Immunity against Delta and Omicron variants elicited by homologous inactivated vaccine booster in kidney transplant recipients.

Background: A third mRNA vaccine booster is recommended to improve immunity against SARS-CoV-2 in kidney transplant recipients (KTRs). However, the immunity against SARS-CoV-2 Ancestral strain and Delta and Omicron variants elicited by the third dose of inactivated booster vaccine in KTRs remains unknown. Methods: The blood parameters related to blood cells count, hepatic function, kidney function, heart injury and immunity were explored clinically from laboratory examinations. SARS-CoV-2 specific antibody IgG titer was detected using an enzyme-linked immunosorbent assay. Cellular immunity was analyzed using interferon-γ enzyme-linked immunospot assay. Results: The results showed that there were no severe adverse effects and apparent changes of clinical laboratory biomarkers in KTRs and healthy volunteers (HVs) after homologous inactivated vaccine booster. A third dose of inactivated vaccine booster significantly increased anti-Ancestral-spike-trimer-IgG and anti-Ancestral-receptor binding domain (RBD)-IgG titers in KTRs and HVs compared with the second vaccination. However, the anti-Delta-RBD-IgG and anti-Omicron-RBD-IgG titers were significantly lower than anti-Ancestral-RBD-IgG titer in KTRs and HVs after the third dose. Notably, only 25.6% (10/39) and 10.3% (4/39) of KTRs had seropositivity for anti-Delta-RBD-IgG and anti-Omicron-RBD-IgG after booster, which were significantly lower than HVs (anti-Delta-RBD-IgG: 100%, anti-Omicron-RBD-IgG: 77.8%). Ancestral strain nucleocapsid protein and spike specific T cell frequency after booster was not significantly increased in KTRs compared with the second dose, significantly lower than that in HVs. Moreover, 33.3% (12/36), 14.3% (3/21) and 14.3% (3/21) of KTRs were positive for the Ancestral strain and Delta and Omicron spike-specific T cells, which were significantly lower than HVs (Ancestral: 80.8%, Delta: 53.8%, and Omicron: 57.7%). Conclusions: A third dose of inactivated booster vaccine may significantly increase humoral immunity against the Ancestral strain in KTRs, while humoral and cellular immunity against the Delta and Omicron variants were still poor in KTRs.

It isn't over ‘till it's over: A continuing concern of the SARS-CoV-2 variants, and miRNAs targeting the S protein as a probable absolute cure

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak which still continues to affect the general population, has mutated day by day and new variants have emerged. More than 40 variants, usually caused by mutations in the spike (S) protein, have been recorded. Observation of S protein mutations in the development of t herapeutic agents will increase success rates. As we identify the three-dimensional (3D) conformation of viruses, it is more and more possible to work on models for understanding molecular interactions. Development of agents for arrays and 3D sequencing of proteins paves the way for potential therapeutic studies against variants. MicroRNAs (miRNAs) seemingly act as a potentially important group of biomolecules in combating uncontrolled cytokine release. Besides antiviral response, miRNAs promise to be powerful therapeutic agents against infections. Studies have shown that miRNAs are able to inhibit the genome directly by miRNA-based treatments as they are sprecific to the SARS-CoV-2 genome. In order to expose this potential, in silico studies before continuing with lab studies are helpful. In our bioinformatics analysis, we proposed to compare the S protein similarities of Delta and Omicron, two of the most common variants, and to detect miRNAs targeting the S protein. The S proteins and coding sequences were compared between the two variants, and differences were determined. Within our analysis, 105 and 109 miRNAs for the Delta and Omicron variants, respectively, were detected.We believe that our study will be a potential guide for deciding on the miRNAs that may most likely have an effect on the management of the infection caused by both variants.

Clinical characteristics and severity of beta and delta variants of SARS-CoV-2 and the effect of vaccine on delta variants.

