Evolving Patterns in COVID-19: The Virus, its Variants and Infectivity-cum-Virulence

The Virus, Variants and Pandemic: COVID-19 as a disease and SARS-CoV-2 as its causative organism, continue to remain an enigma. The pandemic continues to persist over a year with outbreaks and re-emergence involving newer regions and population groups. While we continue to explore the agent factors, disease transmission dynamics, pathogenesis and clinical spectrum of the disease, and therapeutic and vaccine modalities, the grievous nature of the disease is evolving with the genomic mutations and pathophysiological alterations. The Emerging SARS-Cov-2 Variants: Understanding the nucleotide variations in the virus genome provides a useful insight for the changing face of the disease and propagation of the pandemic. The emerging mutations can be interpreted as a strategy through natural selection to facilitate extensive spread of the viral infection. Of late, there is recurrent emergence, accumulation, and onward transmission of various mutations. Among the current major SARS-CoV-2 lineages A, B, B.1, B.1.1, and B.1.177, the lineage -B.1.1.7 is of present concern. Posed by the Mutations: open conformations, of the S protein infectivity the viral into the host cells. variant, named months. A new entrant, the South African variant carries a high infectivity and accompanied by probable high disease severity. There are salient potential consequences of emerging variants including rapid transmission, enhanced disease severity, and diagnostic failure as the variants may evade detection through certain diagnostic tests. Further, they may decrease susceptibility to antiviral drugs and monoclonal antibodies and evade natural or vaccine-induced immunity. Conclusion: Dealing with the Variants: The WHO is working with various countries to amplify and adapt the current surveillance systems to evaluate potential virus variations through ongoing systematic clinical and epidemiologic surveillance. There is need to establish genomic sequencing capacity and access to the sequencing services. Simultaneously, the disease control measures, and intensive public health response are needed to be strengthened to curtail the increased transmissibility associated with the emerging SARS-CoV-2 variants. in COVID-19: The Virus, its Variants and Infectivity-cum-Virulence.

SARS-CoV-2 virus is here to stay for the foreseeable future [1] and continue to create further deterioration and havocs.

Mutations and Variants of SARS-CoV-2
While we continue to explore the agent factors, disease virulence. Looking forward, let us hope that the today's unmet challenges are resolved in near future [2].

The Viral Variants Vs Strains
Being an RNA virus, SARS-CoV-2 has a steady rate of mutations despite presence of the spell-checker, nsp14 protein acting as 3′-5′ exoribonuclease. It is expected and has been observed that the virus accumulates mutations over time. With the mutations, the variants may lose or gain infectivity and virulence. As feared, enhancing the infectivity and virulence due to mutations may pose a heightened challenge for Covid-19 therapeutic and preventive modalities, including vaccines. There is no universally accepted definition for the terms strain, or variant. According to van Regenmortel et al a virus strain is a variant of a given virus that is recognizable because it possesses some unique phenotypic characteristics that remain stable under natural conditions [3]. Whereas the unique phenotypic characteristics and biological properties for a virus strain are different from the compared reference virus, such as the antigenic properties, host range or the disease manifestations it can cause [4]. Further, a virus variant with a simple difference in genome sequence should not be given the status of a separate strain since it lacks a distinct recognizable viral phenotype [5].
Mutations in SARS-CoV-2 are common and over 4,000 mutations have been detected in the spike (S) glycoprotein alone, according to the observations by COVID-19 Genomics UK (COG-UK) Consortium.
Both the Nextstrain and the GISAID clade nomenclatures, in general, aim at a broad categorization of globally circulating diverse SARS-CoV-2 variants, whereas the lineages nomenclature by Rambaut et al has been related to the disease outbreaks and re-emergence.
Trying to simplify the issue, a WHO document has identified six major clades with 14 subclades [9,10] Whereas G251V frequently appears in samples from the United Kingdom, Australia, the United States, and Iceland. The remaining two clades D448del and G392D are smaller and without substantial subclades at this point.

