Comparative analysis of SARS-CoV-2 variants Alpha (B.1.1.7), Gamma (P.1), Zeta (P.2) and Delta (B.1.617.2) in Vero-E6 cells: ultrastructural characterization of cytopathology and replication kinetics

Abstract This study compares the effects of virus-cell interactions among SARS-CoV-2 variants of concern (VOCs) isolated in Brazil in 2021, hypothesizing a correlation between cellular alterations and mortality and between viral load and transmissibility. For this purpose, reference isolates of Alpha, Gamma, Zeta, and Delta variants were inoculated into monolayers of Vero-E6 cells. Viral RNA was quantified in cell supernatants by RT‒PCR, and infected cells were analyzed by Transmission Electron Microscopy (TEM) for qualitative and quantitative evaluation of cellular changes 24, 48, and 72 hours postinfection (hpi). Ultrastructural analyses showed that all variants of SARS-CoV-2 altered the structure and function of mitochondria, nucleus, and rough endoplasmic reticulum of cells. Monolayers infected with the Delta variant showed the highest number of modified cells and the greatest statistically significant differences compared to those of other variants. Viral particles were observed in the cytosol and the cell membrane in 100 % of the cells at 48 hpi. Alpha showed the highest mean particle diameter (79 nm), and Gamma and Delta were the smallest (75 nm). Alpha and Gamma had the highest particle frequency per field at 48 hpi, while the same was observed for Zeta and Delta at 72 hpi and 24 hpi, respectively. The cycle threshold of viral RNA varied among the target protein, VOC, and time of infection. The findings presented here demonstrate that all four VOCs evaluated caused ultrastructural changes in Vero-E6 cells, which were more prominent when infection occured with the Delta variant.

Sub-lineages of the Omicron variant of SARS-CoV-2: characteristic mutations and their relation to epidemiological behavior / Sub-linajes de la variante Ómicron del SARS-CoV-2: mutaciones características y su relación con el comportamiento epidemiológico

Abstract By the end of 2021, the Omicron variant of SARS-CoV-2, the coronavirus responsible for COVID-19, emerges, causing immediate concern, due to the explosive increase in cases in South Africa and a large number of mutations. This study describes the characteristic mutations of the Omicron variant in the Spike protein, and the behavior of the successive epidemic waves associated to the sub-lineages throughout the world. The mutations in the Spike protein described are related to the virus ability to evade the protection elicited by current vaccines, as well as with possible reduced susceptibility to host proteases for priming of the fusion process, and how this might be related to changes in tropism, a replication enhanced in nasal epithelial cells, and reduced in pulmonary tissue; traits probably associated with the apparent reduced severity of Omicron compared to other variants.

Resumen A finales de 2021 surge la variante Omicron del SARS-CoV-2, el coronavirus responsable de la COVID-19, causando preocupación inmediata, debido al aumento explosivo de casos en Suráfrica, y a su gran cantidad de mutaciones. Este estudio describe las mutaciones características de la variante Ómicron en la proteína de la Espiga (S) y el comportamiento de las sucesivas olas epidémicas asociadas a la circulación de sus sub-linajes en todo el mundo. Las mutaciones en la proteína S descritas están relacionadas con su capacidad para evadir la protección provocada por las vacunas actuales, así como su posible susceptibilidad reducida a las proteasas del hospedero para la preparación del proceso de fusión. Se infiere cómo esto podría estar relacionado con su cambio en el tropismo, con una replicación mayor en las células epiteliales nasales y menor en el tejido pulmonar, rasgos probablemente asociados a su aparente menor gravedad en comparación con otras variantes.

Omicron and vaccine booster dose – an update

Mutations in coronavirus is not unheard off. The variant, Omicron B.1.1.529 has overall 50 mutations and is considered as a variant of concern. Though the new variant has shown changes throughout its genome, S gene changes predominate. Significant changes in the S encoding gene, S gene, influences not only the transmissibility properties of SARS-CoV-2 but also the efficacy of existing vaccines. Increased transmissibility and ability of this variant to evade host immune responses conferred either due to past infections or due to vaccination driving increase in number of infections. However, the severity of the infections is low in comparison to its predecessors. A meta-analysis of ten studies analyzing the effect of COVID-19 vaccine booster dose, it was found studies report 10-to-42-fold increase in omicron neutralization. COVID appropriate behaviors, if followed rigidly can bring a meaningful change in the viral spread and resultant health impacts.

The Emergence of Omicron: Challenging Times Are Here Again!