Background: The Delta variant of concern (VOC) is rapidly becoming the dominant strain globally. We report the clinical characteristics and severity of hospitalized patients infected with Delta and Beta VOCs during the local outbreak in Harbin, Heilongjiang Province, China, and the effect of vaccines on the Delta variant. Methods: We collected a total of 735 COVID-19 patients from the First Affiliated Hospital of Harbin Medical University, including 96 cases infected with the Delta VOC and 639 cases infected with the Beta VOC. Demographic, clinical characteristic and laboratory findings were collected and compared. Results: Differences in viral shedding, IgG and IgM levels, and the neutrophil-to-lymphocyte ratio were noted between the Delta and Beta VOCs (p < 0.05). Survival analysis of the two groups revealed longer viral shedding of the Delta VOC (p < 0.05). For the Delta VOC, the longer the vaccination period, the lower the IgG and IgM levels. IgM levels were higher in the convalescent plasma group, whereas lymphocyte counts were lower. Conclusions: Delta VOC virus shedding was longer compared with Beta VOC shedding. Vaccination with inactivated vaccines can reduce the severe illness rate of the Delta VOC. IgG and IgM levels are reduced as the time period between the first and second vaccine doses increases.

Epidemiology, Mutations and Impact of New Omicron Variant (B.1.1.529): A Real Global Threat of Covid-19 Pandemic

The recent emergence of the Omicron variant (B.1.1.529) of SARS-CoV-2 has added alarm to the eternal flame of the global COVID-19 pandemic. Omicron was first identified in Botswana in November 2021. The omicron is thought to be at least three times more infectious than the previous variants. Omicron can cause diseases varying from asymptomatic, mild, and severe infection and people have died from omicron in a second pandemic wave that occurred in March-May 2021. This variant has been detected in more than 77 countries worldwide as per WHO until January 2022. The spike protein is the target of most COVID-19 vaccines and is what the virus uses to unlock access to our body's immune cells, many of which (69-70del (deletion), T95I, G142D/143-145del, K417N, N679K, T478K, N501Y, N655Y, and P681H) overlap with Alpha, Beta, Gamma, or Delta variants. Some spike protein mutations include A67V, DELTA69-70, T95I, G142D/DELTA143-145, DELTA211/L212I, ins214EPE G339D, S371L, S373P, S375F, etc. Remarkable mutations in the furin cleavage site may increase transmissibility and replication as in Alpha (P681H) and Gamma (H655Y, N679K) and affect the binding affinity of ACE-2 receptor. Though, after many ongoing mutations and adaptation, omicron can efficiently breach the host immunity, leading to prolonged, severe infection, causing more mortality and rapid spread. There is still substantial uncertainty based on ongoing genomic changes, the effectiveness of current and upcoming vaccines, and treatment against omicron. Thus omicron has forced on the world a chance to explore the intricacies of the complex immunological mechanism. Copyright © 2022 are reserved by International Journal of Pharmaceutical Sciences and Research. This Journal licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

Unvaccinated Children Are an Important Link in the Transmission of SARS-CoV-2 Delta Variant (B1.617.2): Comparative Clinical Evidence From a Recent Community Surge.

