**4.4. Methods for detection of recombination**

In addition to undergoing mutations, viruses are known to generate new variants through genetic recombination. Genetic recombination refers to the exchange of genetic material between strains of the same or different species of viruses [88]. Within a host, co-infected with viruses, the recombination occurs either by homologous recombination or by reassortment [89]. Homologous recombination can occur between highly similar RNA genomes usually through the process called 'copy-choice' or 'template-switching' mechanism, whereas reas‐ sortment involves exchange of genomic regions between viruses that have segmented genomes. Presence of recombinants can hamper analyses pertaining to molecular clock [90], selection pressure, phylogenetic classification [91, 92] and thus need to be detected prior to such analyses.
