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A cluster of human immunodeficiency virus Type 1 recombinant form escaping detection by commercial genomic amplification assays
Author(s) -
Foglieni Barbara,
Candotti Daniel,
Guarnori Irene,
Raffaele Livia,
Berzuini Alessandra,
Spreafico Marta,
Orani Anna,
Rossotti Roberto,
Rossi Davide,
Allain JeanPierre,
Prati Daniele
Publication year - 2011
Publication title -
transfusion
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.045
H-Index - 132
eISSN - 1537-2995
pISSN - 0041-1132
DOI - 10.1111/j.1537-2995.2010.02942.x
Subject(s) - nat , viremia , recombinant dna , virology , viral load , human immunodeficiency virus (hiv) , nucleic acid test , biology , virus , genome , lentivirus , medicine , viral disease , gene , genetics , covid-19 , disease , computer network , computer science , infectious disease (medical specialty) , pathology
BACKGROUND: Nucleic acid testing (NAT)‐based methods for the detection and quantification of human immunodeficiency virus Type 1 (HIV‐1) RNA are used to increase transfusion safety and to diagnose and manage HIV‐1‐infected patients. We describe a novel HIV‐1 recombinant form associated with lack of reactivity or substantial underestimation of viral load by commercial NAT assays. STUDY DESIGN AND METHODS: We observed a repeat blood donor seroconverting to anti‐HIV in whom HIV RNA was initially undetectable with routine NAT was observed. During donor follow‐up, HIV RNA became detectable, but the viral load was 2 to 3 log lower than measured with other NATs targeting different genome regions. Genome sequencing revealed a novel B/F recombinant with mutations affecting primers and probe annealing accounting for the poor performance of routine NAT. A total of 553 HIV‐1‐infected patients attending the hospital clinic were subsequently tested prospectively using the routine assay and an in‐house assay specifically designed to detect the B/F strains. RESULTS: The routine assay substantially underestimated viremia (1‐5 log) in 19 cases (3.5%), 11 (58%) of which were infected with the same B/F strain observed in the index donor samples. Two other non‐B circulating recombinant forms of HIV‐1 (A/G, B/G subtypes) were identified as poorly detected. Newly introduced NATs targeting two HIV‐1 regions improved assay performance. CONCLUSION: HIV‐1 increasing heterogeneity affects the efficiency of NATs and consequently the safety of the blood supply as well as diagnosis and patient management.