAR, People's Republic of China,<sup>7</sup>Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI, United States,<sup>8</sup>Wisconsin National Primate Research Center, Madison, WI, United States,<sup>9</sup>Papua New Guinea Institute of Medical Research, Goroka, Paula New Guinea,<sup>10</sup>Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.

data/README.md

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+# Data
+
+## Within-host data  
+All within-host variants reported in the manuscript and analyzed are available in "within-host-variants-1%.txt". This data file includes all variants present at a frequency of at least 1% in all human and duck samples. Fastq files were processed and variants called using [this pipeline](https://github.com/lmoncla/illumina_pipeline), briefly outlined below: 
+
+1. Adapter and quality trimming with [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic )
+2. Mapping with [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
+3. Manual inspection of mapping and consensus genome calling with [Geneious](https://www.geneious.com/) 
+4. Re-mapping fastq files called consensus with [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml)
+
+
+### Trimming
+Trimming was performed with [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic ) to remove Illumina adapter sequencing and ends of reads with low quality scores. Reads were trimmed in 5 bp windows to a quality score of Q30, and trimmed reads with length < 100 bp were discarded, using the following command: `java -jar Trimmomatic-0.36/trimmomatic-0.36.jar SE input.fastq output.fastq ILLUMINACLIP:Nextera_XT_adapter.fa:1:30:10 SLIDINGWINDOW:5:30 MINLEN:100`
+
+### Mapping 
+We performed a local mapping of our trimmed reads to reference sequences previously released by [Rith et al.](https://jvi.asm.org/content/88/23/13897.long) using [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml), with the following command:` bowtie2 -x reference_sequence.fasta -U read1.trimmed.fastq,read2.trimmed.fastq -S output.sam --local`
+
+The mapping (bam) file was manually inspected in [Geneious](https://www.geneious.com/). 
+
+### Consensus sequence calling
+Consensus sequences were called in Geneious, with nucleotide sites with <100x coverage called as Ns. Consensus genomes were exported in fasta format and are available [here](https://github.com/blab/h5n1-cambodia/tree/master/data/h5n1-consensus-genomes.fasta).
+
+### Remapping
+To avoid issues with mapping to improper reference sequences, we then remapped each sample's fastq files to its own consensus sequence. These bam files were again manually inspected in Geneious, and a final consensus sequence was called. Those consensus genomes for which we acquired at least 80% full-genome coverage are available [here](https://github.com/blab/mumps-seq/tree/master/data/consensus-genomes) as fasta files. 
+
+### Variant calling
+Variants were called using [Varscan](http://varscan.sourceforge.net/), requiring  minimum coverage of 100x at the polymorphic site, a minimum quality of Q30, and a minimum SNP frequency of 1% with the following command: `java -jar VarScan.v2.3.9.jar mpileup2snp input.pileup --min-coverage 100 --min-avg-qual 30 --min-var-freq 0.01 --strand-filter 1 --output-vcf 1 > output.vcf`
+
+### Amino acid annotation
+Coding region changes were annotated using [this jupyter notebook](https://github.com/blab/h5n1-cambodia/tree/master/scripts).
+
+## Consensus genomes 
+All consensus sequences are available [here](https://github.com/blab/mumps-seq/tree/master/data/consensus-genomes). The fasta header contains the following information: strain name | sample collection date | country of sampling | host species. 
+
+
+## Trees 
+Tree files shown in Figure 1 are available in json format [here](https://github.com/blab/h5n1-cambodia/tree/master/data/tree-jsons). These jsons were generated using the (Nextstrain avian-flu)[https://github.com/nextstrain/avian-flu] pipeline with no geographic or regional subsampling. 