Objective: To evaluate the necessity of Covid-19 vaccination in children aged < 12 y by comparing the clinical characteristics between unvaccinated children aged < 12 y and vaccinated patients aged ≥ 12y during the Delta surge (B.1.617.2) in Putian, Fujian, China. Methods: A total of 226 patients with SARS-Cov-2 Delta variant (B.1.167.2; confirmed by Real-time PCR positivity and sequencing) were enrolled from Sep 10th to Oct 20th, 2021, including 77 unvaccinated children (aged < 12y) and 149 people aged ≥ 12y, mostly vaccinated. The transmission route was explored and the clinical data of two groups were compared; The effect factors for the time of the nucleic acid negativization (NAN) were examined by R statistical analysis. Results: The Delta surge in Putian spread from children in schools to factories, mostly through family contact. Compared with those aged ≥ 12y, patients aged < 12y accounted for 34.07% of the total and showed milder fever, less cough and fatigue; they reported higher peripheral blood lymphocyte counts [1.84 (1.32, 2.71)×10^9/L vs. 1.31 (0.94, 1.85)×10^9/L; p<0.05), higher normal CRP rate (92.21% vs. 57.72%), lower IL-6 levels [5.28 (3.31, 8.13) vs. 9.10 (4.37, 15.14); p<0.05]. Upon admission, their COVID19 antibodies (IgM and IgG) and IgG in convalescence were lower [0.13 (0.00, 0.09) vs. 0.12 (0.03, 0.41), p<0.05; 0.02 (0.00, 0.14) vs. 1.94 (0.54, 6.40), p<0.05; 5.46 (2.41, 9.26) vs. 73.63 (54.63, 86.55), p<0.05, respectively], but longer NAN time (18 days vs. 16 days, p=0.13). Conclusion: Unvaccinated children may be an important link in the transmission of SARS-CoV-2 delta variant (B1.617.2), which indicated an urgent need of vaccination for this particular population.

On the peptide binding affinity changes in population-specific HLA repertoires to the SARS-CoV-2 variants Delta and Omicron.

OBJECTIVE: To investigate the changes of Spike protein-HLA binding affinity profiles between the Wuhan strain and two dominant variants, the Delta and the Omicron strains, among the Taiwanese, the British and the Russian populations. METHODS: The HLA frequencies and the HLA-peptide binding affinity profiles in the T-CoV database were combined to conduct the study. We focused on the public alleles in the three populations (HLA-A, HLA-B, HLA-C, HLA-DRB1, and/or HLA-DPA1/DPB1 alleles) and the altered peptides of the spike protein (compared to the Wuhan strain) in the Delta G/478K·V1 (B.1.617.2 + AY.1 + AY.2) and the Omicron (BA.1) strains. RESULTS: For the Delta strain, tight bindings of the altered peptides to the HLA alleles decrease in all three populations and almost vanish in the Taiwanese population. For the Omicron strain, tight bindings are mostly preserved for both HLA classes and in the Taiwanese and the British populations, with a slight reduction in HLA class II in the Taiwanese (1.4%), while the Russian population preserves a relatively high fraction of tight bindings for both HLA classes. CONCLUSION: We comprehensively reported the changes in the HLA-associated SARS-CoV-2 Spike protein peptide binding profiles among the Taiwanese, the British, and the Russian populations. Further studies are needed to understand the immunological mechanisms and the clinical value of our findings.

The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta variants: A computational approach.

The newly discovered COVID variant B.1.1.529 in Botswana has more than 30 mutations in spike and many other in non-spike proteins, far more than any other SARS-CoV-2 variant accepted as a variant of concern by the WHO and officially named Omicron, and has sparked concern among scientists and the general public. Our findings provide insights into structural modification caused by the mutations in the Omicrons receptor-binding domain and look into the effects on interaction with the hosts neutralizing antibodies CR3022, B38, CB6, P2B-2F6, and REGN, as well as ACE2R using an in silico approach. Computational analysis revealed that the Omicron variant has a higher binding affinity for the human ACE2 receptor than the wild and Delta (AY.1 and AY.2 strains), but lower than the Delta AY.3 strain. MD simulation and docking analysis suggest that the omicron and Delta AY.3 were found to have relatively unstable RBD structures and hampered interactions with antibodies more than wild and Delta (AY.1 and AY.2), which may lead to relatively more pathogenicity and antibody escape. In addition, we observed lower binding affinity of Omicron for human monoclonal antibodies (CR3022, B38, CB6, and P2B2F6) when compared to wild and Delta (AY.1 & AY.2). However, the binding affinity of Omicron RBD variants for CR3022, B38, and P2B2F6 antibodies is lower as compared to Delta AY.3, which might promote immune evasion and reinfection and needs further experimental investigation.

