Comparison of Delta and Omicron variant of COVID-19 infection cases in Montenegro

Introduction/Objective At the end of 2021, Omicron wave (B.1.1.529) SARS-CoV-2 variant superseded the Delta variant (B.1.617). The main goal of the research is to provide a detailed and comprehensive presentation of data related to people infected with the coronavirus in Montenegro. The specific goal of the research is to determine whether virus mutations influenced the course of the epidemic during its two-year duration. Methods This is a retrospective study. We used data from the Institute of Public Health of Montenegro. Our sample consisted of 127,134 people who tested positive for Delta or Omicron infection aged 0–100 years, who had a positive PCR test for COVID-19 between August 17, 2021 and April 17, 2022. Results The respondents aged 40–49 years were taken as a reference group for age. The results showed that the age group from 20 to 29 years old was affected 1.03 times more than the reference group – per-sons belonging to the age group of 30–39 years were affected 1.07 times more than the reference group. The Central region was taken as the reference group for the region. The results showed that people who live in southern region got sick 1.14 times more often and people who live in northern region got sick 1.20 times less than people from the central region. Conclusion The biggest predictor that a person would get sick is the age group. Also, the predictor is the region, and in our research, it was southern region. © 2023, Serbia Medical Society. All rights reserved.

Critical assessment of the impact of vaccine-type and immunity on the burden of COVID-19.

The COVID-19 pandemic continues to have a devastating impact on health systems and economies across the globe. Implementing public health measures in tandem with effective vaccination strategies have been instrumental in curtailing the burden of the pandemic. With the three vaccines authorized for use in the U.S. having varying efficacies and waning effects against major COVID-19 strains, understanding the impact of these vaccines on COVID-19 incidence and fatalities is critical. Here, we formulate and use mathematical models to assess the impact of vaccine type, vaccination and booster uptake, and waning of natural and vaccine-induced immunity on the incidence and fatalities of COVID-19 and to predict future trends of the disease in the U.S. when existing control measures are reinforced or relaxed. The results show a 5-fold reduction in the control reproduction number during the initial vaccination period and a 1.8-fold (2-fold) reduction in the control reproduction number during the initial first booster (second booster) uptake period, compared to the respective previous periods. Due to waning of vaccine-induced immunity, vaccinating up to 96% of the U.S. population might be required to attain herd immunity, if booster uptake is low. Additionally, vaccinating and boosting more people from the onset of vaccination and booster uptake, especially with the Pfizer-BioNTech and Moderna vaccines (which confer superior protection than the Johnson & Johnson vaccine) would have led to a significant reduction in COVID-19 cases and deaths in the U.S. Furthermore, adopting natural immunity-boosting measures is important in fighting COVID-19 and transmission rate reduction measures such as mask-use are critical in combating COVID-19. The emergence of a more transmissible COVID-19 variant, or early relaxation of existing control measures can lead to a more devastating wave, especially if transmission rate reduction measures and vaccination are relaxed simultaneously, while chances of containing the pandemic are enhanced if both vaccination and transmission rate reduction measures are reinforced simultaneously. We conclude that maintaining or improving existing control measures, and boosting with mRNA vaccines are critical in curtailing the burden of the pandemic in the U.S.

SARS-CoV-2 infection among patients with autoimmune rheumatic diseases; comparison between the Delta and Omicron waves in Israel.

OBJECTIVE: The Omicron variant of the coronavirus SARS-CoV-2 (COVID-19) had milder clinical impacts than prior variants. This study aimed to describe the impact of COVID-19 on Autoimmune Rheumatic Disease (ARD) patients during the Delta and Omicron variants waves. METHODS: We used data from Clalit Health Services (CHS), the largest health service in Israel. ARD patients diagnosed with COVID-19 between July 1, 2021, to December 1, 2021, were included in the Delta group. Patients diagnosed between December 2, 2021, to March 31, 2022, were included in the Omicron group based on the predominance of COVID-19 in Israel. The study outcomes were COVID-19-related hospitalization or death. RESULTS: The final study cohort included 8443 actively treated ARD patients diagnosed with COVID-19. 1204 patients were positive during the predefined Delta variant period, and 7249 were positive during the predefined Omicron variant period). Compared to the Delta group, the Omicron group showed a lower rate of COVID-19-related hospitalization (3.9% vs. 1.3% for the Delta Vs. Omicron accordingly, p<0.001) and COVID-19-related death (3.2% vs. 1.1% for the Delta Vs. Omicron accordingly, p<0.001). After applying multivariable regression models, the Omicron group showed a lower risk for COVID-19-related hospitalization (Relative risk 0.4, 95% CI 0.27-0.59) and COVID-19-related mortality (RR 0.48, 95% CI 0.31-0.75). CONCLUSION: ARD patients infected with the COVID-19 Omicron variant had a lower risk of developing COVID-19-related adverse outcomes compared to the Delta variant.

