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2022 ◽  
Author(s):  
Eileen Socher ◽  
Lukas Heger ◽  
Friedrich Paulsen ◽  
Friederike Zunke ◽  
Philipp Arnold

Abstract SARS-CoV-2, the virus which causes the COVID-19 pandemic, changes frequently through the ap-pearance of mutations constantly leading to new variants. However, only few variants evolve as dominating and will be considered as “Variants of Concern” (VOCs) by the world health organization (WHO). At the end of 2020 the alpha (B.1.1.7) variant appeared in the United Kingdom and domi-nated the pandemic situation until mid of 2021 when it was substituted by the delta variant (B.1.617.2) that first appeared in India as predominant variant. At the end of 2021, SARS-CoV-2 omi-cron (B.1.1.529) evolved as the dominating variant. Here, we use in silico modeling and molecular dynamics (MD) simulations of the receptor-binding domain of the viral spike protein and the host cell surface receptor ACE2 to analyze and compare the interaction pattern between the wild type, delta and omicron variants. We identified residue 493 in delta (glutamine) and omicron (arginine) with altered binding properties towards ACE2.


2021 ◽  
Vol 11 (4) ◽  
pp. 1126-1129
Author(s):  
Indrajit Banerjee ◽  
Jared Robinson ◽  
Indraneel Banerjee ◽  
Brijesh Sathian

The SARS-CoV-2 virus which causes the disease termed COVID-19 ripped through the globe in the latter part of 2019 and has left a state of fear, death and destruction in its wake. The Omicron variant was officially announced by the South African authorities on the 24th of November 2021, with the first confirmed sample of the infection being collected on the 9th of November 2021. The initial cases were flagged as a possible new variant due to the stark differences in the presentation and clinical features of the patients. At the time of Omicron’s discovery, the predominant variant circulating within South Africa was the Delta variant B.1.617.2 which typically presented with more severe and stark symptoms.  Omicron spread rapidly within the Southern African content and abroad, principally South Africa, Botswana, Hongkong and Israel were among the first countries to record cases of the new variant. The first European case of the Omicron variant was confirmed on the 26th of November 2021 in Belgium. Towards the end of November 2021 cases of the new variant had been confirmed and recorded in France, the United Kingdom, Germany, Portugal and Scotland. Additional cases of the Omicron variant have been confirmed in Canada and Australia. At this current point in the development of the Omicron upsurge in cases the international community should aim for further vaccinations among their fellow countrymen, but more so vaccine equality should be ensured. Such equality should be ensured in the developing nations as the virus does not respect any boundaries or territories and thus a higher level of vaccination worldwide will confer greater protection to the global community as a whole.


Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2526
Author(s):  
Leira Fernández-Bastit ◽  
Jordi Rodon ◽  
Edwards Pradenas ◽  
Silvia Marfil ◽  
Benjamin Trinité ◽  
...  

Several cases of naturally infected dogs with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported despite the apparently low susceptibility of this species. Here, we document the first reported case of infection caused by the Delta (B.1.617.2) variant of concern (VOC) in a dog in Spain that lived with several household members suffering from Coronavirus Infectious Disease 2019 (COVID-19). The animal displayed mild digestive and respiratory clinical signs and had a low viral load in the oropharyngeal swab collected at the first sampling. Whole-genome sequencing indicated infection with the Delta variant, coinciding with the predominant variant during the fifth pandemic wave in Spain. The dog seroconverted, as detected 21 days after the first sampling, and developed neutralizing antibodies that cross-neutralized different SARS-CoV-2 variants. This study further emphasizes the importance of studying the susceptibility of animal species to different VOCs and their potential role as reservoirs in the context of COVID-19.


2021 ◽  
Author(s):  
Alison Levin-Rector ◽  
Lauren Firestein ◽  
Emily McGibbon ◽  
Jessica Sell ◽  
Sungwoo Lim ◽  
...  

AbstractBackgroundBelief in immunity from prior infection and concern that vaccines might not protect against new variants are contributors to vaccine hesitancy. We assessed effectiveness of full and partial COVID-19 vaccination against reinfection when Delta was the predominant variant in New York City.MethodsWe conducted a case-control study in which case-patients with reinfection during June 15– August 31, 2021 and control subjects with no reinfection were matched (1:3) on age, sex, timing of initial positive test in 2020, and neighborhood poverty level. Conditional logistic regression was used to calculate matched odds ratios (mOR) and 95% confidence intervals (CI).ResultsOf 349,598 adult residents who tested positive for SARS-CoV-2 infection in 2020, did not test positive again >90 days after initial positive test through June 15, 2021, and did not die before June 15, 2021, 1,067 were reinfected during June 15–August 31, 2021. Of 1,048 with complete matching criteria data, 499 (47.6%) were known to be symptomatic for COVID-19-like-illness, and 75 (7.2%) were hospitalized. Unvaccinated individuals, compared with fully vaccinated individuals, had elevated odds of reinfection (mOR, 2.23; 95% CI, 1.90, 2.61), of symptomatic reinfection (mOR, 2.17; 95% CI, 1.72, 2.74), and of reinfection with hospitalization (mOR, 2.59; 95% CI, 1.43, 4.69). Partially versus fully vaccinated individuals had 1.58 (95% CI: 1.22, 2.06) times the odds of reinfection. All three vaccines authorized or approved for use in the U.S. were similarly effective.ConclusionAmong adults with previous SARS-CoV-2 infection, vaccination reduced odds of reinfections when the Delta variant predominated.