A Paradigm Shift in the Combination Changes of SARS-CoV-2 Variants and Increased Spread of Delta Variant (B.1.617.2) across the World.

Since September 2020, the SARS-CoV-2 variants have gained their dominance worldwide, especially in Kenya, Italy, France, the UK, Turkey, Indonesia, India, Finland, Ireland, Singapore, Denmark, Germany, and Portugal. In this study, we developed a model on the frequency of delta variants across 28 countries (R2= 0.1497), displaying the inheritance of mutations during the generation of the delta variants with 123,526 haplotypes. The country-wise haplotype network showed the distribution of haplotypes in USA (10,174), Denmark (5,637), India (4,089), Germany (2,350), Netherlands (1,899), Sweden (1,791), Italy (1,720), France (1,293), Ireland (1,257), Belgium (1,207), Singapore (1,193), Portugal (1,184) and Spain (1,133). Our analysis shows the highest haplotype in Europe with 84% and the lowest in Australia with 0.00001%. A model of scatter plot was generated with a regression line which provided the estimated rate of mutation, including 24.048 substitutions yearly. Our study concluded that the high global prevalence of the delta variants is due to a high frequency of infectivity, supporting the paradigm shift of the viral variants.

Impact of low vaccine coverage on the resurgence of COVID-19 in Central and Eastern Europe.

The coronavirus disease 2019 (COVID-19) pandemic has caused a tremendous global impact both socially and economically. The mechanisms behind the disparity in the severity, vaccine coverage, and variant replacement patterns across European countries are unclear. In this work, we aim to reveal the possible reasons via data visualization and model fitting. We developed a model with a vaccination component to simulate the mortality waves in these countries. Deaths averted by the vaccination campaign were estimated. Finally, we discuss the potential reasons behind the differences in vaccine coverage across European countries. Contemporary transportation and global trade bring significant convenience to our daily life but also facilitate the spread of the novel virus COVID-19 to anywhere globally within a short time. The observations and results in this work highlight the importance of the global campaign to mitigate the COVID-19 pandemic and future pandemics under the One Health approach.

Assessing the Transmissibility of the New SARS-CoV-2 Variants: From Delta to Omicron.

Omicron, the latest SARS-CoV-2 Variant of Concern (VOC), first appeared in Africa in November 2021. At present, the question of whether a new VOC will out-compete the currently predominant variant is important for governments seeking to determine if current surveillance strategies and responses are appropriate and reasonable. Based on both virus genomes and daily-confirmed cases, we compare the additive differences in growth rates and reproductive numbers (R0) between VOCs and their predominant variants through a Bayesian framework and phylo-dynamics analysis. Faced with different variants, we evaluate the effects of current policies and vaccinations against VOCs and predominant variants. The model also predicts the date on which a VOC may become dominant based on simulation and real data in the early stage. The results suggest that the overall additive difference in growth rates of B.1.617.2 and predominant variants was 0.44 (95% confidence interval, 95% CI: -0.38, 1.25) in February 2021, and that the VOC had a relatively high R0. The additive difference in the growth rate of BA.1 in the United Kingdom was 6.82 times the difference between Delta and Alpha, and the model successfully predicted the dominating process of Alpha, Delta and Omicron. Current vaccination strategies remain similarly effective against Delta compared to the previous variants. Our model proposes a reliable Bayesian framework to predict the spread trends of VOCs based on early-stage data, and evaluates the effects of public health policies, which may help us better prepare for the upcoming Omicron variant, which is now spreading at an unprecedented speed.

The dynamics of circulating SARS-CoV-2 lineages in Bogor and surrounding areas reflect variant shifting during the first and second waves of COVID-19 in Indonesia.