Glycogen Synthase Kinase-3 Interaction Domain Enhances Phosphorylation of SARS-CoV-2 Nucleocapsid Protein.

A structural protein of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), nucleocapsid (N) protein is phosphorylated by glycogen synthase kinase (GSK)-3 on the serine/arginine (SR) rich motif located in disordered regions. Although phosphorylation by GSK-3ß constitutes a critical event for viral replication, the molecular mechanism underlying N phosphorylation is not well understood. In this study, we found the putative alpha-helix L/FxxxL/AxxRL motif known as the GSK-3 interacting domain (GID), found in many endogenous GSK-3ß binding proteins, such as Axins, FRATs, WWOX, and GSKIP. Indeed, N interacts with GSK-3ß similarly to Axin, and Leu to Glu substitution of the GID abolished the interaction, with loss of N phosphorylation. The N phosphorylation is also required for its structural loading in a virus-like particle (VLP). Compared to other coronaviruses, N of Sarbecovirus lineage including bat RaTG13 harbors a CDK1-primed phosphorylation site and Gly-rich linker for enhanced phosphorylation by GSK-3ß. Furthermore, we found that the S202R mutant found in Delta and R203K/G204R mutant found in the Omicron variant allow increased abundance and hyper-phosphorylation of N. Our observations suggest that GID and mutations for increased phosphorylation in N may have contributed to the evolution of variants.

Molecular screening of SARS-CoV-2 in dogs and cats from households with infected owners diagnosed with COVID-19 during Delta and Omicron variant waves in Iran.

OBJECTIVE: The emergence of SARS-CoV-2 infection in dogs and cats in different countries worldwide raises concerns that pets are at a higher risk for spreading or transmitting of SARS-CoV-2 to humans and other pets and increased the research works about the zoonotic aspects and natural routes of infection in companion animals. The current study aimed to detect the SARS-CoV-2 in household dogs and cats living with COVID-19 positive owners. METHODS: Deep oropharyngeal and rectal swabs were collected from 30 household pets (20 cats and 10 dogs) living with COVID-19 positive owners from April 2021 to 2022 in Kerman, Iran. All dogs' and cats' samples were tested by real-time reverse transcription polymerase chain reaction for detection of SARS-CoV-2. RESULTS: Two household cats out of 20 examined (10%) were positive for SARS-CoV-2, whereas none of the examined dogs were positive for SARS-CoV-2. The two cats positive for SARS-CoV-2 were symptomatic and suffered from severe anorexia with maximum contact with their infected owners. CONCLUSION: This study reported the presence of SARS-CoV-2 in household cats in close contact with COVID-19 positive owners during the circulation of new SARS-CoV-2 variants (Delta and Omicron) in Iran and suggested that the transmission may have occurred from owners to their cats. Therefore, infected owners should eagerly limit close contact with their pets during COVID-19 illness.

Ethical Issues Involving the Development of COVID-19 Vaccines: Role of Vaccine Development, Clinical Trials, and Speed of Peer Review in Dissuading Public Vaccine Hesitancy

Over 60% of the population in the United States received the SARS-Co-V type 2 messenger RNA (mRNA) vaccine, manufactured by Pfizer-BioNTech and by Moderna. The pace at which these mRNA vaccines have been developed may be alarming to the public when compared with timelines for the development of traditional vaccines for other diseases, eliciting issues of mistrust. Ethical issues arise regarding the pace of vaccine development and have been described and highlighted by the media. In addition, testing and validation of basic science and clinical findings, combined with potential side effects of the mRNA vaccines have contributed to public mistrust of this particular vaccine platform. Here, we focus on the current ethical concerns involved with vaccine development, identify the ethical concerns that mitigate the role of public vaccine hesitancy and efforts to minimize the role of such issues, and address some of the scientific concerns cited by the public in their hesitancy to obtain the mRNA vaccine. Copyright © 2021 by Begell House, Inc.

Molecular dynamic simulation suggests stronger interaction of Omicron-spike with ACE2 than wild but weaker than Delta SARS-CoV-2 can be blocked by engineered S1-RBD fraction.