COVID-19 has been reported to have caused more than 286 million cases and 5.4 million deaths till date. COVID variants have appeared at regular intervals—alpha, beta, gamma, delta and now omicron. ‘Omicron’ is driving the current surge of cases in most countries including India and is poised to replace ‘delta’ the world over. This variant with more than 50 mutations is phylogenetically very diferent from other variants. The omicron variant spreads rapidly with an average doubling time of two days. The disease so far has been mild as compared with delta. Though previous infection and vaccination ofer little or no protection against infection with omicron, they do seem to partially protect against hospitalization and severe disease. Booster vaccinations have not made any notable impact on the spread of omicron and have further worsened global vaccine equity. The indirect consequences of omicron from lockdowns, restrictions, travel bans, economic losses, health care worker infections and overwhelming of health care facilities are likely to be enormous. The direct efects of omicron on children are expected to be mild like with the previous variants. However, the indirect efects on child mental, physical, and social health may be considerable owing to school closures, missed vaccinations, neglect of other diseases, etc. It is, therefore, imperative that governments take rational decisions to navigate the world through this latest crisis.

Detection of the Omicron variant of SARSCoV-2 by restriction analysis targeting the mutations K417N and N440K of the spike protein / Detección de la Variante Ómicron del SARS-CoV-2 por análisis de restricción de dos mutaciones de la proteína de la espiga

Abstract By the end of 2021, the Omicron variant of concern (VOC) emerges in South Africa. This variant caused immediate concern, due to the explosive increase in cases associated with it and the large number of mutations it exhibits. In this study, the restriction sites that allow detecting the mutations K417N and N440K in the Spike gene are described. This analysis allows us to propose a rapid method for the identification of cases infected with the Omicron variant. We show that the proposed methodology can contribute to provide more information on the prevalence and rapid detection of cases of this new VOC.

Resumen Para finales de 2021 surge la variante de preocupación (VOC por sus siglas en inglés) Ómicron en Sudáfrica. Esta variante causó de forma inmediata preocupación, debido al aumento explosivo de casos asociados a ella y al gran número de mutaciones que exhibe. En este estudio, se describen los sitios de restricción que permiten detectar dos de estas mutaciones en el gen de la espiga, las mutaciones K417N y N440K. Este análisis permite proponer un método rápido para la identificación de casos infectados con la variante Ómicron. Mostramos que la metodología propuesta puede contribuir a proporcionar más información sobre la prevalencia y a detectar rápidamente los casos de esta nueva VOC.

Clinical profile of patients infected with suspected SARS-CoV-2 Omicron variant of concern, Tamil Nadu, India, December 2021-January 2022

Background & objectives: COVID-19 cases have been rising rapidly in countries where the SARS-CoV-2 variant of concern (VOC), Omicron (B.1.1.529) has been reported. We conducted a study to describe the epidemiological and clinical characteristics and outcomes of COVID-19 patients with ‘S’ gene target failure (SGTF, suspected Omicron). Furthermore, their clinical outcomes with COVID-19 patients with non-SGTF (non-Omicron) were also compared. Methods: This study was conducted in Tamil Nadu, India, between December 14, 2021 and January 7, 2022 among patients who underwent reverse transcription-PCR testing for SARS-CoV-2 in four laboratories with facilities for S gene screening. Consecutively selected COVID-19 patients with SGTF were telephonically contacted, seven and 14 days respectively after their date of positive result to collect information on the socio-demographic characteristics, previous history of COVID-19, vaccination status and clinical course of illness along with treatment details. To compare their outcomes with non-SGTF patients, one randomly suspected non-Omicron case for every two suspected Omicron cases from the line-list were selected, matching for the date of sample collection and the testing laboratory. Results: A total of 1175 SGTF COVID-19 patients were enrolled for this study. Almost 6 per cent (n=72) reported a history of previous infection. 141 (13.5%) suspected Omicron cases were non-vaccinated, while 148 (14.2%) and 703 (67.4%) had received valid one and two doses of COVID-19 vaccines, respectively. Predominant symptoms reported included fever (n=508, 43.2%), body pain (n=275, 23.4%), running nose (n=261, 22.2%) and cough (n=249, 21.2%). Five (0.4%) of the 1175 suspected Omicron cases required oxygen supplementation as compared to ten (1.6%) of the 634 suspected non-Omicron cases. No deaths were reported among omicron suspects, whereas there were four deaths among suspected non-Omicron cases. Interpretation & conclusions: Majority of the suspected Omicron cases had a mild course of illness. The overall severity of these cases was less compared to the suspected non-Omicron cases.