Background: Indonesia is one of the Southeast Asian countries with high case numbers of COVID-19 with up to 4.2 million confirmed cases by 29 October 2021. Understanding the genome of SARS-CoV-2 is crucial for delivering public health intervention as certain variants may have different attributes that can potentially affect their transmissibility, as well as the performance of diagnostics, vaccines, and therapeutics. Objectives: We aimed to investigate the dynamics of circulating SARS-CoV-2 variants over a 15-month period in Bogor and its surrounding areas in correlation with the first and second wave of COVID-19 in Indonesia. Methods: Nasopharyngeal and oropharyngeal swab samples collected from suspected patients from Bogor, Jakarta and Tangerang were confirmed for SARS-CoV-2 infection with RT-PCR. RNA samples of those confirmed patients were subjected to whole genome sequencing using the ARTIC Network protocol and sequencer platform from Oxford Nanopore Technologies (ONT). Results: We successfully identified 16 lineages and six clades out of 202 samples (male n = 116, female n = 86). Genome analysis revealed that Indonesian lineage B.1.466.2 dominated during the first wave (n = 48, 23.8%) while Delta variants (AY.23, AY.24, AY.39, AY.42, AY.43 dan AY.79) were dominant during the second wave (n = 53, 26.2%) following the highest number of confirmed cases in Indonesia. In the spike protein gene, S_D614G and S_P681R changes were dominant in both B.1.466.2 and Delta variants, while N439K was only observed in B.1.466.2 (n = 44) and B.1.470 (n = 1). Additionally, the S_T19R, S_E156G, S_F157del, S_R158del, S_L452R, S_T478K, S_D950N and S_V1264L changes were only detected in Delta variants, consistent with those changes being characteristic of Delta variants in general. Conclusions: We demonstrated a shift in SARS-CoV-2 variants from the first wave of COVID-19 to Delta variants in the second wave, during which the number of confirmed cases surpassed those in the first wave of COVID-19 pandemic. Higher proportion of unique mutations detected in Delta variants compared to the first wave variants indicated potential mutational effects on viral transmissibility that correlated with a higher incidence of confirmed cases. Genomic surveillance of circulating variants, especially those with higher transmissibility, should be continuously conducted to rapidly inform decision making and support outbreak preparedness, prevention, and public health response.

B.1.617.2 (Delta) Variant of SARS-CoV-2: features, transmission and potential strategies.

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic. With the continuous evolution of the viral genome, SARS-CoV-2 has evolved many variants. B.1.617.2, also called Delta, is one of the most concerned variants. The Delta variant was first reported in India at the end of 2020 but has spread globally, by now, to 135 countries and is not stand still. Delta shared some mutations with other variants, and owned its special mutations on spike proteins, which may be responsible for its strong transmission and increasing virulence. Under these circumstances, a systematic summary of Delta is necessary. This review will focus on the Delta variant. We will describe all the characteristics of Delta (including biological features and clinical characteristics), analyze potential reasons for its strong transmission, and provide potential protective ways for combating Delta.

New Coronavirus Variants are Creating More Challenges to Global Healthcare System: A Brief Report on the Current Knowledge.

The coronavirus is naturally mutating over time and producing new variants. Some of them are more contagious and destructive than previous strains. Also, some variants are capable of therapeutic escaping. Earlier SARS-CoV-2 variants proved that some are supercritical, and newly mutated strains are creating new challenges to the global healthcare systems. Here we aimed to evaluate different coronavirus variants and associated challenges for healthcare systems. We searched for information online and on the PubMed, Scopus, and Embase databases. We found the wild-type virus is more sensitive for neutralization and more controllable than newer variants. The Delta and Omicron variants are more highly transmissible than Alpha, Beta, and Gamma variants. Also, few strains are resistant to neutralization. Therefore, there is a chance of reinfection among the vaccinated population. The transmissibility and resistance of the recently identified Omicron variant is still unclear. The Delta variant is the most dangerous among all variants due to its high transmissibility, disease severity, and mortality rate. For poor and developing countries, oxygen supply, medication, vaccination, and device supply are challenging during epidemic waves. Slowing down the transmission, mass vaccination, vaccine redesign, re-compiling action plans, and following safety guidelines can be effective solutions to the new challenges.