data/consensus-genomes/cambodia-h5n1-mp.fasta

@@ -0,0 +1,26 @@
+>A/Cambodia/X0128304/2013|2013-01-27|cambodia|human
+AGCAAAAGCAGGTAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAAACTTGAGGATGTATTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTTTGACTAAAGGGATCTTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAGAATGCCCTAAATGGAAATGGAGATCCAAATAATATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGAGCTAAGGAGGTCTCACTCAGTTACTCAACAGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACCACGGAAGTGGCTTTTGGCCTAGTGTGTGCCACCTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGGCATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAAAGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCGGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/Cambodia/V0417301/2011|2011-04-16|cambodia|human
+TAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAAACTTGAGGATGTCTTTGCAGGAAAGAACACAGATCTTGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAAGGGATCTTAGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGATTTGTCCAGAACGCCCTAAATGGAAATGGAGATCCAAATAACATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCCAGTTGCATGGGTCTCATTTACAACAGGATGGGAACGGTGACTACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACTTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATTAGACATGAAAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCTAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAACGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTATTGTTGTTGCCGCAAATATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTTTTCAAATGCATTTATCGTCGCCTCAAATACGATTTGAAAAGGGGCCCTGCTACGGCAGGGATACCTGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAGTGCTGTAGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/Cambodia/X0219301/2013|2013-02-18|cambodia|human
+TAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAAACTTGAGGATGTATTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTTTGACTAAAGGGATCTTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAGAATGCCCTAAATGGAAATGGAGATCCAAATAATATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGAGCTAAGGAGGTCTCACTCAGTTACTCAACAGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACCACGGAAGTGGCTTTTGGCCTAGTGTGCGCCACCTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGGCATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAAAGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCGGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTAC
+>A/Cambodia/W0112303/2012|2012-01-10|cambodia|human
+AGCAAAAGCAGGTAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGATCGCACAGAAACTTGAGGATGTCTTTGCAGGAAAGAACACAGATCTTGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAAGGGATCTTAGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAGAACGCCCTAAATGGAAATGGAGATCCAAATAACATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACTGTGACTACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACTTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGACATGAAAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCTAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCATACCAGAAACGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTATTGTTGTTGCCGCAAATATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTTTTCAAATGCATTTATCGTCGCCTCAAATACGATTTGAAAAGGGGCCCTGCTACGGCAGGGATACCTGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAGTGCTGTAGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/Cambodia/X0125302/2013|2013-01-25|cambodia|human
+TAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAAACTTGAGGATGTATTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTTTGACTAAAGGGATCTTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAGAATGCCCTAAATGGAAATGGAGATCCAAATAATATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGAGCTAAGGAGGTCTCACTCAGTTACTCAACAGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACCACGGAAGTGGCTTTTGGCCTAGTGTGTGCCACCTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGGCATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAAAGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCGGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/Cambodia/X1030304/2013|2013-10-25|cambodia|human
+GCAAAAGCAGGTAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAAACTTGAGGATGTATTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTTTGACTAAAGGGATCTTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAGAATGCCCTAAATGGAAATGGAGATCCAAATAATATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGAGCTAAGGAGGTCTCACTCAGTTACTCAACAGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACCACGGAAGTGGCTTTTGGCCTAGTGTGTGCCACCTGTGAGCAGATTGCGGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGGCATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAAAGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCGGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/Cambodia/V0401301/2011|2011-03-31|cambodia|human
+AGCAAAAGCAGGTAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAAACTTGAGGATGTCTTTGCAGGGAAAAACACAGATCTTGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAAGGGATCTTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAGAACGCCCTAAATGGAAATGGAGATCCAAATAACATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACTACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACCTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACTATCACCAACCCACTAATCAGACATGAAAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCGGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTTTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAACGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTATTGTTGTTGCCGCAAATATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTCCAAATGCATTTATCGTCGCCTTAAATACGATTTGAAAAGAGGCCCTGCTACGGCAGGGATACCTGAGTCTATGAGGGAAGAGTACCGGCAGGAGCAGCAGAGTGCTGTAGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/Cambodia/X0207301/2013|2013-02-06|cambodia|human
+AGCAGGTAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAAGCTTGAGGATGTATTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTTTGACTAAAGGGATCTTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAGAATGCCCTAAATGGAAATGGAGATCCAAATAATATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGAGCTAAGGAGGTCTCACTCAGTTACTCAACAGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACCACGGAAGTGGCTTTTGGCCTAGTGTGTGCCACCTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGGCATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAAAGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCGGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/duck/Cambodia/381W11M4/2013|2013-03-15|cambodia|avian
+GCAGGTAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAAACTTGAGGATGTATTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCTTGTCACCTTTGACTAAAGGGATCTTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAGAATGCCCTAAATGGAAATGGAGATCCAAATAATATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGAGCTAAGGAGGTCTCACTCAGTTACTCAACAGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACCACGGAAGTGGCTTTTGGCCTAGTGTGCGCCACCTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGGCATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAAAGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCGGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCT
+>A/duck/Cambodia/PV027D1/2010|2010-04-30|cambodia|avian
+AGCAAAAGCAGGTAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAAACTTGAGGATGTCTTTGCAGGAAAGAACACAGATCTTGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAAGGGATCTTAGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAGAACGCCCTAAATGGAAATGGAGATCCAAATAACATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACTACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACTTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGACATGAAAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCTAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAACGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTATTGTTGTTGCCGCAAATATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTTTTCAAATGCATTTATCGTCGCCTCAAATACGATTTGAAAAGGGGCCCTGCTACGGCAGGGATACCTGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAGTGCTGTAGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/duck/Cambodia/083D1/2011|2011-09-08|cambodia|avian
+ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGATCGCGCAGAAACTTGAAGATGTCTTTGCAGGAAAGAACACAGATCTTGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTCTGACTAAAGGGATCTTAGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGCTTTGTCCAGAACGCCCTAAATGGAAATGGAGATCCAAATAACATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGGGCTAAGGAGGTCGCACTCAGCTACTCAACCGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACTACAGAAGTGGCTTTTGGCCTAGTGTGTGCCACTTGTGAGCAGATTGCTGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGACATGAAAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCTAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAACGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTATTGTTGTTGCCGCAAATATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTTTTCAAATGCATTTATCGTCGCCTCAAATACGATTTGAAAAGGGGCCCTGCTACGGCAGGGATACCTGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAGTGCTGTAGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/duck/Cambodia/Y0224301/2014|2014-02-18|cambodia|avian
+GGTAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAAACTTGAGGATGTATTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTTTGACTAAAGGGATATTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAGAATGCCCTAAATGGAAATGGAGATCCAAATAATATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGAGCTAAGGAGGTCTCACTCAGTTACTCAACAGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACGGTGACCACGGAAGTGGCTTTTGGCCTAGTGTGTGCCACCTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGACATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCGGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGAACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAAAGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCGGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTACT
+>A/duck/Cambodia/Y0224304/2014|2014-02-19|cambodia|avian
+TAGATGTTGAAAGATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTCTCTATCATCCCATCAGGCCCCCTCAAAGCCGAGATCGCACAGAAACTTGAGGATGTATTTGCAGGAAAGAACACCGATCTCGAGGCTCTCATGGAGTGGCTAAAGACAAGACCAATCCTGTCACCTTTGACTAAAGGGATCTTGGGATTTGTATTCACGCTCACCGTGCCCAGTGAGCGAGGACTGCAGCGTAGACGTTTTGTCCAGAATGCCCTAAATGGAAATGGAGATCCAAATAATATGGATAGGGCAGTTAAGCTATATAAGAAGCTGAAAAGAGAAATAACATTCCATGGAGCTAAGGAGGTCTCACTCAGTTACTCAACAGGTGCACTTGCCAGTTGCATGGGTCTCATATACAACAGGATGGGAACAGTGACCACGGAAGTGGCTTTTGGCCTAGTGTGTGCCACCTGTGAGCAGATTGCAGATTCACAGCATCGGTCTCACAGACAGATGGCAACCATCACCAACCCACTAATCAGACATGAGAACAGAATGGTGCTGGCCAGCACTACAGCTAAGGCTATGGAGCAGATGGCGGGATCAAGTGAGCAGGCAGCAGAAGCCATGGAGATCGCCAATCAGGCTAGGCAGATGGTGCAGGCAATGAGGACAATTGGGACTCATCCTAACTCTAGTGCTGGTCTGAGAGATAATCTTCTTGAAAATTTGCAGGCCTACCAGAAAAGAATGGGAGTGCAGATGCAACGATTCAAGTGATCCTCTTGTTGTTGCCGCAAGTATCATTGGGATCTTGCACTTGATATTGTGGATTCTTGATCGTCTTTTCTTCAAATGCATTTATCGTCGCCTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGGGTACCGGAGTCTATGAGGGAAGAGTACCGGCAGGAACAGCAGAATGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAATTGGAGTAAAAAACTACCTTGTTTCTAC