2021 ◽  
Author(s):  
Kerstin Klaser ◽  
Erika Molteni ◽  
Mark S Graham ◽  
Liane S Canas ◽  
Marc F Osterdahl ◽  
...  

Background The Delta (B.1.617.2) variant became the predominant UK circulating SARS-CoV-2 strain in May 2021. How Delta infection compares with previous variants is unknown. Methods This prospective observational cohort study assessed symptomatic adults participating in the app-based COVID Symptom Study who tested positive for SARS-CoV-2 from May 26 to July 1, 2021 (Delta overwhelmingly predominant circulating UK variant), compared (1:1, age- and sex-matched) with individuals presenting from December 28, 2020 to May 6, 2021 (Alpha (B.1.1.7) predominant variant). We assessed illness (symptoms, duration, presentation to hospital) during Alpha- and Delta-predominant timeframes; and transmission, reinfection, and vaccine effectiveness during the Delta-predominant period. Findings 3,581 individuals (aged 18 to 100 years) from each timeframe were assessed. The seven most frequent symptoms were common to both variants. Within the first 28 days of illness, some symptoms were more common with Delta vs. Alpha infection (including fever, sore throat and headache) and vice versa (dyspnoea). Symptom burden in the first week was higher with Delta vs. Alpha infection; however, the odds of any given symptom lasting ≥7 days was either lower or unchanged. Illness duration ≥28 days was lower with Delta vs. Alpha infection, though unchanged in unvaccinated individuals. Hospitalisation for COVID-19 was unchanged. The Delta variant appeared more (1.47) transmissible than Alpha. Re-infections were low in all UK regions. Vaccination markedly (69-84%) reduced risk of Delta infection. Interpretation COVID-19 from Delta or Alpha infections is clinically similar. The Delta variant is more transmissible than Alpha; however, current vaccines show good efficacy against disease. Funding UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare, UK National Institute for Health Research, UK Medical Research Council, British Heart Foundation, Alzheimer's Society, and ZOE Limited.


Diagnostics ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2092
Author(s):  
Rama Devudu Puligedda ◽  
Fetweh H. Al-Saleem ◽  
Cristoph Wirblich ◽  
Chandana Devi Kattala ◽  
Marko Jović ◽  
...  

Efforts to control SARS-CoV-2 have been challenged by the emergence of variant strains that have important implications for clinical and epidemiological decision making. Four variants of concern (VOCs) have been designated by the Centers for Disease Control and Prevention (CDC), namely, B.1.617.2 (delta), B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma), although the last three have been downgraded to variants being monitored (VBMs). VOCs and VBMs have shown increased transmissibility and/or disease severity, resistance to convalescent SARS-CoV-2 immunity and antibody therapeutics, and the potential to evade diagnostic detection. Methods are needed for point-of-care (POC) testing to rapidly identify these variants, protect vulnerable populations, and improve surveillance. Antigen-detection rapid diagnostic tests (Ag-RDTs) are ideal for POC use, but Ag-RDTs that recognize specific variants have not yet been implemented. Here, we describe a mAb (2E8) that is specific for the SARS-CoV-2 spike protein N501 residue. The 2E8 mAb can distinguish the delta VOC from variants with the N501Y meta-signature, which is characterized by convergent mutations that contribute to increased virulence and evasion of host immunity. Among the N501Y-containing mutants formerly designated as VOCs (alpha, beta, and gamma), a previously described mAb, CB6, can distinguish beta from alpha and gamma. When used in a sandwich ELISA, these mAbs sort these important SARS-CoV-2 variants into three diagnostic categories, namely, (1) delta, (2) alpha or gamma, and (3) beta. As delta is currently the predominant variant globally, they will be useful for POC testing to identify N501Y meta-signature variants, protect individuals in high-risk settings, and help detect epidemiological shifts among SARS-CoV-2 variants.