Pathogenetic factors fanning the flames of COVID-19 to cause rhino-orbito-cerebral mucormycosis: An observational study.

BACKGROUND AND AIMS: Published studies on coronavirus disease 19 (COVID-19) associated rhino-orbito-cerebral mucormycosis (CAROCM) were primarily descriptive. Therefore, we aimed to identify features of COVID-19 that could predispose to CAROCM and explore the pathogenic pathways. PATIENTS AND METHODS: This retrospective hospital-based study was done during the first (March 2020 - January 2021) and the second (February 2021 - June 2021) waves of the COVID-19 pandemic. Subjects were grouped into four categories: first-wave CAROCM (n-4); second-wave CAROCM (n-27); first-wave non-mucor COVID (n-75), and second-wave non-mucor COVID (n-50). Data elements included age, gender, comorbidities, COVID-19 severity, steroid therapy, peak values of interleukin-6 (IL-6), serum ferritin and D-dimer, nadir values of absolute lymphocyte count (ALC), absolute neutrophil count (ANC) and platelet count (Pl. C). RESULTS: Thirty-one patients of CAROCM were included. The mean (SD) age was 51.26 (11.48) years. 27 (87.1%) were aged ≥ 40 years and males. Severe COVID-19 was seen more often in the second wave than the first wave (P-0.001). CAROCM group was significantly younger (P-0.008) and showed a higher incidence of uncontrolled diabetes (P-0.001) and renal dysfunction (P-0.004) than non-mucor COVID. While IL-6, ferritin and D-dimer were significantly elevated in CAROCM than non-mucor COVID, clinical severity, ANC, ALC and Pl. C showed no significant difference. CONCLUSION: CAROCM is seen often in middle-aged diabetic males with uncontrolled hyperglycaemia, diabetic ketoacidosis, renal dysfunction and those infected by more transmissible delta variants and treated with steroids. IL-6, D-dimer, serum ferritin are more often elevated in CAROCM and might play a pathogenic role.

The Second Wave of COVID-19 in South and Southeast Asia and the Effects of Vaccination.

Background: By February 2021, the overall impact of coronavirus disease 2019 (COVID-19) in South and Southeast Asia was relatively mild. Surprisingly, in early April 2021, the second wave significantly impacted the population and garnered widespread international attention. Methods: This study focused on the nine countries with the highest cumulative deaths from the disease as of August 17, 2021. We look at COVID-19 transmission dynamics in South and Southeast Asia using the reported death data, which fits a mathematical model with a time-varying transmission rate. Results: We estimated the transmission rate, infection fatality rate (IFR), infection attack rate (IAR), and the effects of vaccination in the nine countries in South and Southeast Asia. Our study suggested that the IAR is still low in most countries, and increased vaccination is required to prevent future waves. Conclusion: Implementing non-pharmacological interventions (NPIs) could have helped South and Southeast Asia keep COVID-19 under control in 2020, as demonstrated in our estimated low-transmission rate. We believe that the emergence of the new Delta variant, social unrest, and migrant workers could have triggered the second wave of COVID-19.

Antibody Response of BNT162b2 and CoronaVac Platforms in Recovered Individuals Previously Infected by COVID-19 against SARS-CoV-2 Wild Type and Delta Variant.

