Challenges in Virus Detection and Identification

Challenges in Virus Detection and Identification

• LAMP shows sensitivity comparable to qPCR and is less affected by inhibitors like phenols and tannins than PCR.
• High sensitivity of amplification techniques can lead to false positives due to contamination and cross-contamination.
• Genetic variability within virus species and relationships with other species affect accuracy of detection methods.
• Specific binding-based methods may fail to detect dissimilar virus variants, leading to false negatives.
• False positives can occur due to cross-reactions of antibodies with related viruses.
• Genetic variation of viruses is often overlooked in detection protocols, impacting accuracy in different geographical areas and with divergent variants.
• Accurate probes or primers for a virus require understanding genetic variation and structure, obtained from nucleotide sequences in databases like GenBank.
• Nucleotide diversity and structure can be analyzed using MEGA X software and CLUSTALW algorithm.
• Phylogenetic trees can visualize genetic structure and relationships, aiding in the development of accurate detection methods.
• For universal virus detection by PCR, degenerate primers covering genetic variation among available sequences should be designed.
• Molecular hybridization for probe design should consider genetic diversity across the genome due to selective pressures or recombination.
• HTS provides unbiased virus identification with high sensitivity, but validation with other techniques is necessary to avoid false positives.