In silico analysis of amino acid variation in human respiratory syncytial virus: insights into immunodiagnostics

Abstract

BACKGROUND The highly contagious nature of human respiratory syncytial virus (HRSV) and the gravity of its infection in newborns and vulnerable adults pose a serious public health problem. Thus, a rapid and sensitive diagnostic test for viral detection that can be implemented upon the first appearance of symptoms is needed. The genetic variation of the virus must be considered for immunodiagnostic purposes.OBJECTIVES To analyse HRSV genetic variation and discuss the possible consequences for capture immunoassay development.METHODS We performed a wide analysis of N, F and G protein variation based on the HRSV sequences currently available in the GenBank database. We also evaluated their similarity with homologous proteins from other viruses.FINDINGS The mean amino acid divergences for the N, F, and G proteins between HRSV-A and HRSV-B were determined to be approximately 4%, 10% and 47%, respectively. Due to their high conservation, assays based on the full-length N and F proteins may not distinguish HRSV from human metapneumovirus and other Mononegavirales viruses, and the full-length G protein would most likely produce false negative results due to its high divergence.MAIN CONCLUSIONS We have identified specific regions in each of these three proteins that have higher potential to produce specific results, and their combined utilisation should be considered for immunoassay development.

A potent broadly neutralizing human RSV antibody targets conserved site IV of the fusion glycoprotein

“…Out of these 3,058 contained the complete extracellular domain and had no ambiguous amino acids in antigenic site IV. Genbank entry AHA61614 was excluded from analysis due to an atypically large degree of sequence divergence from other RSV A and RSV B sequences according to our own analysis and as reported in Souza, et al 42 .The sequences were aligned using a modified Seq2Logo program 43 and the amino acid frequency at each position was determined. RSV F glycoprotein sequences from an additional panel of 47 clinical isolates were sequenced.…”

Recommendations for respiratory syncytial virus surveillance at the national level

“…RSV antigen detection by RADT through antigen capture and by DFA/IFA through antigen detection in infected cells by monoclonal antibodies are both less sensitive than qRT-PCR [ 70 ]. They suffer from higher false positive results due to cross-reactivity with similar proteins of related viruses, and higher false negative results mostly due to antigenic variation among viruses [ 71 ]. The protein most often targeted is the F-protein, but the N-protein and G-protein are also used.…”

“…Mutations in the genes coding for these proteins may result in changes in antigenic epitopes used by the detecting antibodies. A recent study concluded that for optimal development of monoclonal antibodies, only selected regions of F and N should be used and combined with selected regions of G. This is because F and N of RSV and of human metapneumovirus (hMPV) are highly related and can cause false positivity [71]. Indeed, this type of targeted development of monoclonal antibodies, although against other proteins, was shown to result in higher sensitivity and specificity in the ELISA format [72].…”

Expert consensus on the diagnosis, treatment, and prevention of respiratory syncytial virus infections in children

“…RSV antigen detection by RADTs via antigen capture and by DFAs via monoclonal antibodies for antigen detection in infected cells are both less sensitive than quantitative reverse transcription polymerase chain reactions (qRT‒PCRs) [ 47 – 54 ]. They are prone to higher false-positive results owing to cross-reactivity with similar proteins of related viruses, such as human metapneumovirus, and higher false-negative results, mainly owing to antigenic variation among viruses [ 55 ]. RADTs are still employed because they are less costly and require less time, expertise, and maintenance than qRT‒PCRs.…”