Vaccinating recovered patients previously infected by COVID-19 with mRNA vaccines to boost their immune response against wild-type viruses (WT), we aimed to investigate whether vaccine platform and time of vaccination affect immunogenicity against the SARS-CoV-2 WT and Delta variant (DV). Convalescent patients infected by COVID-19 were recruited and received one booster dose of the BNT162b2 (PC-B) or CoronaVac (PC-C) vaccines, while SARS-CoV-2 naïve subjects received two doses of the BNT162b2 (CN-B) or CoronaVac (CN-C) vaccines. The neutralizing antibody in sera against the WT and DV was determined with live virus neutralization assay (vMN). The vMN geometric mean titre (GMT) against WT in recovered individuals previously infected by COVID-19 reduced significantly from 60.0 (95% confidence interval (CI), 46.5-77.4) to 33.9 (95% CI, 26.3-43.7) at 6 months post recovery. In the PC-B group, the BNT162b2 vaccine enhanced antibody response against WT and DV, with 22.3-fold and 20.4-fold increases, respectively. The PC-C group also showed 1.8-fold and 2.2-fold increases for WT and DV, respectively, after receiving the CoronaVac vaccine. There was a 10.6-fold increase in GMT in the CN-B group and a 1.3-fold increase in the CN-C group against DV after full vaccination. In both the PC-B and PC-C groups, there was no difference between GMT against WT and DV after vaccination. Subjects in the CN-B and CN-C groups showed inferior GMT against DV compared with GMT against WT after vaccination. In this study, one booster shot effectively enhanced the pre-existing neutralizing activity against WT and DV in recovered subjects.

Codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spreads all over the world and brings great harm to humans in many countries. Many new SARS-CoV-2 variants appeared during its transmission. In the present study, the Delta variants (B.1.617.2) of SARS-CoV-2, which have appeared in many countries, were considered for analysis. In order to evaluate the evolutionary divergence of the Delta variants(B.1.617.2), the codon usage divergence in Delta variants (B.1.617.2) of SARS-CoV-2 was compared to that of the SARS-CoV-2 genomes emerged before June 2020. All Delta variants (B.1.617.2) and 350 early genomes of SARS-CoV-2 in the NCBI database were downloaded. Codon usage pattern including the basic composition, the GC ratio of the third position (GC3) and the first two positions (GC12) in codons, overall GC contents, the effective number of codons (ENC), the codon bias index (CBI), the relative synonymous codon usage (RSCU) values, etc., of all concerned important gene sequences were all calculated. Codon usage divergence of them was calculated via summing their standard deviations. The results suggested that base compositions in both Delta variants (B.1.617.2) of SARS-CoV-2 and the early SARS-CoV-2 genomes were similar to each other. However, the internal codon usage divergence for most genes in Delta variants (B.1.617.2) was significantly wider than that of SARS-CoV-2. The RSCU values were further used to explore the synonymous and non-synonymous mutations in the sequences of the Delta variants (B.1.617.2), and the results showed the synonymous mutations are more obvious than the non-synonymous in the concerned sequences. The related codon usage divergence analysis is helpful for further study on the adaptability and disease prognosis of the SARS-CoV-2 variants.

Differences in the case fatality risks associated with SARS-CoV-2 Delta and non-Delta variants in relation to vaccine coverage: An early ecological study in the United Kingdom.

The circulation of SARS-CoV-2 Delta (i.e., B.1.617.2) variants challenges the pandemic control. Our analysis showed that in the United Kingdom (UK), the reported case fatality ratio (CFR) decreased from May to July 2021 for non-Delta variant, whereas the decreasing trends of the CFR of Delta variant appeared weak and insignificant. The association between vaccine coverage and CFR might be stratified by different circulating variants. Due to the limitation of ecological study design, the interpretation of our results should be treated with caution.

SARS-CoV-2 variants and environmental effects of lockdowns, masks and vaccination: a review.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously evolving and four variants of concern have been identified so far, including Alpha, Beta, Gamma and Delta variants. Here we review the indirect effect of preventive measures such as the implementation of lockdowns, mandatory face masks, and vaccination programs, to control the spread of the different variants of this infectious virus on the environment. We found that all these measures have a considerable environmental impact, notably on waste generation and air pollution. Waste generation is increased due to the implementation of all these preventive measures. While lockdowns decrease air pollution, unsustainable management of face mask waste and temperature-controlled supply chains of vaccination potentially increases air pollution.