Computational protocol: Increased Cytomegalovirus Secretion and Risks of Infant Infection by Breastfeeding Duration From Maternal Human Immunodeficiency Virus Positive Compared to Negative Mothers in Sub-Saharan Africa

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Protocol publication

[…] Human cytomegalovirus gO (UL74 gene) genotyping was performed on a subset of 34 milk samples with sufficient remaining volume. Based on translated amino acid sequences, HCMV gO (UL74 gene) has 8 distinct genotypes: gO1a, gO1b, gO1c, gO2a, gO2b, gO3, gO4, and gO5 [, ]. We used PCR-based genotyping with the gOup/gOlw primers, which detected all 8 gO genotypes. Nucleotide sequences were determined using Sanger methods [, ] and compiled using ChromasPro software. Multiple alignments used CLUSTAL and phylogenetic analysis via maximum-likelihood methods in MEGA6 []. […]

Pipeline specifications

Software tools ChromasPro, MEGA
Application Phylogenetics
Organisms Homo sapiens, Human immunodeficiency virus 2, Human betaherpesvirus 5
Diseases Cytomegalovirus Infections, HIV Infections