Datasets Comparison

HAdV Genetic Diversity Assessment Two approaches strategies were used to select representative worldwide human adenovirus (HAdV) sequences. The first approach consisted of a bibliographic search of respiratory HAdV epidemiology in different geographical locations performed in Pubmed. The second approach included searches in Nuccore (https://ncbi.nlm.nih.gov/nuccore). For this strategy several keyword combinations were tested. Best results were achieved with “human Adenovirus” OR “mastadenovirus” AND “hexon” AND a number or name indicating the type and or adenovirus species. Several genotypes had received different names over the time (e.g. genome type 11a and genotype 55) thus requiring several searches to include these sequences. All searches were perform on July 23th 2019. Because some of the downloaded sequences were suspiciously divergent a pairwise alignment of each sequence against the reference dataset was performed with FASTA36 software [1] to both unequivocally assign genotype and region. Genotype was assigned by sequence identity. A minimum 80% sequence coverage of the partial hexon region (HVR 1-6) was required for inclusion in the final dataset. With this procedure we were able to use some sequences that were erroneously annotated as belonging to a different genotype (even species) and parts of sequences that were uploaded as a concatenation of different genomic regions.

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Respiratory Virology

Creative Commons Attribution 4.0 International

HAdV Genetic Diversity Assessment Two approaches strategies were used to select representative worldwide human adenovirus (HAdV) sequences. The first approach consisted of a bibliographic search of respiratory HAdV epidemiology in different geographical locations performed in Pubmed. The second approach included searches in Nuccore (https://ncbi.nlm.nih.gov/nuccore). For this strategy several keyword combinations were tested. Best results were achieved with “human Adenovirus” OR “mastadenovirus” AND “hexon” AND a number or name indicating the type and or adenovirus species. Several genotypes had received different names over the time (e.g. genome type 11a and genotype 55) thus requiring several searches to include these sequences. All searches were perform on July 23th 2019. Because some of the downloaded sequences were suspiciously divergent a pairwise alignment of each sequence against the reference dataset was performed with FASTA36 software [1] to both unequivocally assign genotype and region. Genotype was assigned by sequence identity. A minimum 80% sequence coverage of the partial hexon region (HVR 1-6) was required for inclusion in the final dataset. With this procedure we were able to use some sequences that were erroneously annotated as belonging to a different genotype (even species) and parts of sequences that were uploaded as a concatenation of different genomic regions.

, ,

Respiratory Virology

Creative Commons Attribution 4.0 International