Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape

Bhattacharya, Manojit; Chatterjee, Srijan; Sharma, Ashish Ranjan; Lee, Sang-Soo; Chakraborty, Chiranjib

doi:10.1007/s12223-022-01001-3

Cited by 30 publications

(24 citation statements)

References 66 publications

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“…Furthermore, ΔE156/F157 and R158G contribute to increased infectivity [ 98 ]. The L452R and T478K S protein RBD mutations are reported to improve transmission and confer immune evasion [ 73 , 99 , 100 ]. L452R is also reported to reduce the effectiveness of antibodies induced by vaccination or natural infection [ 101 ].…”

Section: Discussionmentioning

confidence: 99%

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

Chrysostomou¹,

Vrancken²,

Haralambous³

et al. 2022

Viruses

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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.

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Section: Discussionmentioning

confidence: 99%

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

Chrysostomou¹,

Vrancken²,

Haralambous³

et al. 2022

Viruses

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“…During the Omicron outbreak, Brazil and India had a lower number of daily deaths than the other countries did [ 15 , 64 ]. Similarly, the degree of the severity of the illness was much lower than it was during the Delta outbreak [ 65 ]. The vaccine’s effectiveness also decreased much faster for the Omicron variant than it did for the pre-Omicron variants, and people infected with pre-Omicron variants have only 15% protection against the BA.4 and BA.5 variants.…”

Section: Omicron Variant-associated Disease Intensitymentioning

confidence: 99%

A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

Chatterjee

Bhattacharya

Nag

et al. 2023

Viruses

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157

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The COVID-19 pandemic has created significant concern for everyone. Recent data from many worldwide reports suggest that most infections are caused by the Omicron variant and its sub-lineages, dominating all the previously emerged variants. The numerous mutations in Omicron’s viral genome and its sub-lineages attribute it a larger amount of viral fitness, owing to the alteration of the transmission and pathophysiology of the virus. With a rapid change to the viral structure, Omicron and its sub-variants, namely BA.1, BA.2, BA.3, BA.4, and BA.5, dominate the community with an ability to escape the neutralization efficiency induced by prior vaccination or infections. Similarly, several recombinant sub-variants of Omicron, namely XBB, XBD, and XBF, etc., have emerged, which a better understanding. This review mainly entails the changes to Omicron and its sub-lineages due to it having a higher number of mutations. The binding affinity, cellular entry, disease severity, infection rates, and most importantly, the immune evading potential of them are discussed in this review. A comparative analysis of the Delta variant and the other dominating variants that evolved before Omicron gives the readers an in-depth understanding of the landscape of Omicron’s transmission and infection. Furthermore, this review discusses the range of neutralization abilities possessed by several approved antiviral therapeutic molecules and neutralizing antibodies which are functional against Omicron and its sub-variants. The rapid evolution of the sub-variants is causing infections, but the broader aspect of their transmission and neutralization has not been explored. Thus, the scientific community should adopt an elucidative approach to obtain a clear idea about the recently emerged sub-variants, including the recombinant variants, so that effective neutralization with vaccines and drugs can be achieved. This, in turn, will lead to a drop in the number of cases and, finally, an end to the pandemic.

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“…Magazine et al reported more related mutations located in the S1 subunit of the spike protein such as 69-70del, 144del, and 156del, including N501Y and D614G, between the Alpha and Omicron variants when compared with other variants, which play an essential role in enhancing viral replication and increasing transmission [ 75 , 76 , 77 ]. The 1.617.1/2 variant developed several mutations in the viral genome that resulted in many significant features [ 78 ]. The Delta spike mutation P681R, located at the furin cleavage site, enhances the cleavage of the full-length spike to S1 and S2 subunits, which improves cell-surface-mediated viral entry [ 79 ].…”

Section: Discussionmentioning

confidence: 99%

“…The Delta spike mutation P681R, located at the furin cleavage site, enhances the cleavage of the full-length spike to S1 and S2 subunits, which improves cell-surface-mediated viral entry [ 79 ]. The L452R and T478K mutations enhance ACE receptor affinity by altering the receptor-binding domain (RBD) and developing immune invasion (both immune and vaccine escape) due to changes in the epitope of the spike protein [ 78 ]. Immune invasion results in a higher viral load and a longer viral shedding time [ 73 ].…”

Section: Discussionmentioning

confidence: 99%

Characteristics, Outcomes, and Factors Affecting Mortality in Hospitalized Patients with CAP Due to Different Variants of SARS-CoV-2 and Non-COVID-19 CAP

Tongsengkee

Surasombatpattana

Tanomkiat

et al. 2023

JCM

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The study was conducted from October 2020 to March 2022 in a province in southern Thailand. The inpatients with community-acquired pneumonia (CAP) and more than 18 years old were enrolled. Of the 1511 inpatients with CAP, COVID-19 was the leading cause, accounting for 27%. Among the patients with COVID-19 CAP, mortalities, mechanical ventilators, ICU admissions, ICU stay, and hospital costs were significantly higher than of those with non-COVID-19 CAP. Household and workplace contact with COVID-19, co-morbidities, lymphocytopenia and peripheral infiltration in chest imaging were associated with CAP due to COVID-19. The delta variant yielded the most unfavorable clinical and non-clinical outcomes. While COVID-19 CAP due to B.1.113, Alpha and Omicron variants had relatively similar outcomes. Among those with CAP, COVID-19 infection as well as obesity, a higher Charlson comorbidity index (CCI) and APACHE II score were associated with in-hospital mortality. Among those with COVID-19 CAP, obesity, infection due to the Delta variant, a higher CCI and higher APACHE II score were associated with in-hospital mortality. COVID-19 had a great impact on the epidemiology and outcomes of CAP.

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Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape

Cited by 30 publications

References 66 publications

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern

A Detailed Overview of SARS-CoV-2 Omicron: Its Sub-Variants, Mutations and Pathophysiology, Clinical Characteristics, Immunological Landscape, Immune Escape, and Therapies

Characteristics, Outcomes, and Factors Affecting Mortality in Hospitalized Patients with CAP Due to Different Variants of SARS-CoV-2 and Non-COVID-19 CAP

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