Melioidosis is caused by Burkholderia pseudomallei which can be found in water and soil, as well as in animals. This study was carried out to study the spatial distributions of the cases and their sequence types (ST) from the isolates. The cases were taken from the Hospital USM admission records from the years 2014 to 2019. There were 70 cases which from these cases 33 bacterial isolates were included in this study. Multi-locus Sequence Typing (MLST) was performed to the isolates. As the results, six novel STs were discovered. The cases were found to be clustered and concentrated in the northern part of the state. This study had revealed 15 different STs however, the predominant variant, ST371 (n=6) were found to be distributed in a dispersed manner. Meanwhile, the novel STs were found distributed sporadically in few districts of the state.


Author(s):  
Sadia Choudhury Shimmi ◽  
M Tanveer Hossain Parash

The Delta variant is currently the highly contagious predominant variant of the SARSCoV-2 virus worldwide that causes severe illness more than the previous variants in unvaccinated people (CDC, 2021). At a White House briefing, the National Institute of Allergy and Infectious Diseases director, Anthony Fauci, predicted that there would be an increase in the number of child hospitalisation proportionate to the increased number of children getting infected with the Delta variant (Press briefing White House, 2021). In response to this situation, the FDA (U.S. Food and Drug Administration) approved Pfizer-BioNTech and Moderna vaccines for children aged 12 – 17 years. Vaccines in children aged 5 – 11 years are currently under clinical trial (Sick-Samuels & Messina, 2021).


COVID ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 423-434
Author(s):  
Samrat Paudel ◽  
Amol Dahal ◽  
Hitesh Kumar Bhattarai

Nepal has suffered two waves of SARS-CoV-2 infections, one in the year 2020 and another in the year 2021. Although the government of Nepal keeps a detailed record of daily coronavirus infections and deaths throughout the country, and publishes the result every day, genomic surveillance of mutants in the country has lagged behind. Sequencing of COVID-19 samples has been conducted sporadically during the pandemic. From the GISAID database, 127 high-quality sequences deposited by different health authorities in Nepal were collected and analyzed. From the analysis, it can be concluded that at least two variants of concern, alpha and delta, and one variant of interest, kappa, were detected in Nepal in 2021. As in other countries, the delta variant outcompeted the kappa and alpha variants and by July 2021 had established itself as the dominant variant. It can be hypothesized that the second wave in Nepal was primarily caused by the delta variant. Further, phylogenetic tree analysis suggests cases of local transmission and global transmission of coronavirus. This analysis reveals the global nature of the disease, where variants arising in one part of the world can quickly spread to other parts of the world and can also spread through individual communities. This paper highlights a need to structure public policy of Nepal to target the delta variant since it has become the predominant variant in Nepal. A further policy suggestion is to appropriately sample and sequence genomes of SARS-CoV-2 at regular intervals to understand the dynamics of variants in the population.


2021 ◽  
Author(s):  
Paul M McKeigue ◽  
David McAllister ◽  
Sharon J Hutchinson ◽  
Chris Robertson ◽  
Diane Stockton ◽  
...  

Objectives - To investigate: (1) whether vaccine efficacy against severe COVID-19 has decreased since Delta became the predominant variant; (2) whether efficacy wanes with time since second dose. Design - Matched case-control study. Setting - Population of Scotland from 1 December 2020 to 19 August 2021. Main outcome measure - Severe COVID-19, defined as cases with entry to critical care or fatal outcome. Results - Efficacy of vaccination against severe COVID-19 decreased in May 2021 coinciding with the replacement of the B.1.1.7 (Alpha) by the B.1.617.2 (Delta) variant in Scotland, but this decrease was reversed over the next month. In the most recent time window, the efficacy of two doses against severe COVID-19 was 91% (95 percent CI 86% to 95%) for the AstraZeneca product and 92% (95 percent CI 85% to 95%) for mRNA (Pfizer or Moderna) products. Against the broader category of hospitalised or fatal COVID-19, efficacy in this time window was slightly lower: 88% (95 percent CI 85% to 90%) for the AstraZeneca product, 91% (95 percent CI 88% to 93%) for mRNA vaccines. Efficacy against COVID-19 declined rapidly in the first two months since second dose but more slowly thereafter. For hospitalised or fatal COVID-19 the model best supported by the data was one in which efficacy was the sum of a rapidly waning effect with half-life of 17 (95% CI 9 to 39) days and a time-invariant efficacy of 83%. Conclusions - These results are reassuring with respect to concerns that efficacy against severe COVID-19 might have fallen since the Delta variant became predominant. Although there is considerable uncertainty attached to any extrapolation into the future, these results suggest that the rapid early waning of efficacy against hospitalised COVID-19 after the second dose tapers off within a few months. This weakens the rationale for policies based on delivering booster doses to the entire population, rather than to vulnerable individuals for focused protection.


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