Mutations and Variation in SARS-CoV-2
Understanding the nucleotide variations in the SARS-CoV-2 genome provides a useful insight for evolution of the disease and propagation of the pandemic [11]. The early variations have made their way almost unnoticed as the virus spread around the world. Whereas most variations or mutations have no impact on the viral ability to transmit or cause disease, certain mutations appear to have impact on transmissibility, infectivity, or lethality.
Some of these mutations have possibly arisen as a result of the virus evolving from immune selection pressure in infected individuals and are more prevalent in patients with mild than those with severe disease. In general, the mutations can be interpreted as a strategy through natural selection to facilitate extensive spread of the viral infection. As such the SARS-CoV-2 virus has a low mutation rate by virtue of the nsp14 protein acting as 3′-5′ exoribonuclease on both single-stranded and double-stranded RNA during the viral replication cycle [12]. Still its large genome appears to facilitate recombination, insertions, and deletions. Andrés et al have noted that the viral S protein accumulates deletions upstream and close to the S1/S2 cleavage site [13]. Further, SARS-CoV-2 can resort to RNA viral evolution through recombination (synthesis of chimeric RNA molecules from two different progeny genomes) and reassortment (the packaging within a single virion of genomic segments from different progeny viruses).
In general, the Single Nucleotide Variations (SNVs) as SARS-CoV-2 Spike amino acid replacements in the Receptor Binding Domain (RBD) occur relatively frequently [14]. There is recurrent emergence and significant onward transmission of a six-nucleotide deletion in the S gene resulting in loss of two amino acids labelled as ΔH69/ΔV70. This deletion often co-occurs with the receptor binding motif amino acid replacements N501Y, N439K and Y453F. As such, these deletions have been found in a small percentage (2.2%) of the samples [15]. Among the Current major SARS-CoV-2 Lineages A, B, B.1, B.1.1, and B.1.177, the lineage -B.1.1.7, of present concern.
First sequenced in the UK on 20 Sep 2020, it is spreading to other countries and has been discovered in Denmark, the Netherlands, Italy, Israel, Australia, Hong Kong, Singapore, Japan, and the USA.
The other countries are being increasingly involved. Using the complete sequences of 1,932 SARS-CoV-2 genomes, six types of the variants have been identified. The 13 signature variations in the form of SNVs in protein coding regions and one SNV in the 5′ untranslated region (UTR) provide interpretation for the six types (types I to VI). The type VI, characterized by the four signature SNVs C241T (5′UTR), C3037T (nsp3 F924F), C14408T (nsp12 P4715L), and A23403G (Spike D614G), with strong allelic associations, first reported in China, has become the dominant type world over.
Out of these, C241T is in the 5′ UTR appears to be of uncertain significance. The other three SNVs, 3037T-14408T-23403G characterising the increasing frequency of the type VI, in majority of samples from various regions indicate a possible fitness gain for the virus. Further, it has been noted that the variants missing one or two of these signature SNVs fail to persist or wiped out by other evolutionary more fit variants [16]. Taking a note of the major mutations, their lineages and effects on disease transmissibility is important to understand the changing face of the pandemic (Table 1).

Emergence of the D614G Variant
The genomic analysis of various samples for SARS-CoV-2 from several regions has found an increased proportion of some particular variants. One such variant is the D614G mutation in the C-terminal end of the S1 domain and in proximity to the S2 subunit. In short called the G variant, it has increased in prevalence during the pandemic, probably after initially arising in China and then spreading to Italy in January and later globally to become the dominant form in the pandemic [17]. The SARS-CoV-2 G variant is part of the G clade by GISAID and the B1 clade by the Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN).
The variant is associated with the faster viral transmission and harbouring and discharge of higher viral loads by virtue of higher binding to the ACE2 receptor and higher protein stability [18]. In addition, it is associated with reduced S1 Shedding.  [20]. Experimentally, the D614G variant was found to be equally sensitive to neutralizing antibodies and did not cause more severe disease than the ancestral variant in hamsters, an observation supporting current findings in humans [21]. As shown, the SARS- In general, the D614G mutation leads to more open RBD conformations, increases density of the S protein and disease infectivity by facilitating the viral entry into the host cells [22].
Further, this mutation is often accompanied by other mutations involving parts of the SARS-CoV-2 genome. Epidemiologically, the rapid spread of D614G was first spotted in early samples collected from China and Germany. In due course, it has become the dominant strain across the European continent, Australia, Canada, and parts of the United States, and probably rest of the world regions. It appears that D614G represents a more transmissible form of SARS-CoV-2, which has emerged as a product of natural selection [18].
There is a potential concern that a similar situation may occur with the VUI-202012/01 or B.1.1.7 variant. selected several times appears to imply its fitness for the virus.

