HIV-1 protein coding sequences are present in relevant bacteria

Human Immunodeficiency Virus (HIV) is a retrovirus that attacks the immune system, causing acquired immunodeficiency syndrome (AIDS). Early diagnosis and treatment of HIV infected individuals are considered key to reduce HIV transmission and developing AIDS. Therefore, HIV diagnostics play an important role in the battle against AIDS. HIV tests are regarded as reliable and very specific. However, false-positive results are known to occur, usually caused by infections with unrelated pathogens leading to cross-reactive antibodies. In this work, we found through TBLASTN searches that the genome of several bacterial species, most frequently Klebsiella pneumoniae and Escherichia coli, contain segments matching HIV-1 proteins, including p24 and other proteins relevant for HIV testing, with a high degree of similarity (sequence identity > 95 %). The presence of HIV-1 in these bacteria of the human microbiota does not appear to be an artifact, since HIV-1 proteins were detected in different isolates of the same species. The proteome of other common viruses, particularly Influenza A virus and Hepatitis B virus, was also detected in bacterial genomes, but to a much lesser extent. Overall, our findings support that some bacteria can acquire HIV-1 genetic material and could interfere with HIV testing, causing false-positives.