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Whole genome sequencing and phylogenetic analysis of Human metapneumovirus strains from Kenya and Zambia
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Kamau, Everlyn, Oketch, John W., de Laurent, Zaydah R., Phan, My V. T., Agoti, Charles N., Nokes, D. James and Cotton, Matthew (2020) Whole genome sequencing and phylogenetic analysis of Human metapneumovirus strains from Kenya and Zambia. BMC Genomics, 21 (5). doi:10.1186/s12864-019-6400-z ISSN 1471-2164.
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Official URL: https://doi.org/10.1186/s12864-019-6400-z
Abstract
Background
Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in young children. Whole genome sequencing enables better identification of transmission events and outbreaks, which is not always possible with sub-genomic sequences.
Results
We report a 2-reaction amplicon-based next generation sequencing method to determine the complete genome sequences of five HMPV strains, representing three subgroups (A2, B1 and B2), directly from clinical samples. In addition to reporting five novel HMPV genomes from Africa we examined genetic diversity and sequence patterns of publicly available HMPV genomes. We found that the overall nucleotide sequence identity was 71.3 and 80% for HMPV group A and B, respectively, the diversity between HMPV groups was greater at amino acid level for SH and G surface protein genes, and multiple subgroups co-circulated in various countries. Comparison of sequences between HMPV groups revealed variability in G protein length (219 to 241 amino acids) due to changes in the stop codon position. Genome-wide phylogenetic analysis showed congruence with the individual gene sequence sets except for F and M2 genes.
Conclusion
This is the first genomic characterization of HMPV genomes from African patients.
| Item Type: | Journal Article | |||||||||
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| Subjects: | Q Science > QH Natural history > QH426 Genetics R Medicine > RA Public aspects of medicine |
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| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | |||||||||
| Library of Congress Subject Headings (LCSH): | Paramyxoviruses -- Genetics, Respiratory organs -- Diseases, Variation (Biology), Genetics, Genomes | |||||||||
| Journal or Publication Title: | BMC Genomics | |||||||||
| Publisher: | BioMed Central Ltd. | |||||||||
| ISSN: | 1471-2164 | |||||||||
| Official Date: | 2 January 2020 | |||||||||
| Dates: |
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| Volume: | 21 | |||||||||
| Number: | 5 | |||||||||
| DOI: | 10.1186/s12864-019-6400-z | |||||||||
| Status: | Peer Reviewed | |||||||||
| Publication Status: | Published | |||||||||
| Access rights to Published version: | Open Access (Creative Commons) | |||||||||
| Date of first compliant deposit: | 16 December 2019 | |||||||||
| Date of first compliant Open Access: | 11 May 2020 | |||||||||
| RIOXX Funder/Project Grant: |
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