Algorithm steps:

structures of both viruses and hosts. Environmental factors like salinity also influenced the viral persistence and hence their diversity. Technological advances in viral metagenomics would help to unravel the underlying rules of viral evolution and ecology, the so-called

A key event during any viral infection is the interaction of viruses with the host receptors on the plasma membrane. This serves as an entry point for viruses to access resources of the host cell and is very crucial for tropism. This interaction is known to be very specific and is responsible for activation of the signalling processes that recruit cellular machinery of the host for viral replication. The specificity of receptor binding defines host range that a virus can infect and the extent of tissue tropism that a virus can display. Switching of receptors thus enables the virus to increase its host range and/or gain access to the previously unaffected cell

*HIV-1* enters the target host cell by binding to CD4 receptor along with a co-receptor (in majority of cases, chemokine C-C motif receptor 5 (CCR5)) using its spike protein. Monitoring of the co-receptor usage using phenotype-based assays provided clues for the likely shift from CCR5 to chemokine C-X-C motif receptor 4 (CXCR4). However, due to the low resolution of these procedures, this transition could not be captured effectively. NGS of the variable loop region (V3) of the envelope gene containing determinants of coreceptor usage revealed the stepwise mutational pathway involved in the transition from CCR5 to CXCR4 [71]. The observation of the low-frequency intermediate variants provid‐ ed an insight into the fitness landscape of *HIV-1* and provided clues to tackle the disease

The *de novo* sequencing approach has helped to analyse the heterogeneity of *Influenza A virus* (strain A/Nagano/RC1-L/200 or H1N1) isolated from 2009 pandemic. The amino acid changes in haemagglutinin protein (G172E and G239N) were observed to be associated with the

Bioinformatics approaches help to estimate and analyse population diversity by studying genetic recombination, mutation, selection and, thereby, assist in correlation of genotype to phenotype. The methods relevant to these aspects are discussed below with emphasis on the

'Genomic rulebook of viruses' [70].

progression in a rational manner.

**4. Bioinformatics methods for viral genomics**

*3.5.2. Immune escape*

immune escape [72].

analysis of viral populations.

*3.5.1. Receptor switching*

types.

**3.5. Genotype–phenotype correlation studies**

182 Next Generation Sequencing - Advances, Applications and Challenges

