This chapter discusses the SARS-CoV-2 variants and their immune evasion strategies, shedding light on the dynamic nature of the COVID-19 pandemic. The ecological dynamics and viral evolution of SARS-CoV-2 are explored, considering carriers of infection, individual immunity profiles, and human movement as key factors in the emergence and dissemination of variants. The chapter discusses SARS-CoV-2 mutation, including mutation rate, substitution rate, and recombination, influencing genetic diversity and evolution. Transmission bottlenecks are highlighted as determinants of dominant variants during viral spread. The evolution phases of the pandemic are outlined, from limited early evolution to the emergence of notable changes like the D614G substitution and variants with heavy mutations. Variants of Concern (VOCs), including Alpha, Beta, Gamma, and the recent Omicron variant, are examined, with insights into inter-lineage and intra-lineage dynamics. The origin of VOCs and the Omicron variant is explored, alongside the role of the furin cleavage site (FCS) in variant emergence. The impact of structural and non-structural proteins on viral infectivity is assessed, as well as innate immunity evasion strategies employed by SARS-CoV-2 variants. The chapter concludes by considering future possibilities, including ongoing virus evolution, the need for surveillance, vaccine development, and public health measures.

With severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as an emergent human virus since December 2019, the world population is susceptible to coronavirus disease 2019 (COVID-19). SARS-CoV-2 has higher transmissibility than the previous coronaviruses, associated by the ribonucleic acid (RNA) virus nature with high mutation rate, caused SARS-CoV-2 variants to arise while circulating worldwide. Neutralizing antibodies are identified as immediate and direct-acting therapeutic against COVID-19. Single-domain antibodies (sdAbs), as small biomolecules with non-complex structure and intrinsic stability, can acquire antigen-binding capabilities comparable to conventional antibodies, which serve as an attractive neutralizing solution. SARS-CoV-2 spike protein attaches to human angiotensin-converting enzyme 2 (ACE2) receptor on lung epithelial cells to initiate viral infection, serves as potential therapeutic target. sdAbs have shown broad neutralization towards SARS-CoV-2 with various mutations, effectively stop and prevent infection while efficiently block mutational escape. In addition, sdAbs can be developed into multivalent antibodies or inhaled biotherapeutics against COVID-19.

The SARS-CoV-2 Variants of Concern tracking via Whole Genome Sequencing represents a pillar of public health measures for the containment of the pandemic. The ability to track down the lineage distribution on a local and global scale leads to a better understanding of immune escape and to adopting interventions to contain novel outbreaks. This scenario poses a challenge for NGS laboratories worldwide that are pressed to have both a faster turnaround time and a high-throughput processing of swabs for sequencing and analysis. In this study, we present an optimization of the Illumina COVID-seq protocol carried out on thousands of SARS-CoV-2 samples at the wet and dry level. We discuss the unique challenges related to processing hundreds of swabs per week such as the tradeoff between ultra-high sensitivity and negative contamination levels, cost efficiency and bioinformatics quality metrics.

One SARS-CoV-2-positive sample demonstrated impaired detection of the N1 target by RT-PCR using US CDC primer/probe sets. A 3 nucleotide deletion was discovered that overlaps the forward primer binding site. This finding underscores the importance of continued SARS-CoV-2 mutation surveillance and assessment of the impact on diagnostic test performance.

BACKGROUND: Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has become a worldwide pandemic and created an utmost crisis across the globe. To mitigate the crisis, the design of vaccines is a crucial solution. The frequent mutation of the virus demands generalized vaccine candidates, which would be effective for all mutated strains at present and for the strains that would evolve due to further new mutations in the virus.
OBJECTIVE: The objective of this study is to identify more frequently occurring mutated variants of SARS-CoV-2 and to suggest peptide vaccine candidates effective in common against the viral strains considered.
METHODS: In this study, we have identified all currently prevailing mutated strains of SARS-CoV-2 through 2D Polar plot and Quotient Radius〖(q〗_R) characterization descriptor. Then, by considering the top eight mutation strains, which are significant due to their frequency of occurrence, peptide regions suitable for vaccine design have been identified with the help of a mathematical model - 2D Polygon Representation, followed by the evaluation of epitope potential and ensuring that there is no case of any autoimmune threat. Lastly, in order to verify whether this entire approach is applicable for vaccine design against any other virus in general, we have made a comparative study between the peptide vaccine candidates prescribed for the Zika virus using the current approach and a list of potential vaccine candidates for the same already established in the past.
RESULTS: We have finally suggested three generalized peptide regions which would be suitable as sustainable peptide vaccine candidates against SARS-CoV-2 irrespective of its currently prevailing strains as well any other variant of the same that may appear in the future. We also observed that during the comparative study using the case of E protein of Zika virus, the peptide regions suggested using the new approach matched with the already established results.
CONCLUSIONS: The study, therefore, illustrates an approach that would help in developing peptide vaccine against SARS-CoV-2 by suggesting those peptide regions which can be targeted irrespective of any mutated form of this virus. The consistency with which this entire approach was also able to figure out similar vaccine candidates for Zika virus with utmost accuracy proves that this protocol can be extended for peptide vaccine design against any other virus in the future.

Tracking the genetic variability of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is a crucial challenge. Mainly to identify target sequences in order to generate robust vaccines and neutralizing monoclonal antibodies, but also to track viral genetic temporal and geographic evolution and to mine for variants associated with reduced or increased disease severity. Several online tools and bioinformatic phylogenetic analyses have been released, but the main interest lies in the Spike protein, which is the pivotal element of current vaccine design, and in the Receptor Binding Domain, that accounts for most of the neutralizing the antibody activity.
Here, we present an open-source bioinformatic protocol, and a web portal focused on SARS-CoV-2 single mutations and minimal consensus sequence building as a companion vaccine design tool. Furthermore, we provide immunogenomic analyses to understand the impact of the most frequent RBD variations.
Results on the whole GISAID sequence dataset at the time of the writing (October 2020) reveals an emerging mutation, S477N, located on the central part of the Spike protein Receptor Binding Domain, the Receptor Binding Motif. Immunogenomic analyses revealed some variation in mutated epitope MHC compatibility, T-cell recognition, and B-cell epitope probability for most frequent human HLAs.
This work provides a framework able to track down SARS-CoV-2 genomic variability.