DOI: 10.5061/dryad.r2280gbcw
title: Information and sequences of the six lineages identified in the H1N1 influenza A virus

description: The influenza virus mutates and spreads rapidly, making it an ideal model
 for studying evolutionary and ecological processes. The ecological factors
 and processes by which different lineages compete or coexist within hosts,
 through time and across geographical space are poorly known. We
 hypothesize that competition would be higher for influenza viruses sharing
 the same host than those sharing different hosts (Host Barrier
 Hypothesis), or for influenza viruses with a higher cross-region
 transmission intensity than those with a lower cross-region transmission
 intensity (Geographic Barrier Hypothesis). Using available sequences of
 influenza A (H1N1) virus in GenBank we identified six lineages of H1N1 and
 twelve clades with several replacement events. We found the human-hosted
 lineages had a higher cross-region transmission intensity than
 swine-hosted lineages. The estimated co-occurrence probability of lineages
 sharing the same host is much lower than those sharing different hosts,
 and human-hosted lineages had lower co-occurrence probability and genetic
 diversity than swine-hosted lineages. Our results indicate that H1N1
 lineages sharing the same host or having a higher cross-region
 transmission intensity experienced a higher competition and extinction
 pressure. Our study highlights the significant roles of the host and
 geographic barriers in shaping the competition, extinction and coexistence
 patterns of H1N1 lineages or clades.
description: We collected
 H1N1 IAV sequence data from GenBank (https://www.ncbi.nlm.nih.gov/) and
 extracted the sequences encoding Hemagglutinin (HA). The datasets included
 32,759 H1N1 virus records from the first case reported on May 11, 1918, to
 the latest case reported on October 30, 2018 and included the sampling
 location and date information for each report. We assigned the sampling
 location with the latitude and
 longitude based on the administrative center
 coordinates. We excluded samples without accurate
 sampling dates (i.e. daily resolution) or strain codes, as well as those
 with sequence &lt; 1600 bp (making up 29.8% of the total sequences) in
 length. To reduce the impacts of sampling effort bias on the research, we
 only used one sample from the same place in the same month (25.9% of total
 sequences were removed). Finally, 6097 samples of H1N1 virus from 1279
 locations were used (Fig. S1). For subsequent analysis at the amino acid
 codon level, all sequences were aligned using an H1N1 sequence
 (A/swine/Hong Kong/61/1977) as a template sequence and all GAPs and
 redundant bases were manually deleted according to the template sequence
 so that the sequence could be converted to codons. We
 divided the cleaned sequences into three host types: human, swine and
 avian based on the sample’s host type. We calculated the genetic distance
 (GD) between each sequence and the oldest sequence (A/swine/Hong Kong/61/1977) in
 all cleaned sequences. Then we plotted GD vs. sampling date separately for
 each host type. Based on the molecular clock theory, the mutation rate of
 H1 can be considered constant, and six lineages were readily identified
 using linear relationships between GD and sampling time (see Fig. 1A).
 According to the similarities and differences when influenza viruses
 infect their hosts, influenza virus hosts are generally divided into three
 categories: humans, pigs and birds，and most of the spread of influenza A
 viruses occurs between the same host categories. Thus, we use the
 following criteria to identify the lineage of the samples: (1) infect the
 same host categories; (2) the samples form close and continuous cluster on
 the two-dimensional space formed by GD and sampling time.
description: The explanation of each variable in the dataset is as
 follows: id: the virus name lat:
 latitude lon: longitude time:
 sampling time of the virus seqs: aligned HA-gene
 sequences of the virus host: host type
 year: sampling year