Emergence of VUI-202012/01 Variant
Presently the preliminary epidemiologic indicators suggest the

The New Brazilian Variant
The new variant, also called P.  [37].
This variant appears to have evolved during the recent months.
It has been associated with a case of reinfection in a 28-yearold female healthcare worker and possibly confers resistance to neutralising antibodies. alter the infectivity and disease severity [42]. This represents about 3.6% of total global cases and is far too low than the predicted up to 70 million Africans may be infected with SARS-CoV-2 with more than 3 million deaths by June 2020 [44]. A sero-survey study for measuring the occurrence of SARS-CoV-2 antibodies in blood donors in Kenya has highlighted that the incidence of SARS-CoV-2 infection is much higher than expected from case numbers [45]. Similarly, in October 2020, Mozambique reported less than 3000 confirmed cases of COVID-19; however, sero-surveys have found the actual transmission much higher [46].

The COVID-19 pandemic in Africa and Asia
This suggests that there may be more infections than documented.

The Ill-defined and Short-lived Immune Response
In the experimental studies using animals and cell cultures, along with the latest molecular techniques, and in small human clinical studies, the immune response to SARS-CoV-2 has been recognized [48]. Further, the animal studies in mice, primate studies in monkeys and human clinical studies have documented that those who received one of the experimental RNA vaccines, produced antibodies that proved more potent at blocking G viruses than D viruses [49].

The Effect of Mutations on COVID-19 Vaccines
Presently, the researchers as well as clinicians are most concerned about several mutations occurring in group in the S protein.
The accumulation of multiple mutations as in the British variant or South African variant is more of a concern and could potentially impede immune protection. Another unresolved issue is the concern that the mutations can have far-reaching consequences for the human health in form of delayed disease complications.
There is a chance that vaccines currently being administered in the country may not provide sufficient immunity against new variants emerging in both the UK and South Africa. Though, there is no evidence that the vaccines currently being administered will not be able to protect against these new variants. 12 weeks, will allow more people to get the protection of at least one dose [51]. There are concerns that the plan is different from the efficacy trials and may lead to unchartered course of immune response. In addition, the approach could foster vaccine-resistant forms and increase the potential for escape mutants by having so many people with incomplete protection into a community swamped with SARS-CoV-2 infections. There is another concern, the vaccination programme is covering the elderly citizens first, in whom the immune system does not function so well, and some may inevitably contract the disease while waiting for their second dose of vaccine which may also erode confidence in the vaccines.

The RBD and Non-RBD Mutations
The RBD of the S protein in SARS-CoV-2 plays a crucial role in binding with the hACE2 receptors required for viral entry. The intricate ACE2 receptor recognition mechanism of the SARS-CoV-2 virus regulates its infectivity and pathogenesis [54]. The mutations involving the RBD, thus, are associated with altered infectivity and possibly disease severity. On the other hand, the mutations distal to the RBD also impact the transmissibility and the antibody also appear to target non-RBD regions. A mutation in non-RBD region may lead to polybasic cleavage sites enhancement, via electrostatic interactions and hydration and influence the RBD-ACE2 binding affinity [55]. It has been noted that certain mutations in the new variants affect genomic targets used by the PCR tests. This may affect the ability of some tests to detect the virus. However, because most PCR tests detect more than one gene target, there is a small chance of a false negative result. Further, the mutations in various viral genes that help build glycan chains may influence the individual immune response, which is a serious concern relating to the antibody response to vaccines.
Recently, the actual sequence of the Pfizer mRNA vaccine was released [56]. The main difference in the vaccine code is that uracil has been replaced by 1-methyl-3'-pseudouridylyl, labelled as Ψ [57]. As such, the Ψ is accepted as normal uracil by the immune e) Likelihood of evading natural or vaccine-induced immunity. The multiple mutations in the S protein may confer ability to evade immunity induced by vaccines or by natural infection.

The Impact of SARS-CoV-2 Variants
The WHO is working with various countries to identify how Simultaneously, there is need to reduce transmission of SARS-CoV-2 by using established disease control measures as well as avoiding introductions to animal populations as part of the global strategy to reduce the occurrence of mutations that may have potential negative public health implications [61]. Further, the increased transmissibility has potential for higher case incidence, leading to increased COVID-19 related hospitalizations, morbidity, and deaths. As warned by the WHO, a more intensive public health response may be necessary to control variant transmission.