The SARS-CoV-2 claimed millions of lives, globally. Occurring from Wuhan (wild type) in December, 2019, it constantly mutated to Omicron (B.1.1.529), the predecessor to Delta. Omicron having ~ 32 spike mutations has variable infectivity-multiplicity-immuno-invasive properties. Understanding of its mutational effect on ACE2-binding/disease severity and developing preventive/therapeutic strategies are important. The binding affinities of Wuhan/Delta/Omicron spikes (PDB/GISAID/SWISS-MODEL) were docked (HADDOCK2.4) with ACE2 and compared by competitive-docking (PRODIGY). The protein structural stability was verified by kinetic-data/Ramachandran-plot (Zlab/UMassMedBioinfo). After several trials, a 59 amino acid (453ARG-510VAL) peptide-cut (Expasy-server) of the wild-type spike RBD with some desired mutants (THR500SER/THR500GLY/THR500ALA/THR500CYS) was blindly/competitively docked (PyMOL-V2.2.2) to block the Omicron-ACE2 binding. We examined molecular dynamic simulation (iMOD-server, with 9000 cycles/300 k-heating/1 atm pressure for system equilibration for 50 ns-run) of ACE2 and two CUTs with different SARS-CoV-2 variants. The binding-affinity of Omicron-ACE2 is slightly higher than the rest two in competitive docking setup. During individual (1:1) docking, Omicron showed little higher than wild type but much weaker binding affinity than Delta. Competitive docking suggests ten H-bonding (1.3-2.4 Å) with highly favorable energy values/Van-der-Walls-force/Haddock score for more stable-binding of Omicron-RBD with ACE2. Blind docking of different CUTs (wild/mutants) and Omicron to ACE2 completely rejected the Omicron-RBD from ACE2-target. The best blocking/binding affinity of -16.4 and -13 kcal/mole were observed in the case of THR500SER and THR500GLY, respectively, with multiple H-bonding 1.9-2.2 Å. These are supported by the MD-simulation results. So, the spike binding affinities were Delta > Omicron > wild in 1:1 docking with ACE2. Considering the wild type is non-existing nowadays, Omicron showed less ACE2 binding properties. The 59 cut of spike-RBD and its mutant THR500SER/THR500GLY may be further screened as universal blockers of this virus. Supplementary Information: The online version contains supplementary material available at 10.1007/s11224-022-02022-x.

Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing.

OBJECTIVES: To describe Delta/Omicron SARS-CoV-2 variants co-infection detection and confirmation during the fifth wave of COVID-19 pandemics in France in 7 immunocompetent and epidemiologically unrelated patients. METHODS: Since December 2021, the surveillance of Delta/Omicron SARS-CoV-2 variants of concern (VOC) circulation was performed through prospective screening of positive-samples using single nucleotide polymorphism (SNP) PCR assays targeting SARS-CoV-2 S-gene mutations K417N (Omicron specific) and L452R (Delta specific). Samples showing unexpected mutational profiles were further submitted to whole genome sequencing (WGS) using three different primer sets. RESULTS: Between weeks 49-2021 and 02-2022, SARS-CoV-2 genome was detected in 3831 respiratory samples, of which 3237 (84.5%) were screened for VOC specific SNPs. Unexpected mutation profiles suggesting a dual Delta/Omicron population were observed in 7 nasopharyngeal samples (0.2%). These co-infections were confirmed by WGS. For 2 patients, the sequence analyses of longitudinal samples collected 7 to 11 days apart showed that Delta or Omicron can outcompete the other variant during dual infection. Additionally, for one of these samples, a recombination event between Delta and Omicron was detected. CONCLUSIONS: This work demonstrates that SARS-CoV-2 Delta/Omicron co-infections are not rare in high virus co-circulation periods. Moreover, co-infections can further lead to genetic recombination which may generate new chimeric variants with unpredictable epidemic or pathogenic properties that could represent a serious health threat.

A Newly Engineered A549 Cell Line Expressing ACE2 and TMPRSS2 Is Highly Permissive to SARS-CoV-2, Including the Delta and Omicron Variants.

New variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue to emerge, causing surges, breakthrough infections, and devastating losses-underscoring the importance of identifying SARS-CoV-2 antivirals. A simple, accessible human cell culture model permissive to SARS-CoV-2 variants is critical for identifying and assessing antivirals in a high-throughput manner. Although human alveolar A549 cells are a valuable model for studying respiratory virus infections, they lack two essential host factors for SARS-CoV-2 infection: angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). SARS-CoV-2 uses the ACE2 receptor for viral entry and TMPRSS2 to prime the SARS-CoV-2 spike protein, both of which are negligibly expressed in A549 cells. Here, we report the generation of a suitable human cell line for SARS-CoV-2 studies by transducing human ACE2 and TMPRSS2 into A549 cells. We show that subclones highly expressing ACE2 and TMPRSS2 ("ACE2plus" and the subclone "ACE2plusC3") are susceptible to infection with SARS-CoV-2, including the delta and omicron variants. These subclones express more ACE2 and TMPRSS2 transcripts than existing commercial A549 cells engineered to express ACE2 and TMPRSS2. Additionally, the antiviral drugs EIDD-1931, remdesivir, nirmatrelvir, and nelfinavir strongly inhibit SARS-CoV-2 variants in our infection model. Our data show that ACE2plusC3 cells are highly permissive to SARS-CoV-2 infection and can be used to identify anti-SARS-CoV-2 drugs.