Five patients with novel coronavirus Omicron variant of concern infection / 中华危重病急救医学

Objective:To analyze clinical characteristics of patients with novel coronavirus Omicron variant of concern infection, and to provide practical data and experience for subsequent clinical treatment.Methods:A retrospective analysis was performed for the clinical data of 5 cases with novel coronavirus Omicron variant of concern infection treated in the First Hospital of Jiaxing from December 18, 2021 to January 28, 2022. The patients' clinical data were recorded, including gender, age, length of hospital stay, vaccination status, clinical symptoms, laboratory indicators [white blood cell count (WBC), lymphocyte count (LYM), eosinophil count (EOS), hypersensitivity C-reactive protein (hs-CRP), novel coronavirus antibody immunoglobulin (IgG and IgM)], chest CT, treatment course and disease outcome.Results:All 5 patients were male, aged 24-37 years old. Four patients were vaccinated with novel coronavirus vaccine (one patient received 3 doses of the vaccine and 3 patients received only the first 2 doses of the vaccine), and no infection was found in chest CT. Laboratory examination showed that WBC, LYM, EOS and hs-CRP levels were normal, and only showed mild symptoms of upper respiratory tract infection. One patient was not vaccinated with novel coronavirus vaccine, and signs of viral pneumonia could be seen in chest CT, laboratory examination showed that WBC and hs-CRP levels increased, suggesting that bacterial infection, fever, cough, sputum and other respiratory symptoms were obvious, and the treatment time was long. All 5 patients were treated with Chinese medicine Lotus antipyretic and Baihu Yinqiao decoction based on routine antiviral therapy.Conclusions:Patients with novel coronavirus Omicron variant of concern infection vaccinated with the novel coronavirus vaccine have milder clinical symptoms, with less obvious chest CT findings and faster recovery. Chinese medicine Lotus antipyretic and Baihu Yinqiao decoction has obvious therapeutic effect on such patients.

Clinical and epidemiological aspects of Delta and Gamma SARS-CoV-2 variant of concern from the western Brazilian Amazon

BACKGROUND The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become a major concern contributing to increased morbidity and mortality worldwide. OBJECTIVES Here we describe the replacement of the Gamma variant of concern (VOC) with Delta in the western Brazilian Amazon. METHODS In this study, we analysed 540 SARS-CoV-2 positive samples determined by qualitative real-time RT-PCR selected in the state of Rondônia between June and December 2021. The positive cohort was sequenced through next-generation sequencing (NGS) and each sample was quantified using real-time RT-qPCR, the whole genome sequence was obtained, SARS-CoV-2 lineages were classified using the system Pango and the maximum likelihood (ML) method was used to conduct phylogenetic analyses. FINDINGS A total of 540 high-quality genomes were obtained, where the Delta VOC showed the highest prevalence making up 72%, with strain AY.43 being the most abundant, while the Gamma VOC was present in 28%, where the P.1 strain was the most frequent. In this study population, only 32.96% (178/540) had completed the vaccination schedule. MAIN CONCLUSIONS This study highlighted the presence of Gamma and Delta variants of SARS-CoV-2 in RO. Furthermore, we observed the replacement of the Gamma VOC with the Delta VOC and its lineages.

Analytical evaluation of thirty-two severe acute respiratory syndrome 2 lateral flow antigen tests demonstrates sensitivity remains with the SARS-CoV-2 Gamma lineage

ABSTRACT Background: The emergence of variants of concern (VOCs) requires an ongoing assessment of the performance of antigen lateral flow tests (Ag-RDTs). The limit of detection (LOD) of 32 Ag-RDTs was evaluated using the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Gamma variant. Methods: Ag-RDTs were performed according to the manufacturer's instructions with a clinical isolate of the Gamma variant. Results: Twenty-eight of the 32 Ag-RDTs exceeded the World Health Organization criteria. Conclusions: This comprehensive analytical evaluation of Ag-RDTs demonstrated that the test performance was maintained with Gamma VOC.

Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq

Abstract Despite vaccine development and vaccination programs underway around the globe, the coronavirus disease 2019 (COVID-19) pandemic has not been controlled as the SARS-CoV-2 virus is evolving and new variants are emerging. This study was conducted to sequence and molecularly characterize the representing samples from the early fourth SARS-CoV-2 wave in Iraq. Here, we have performed next-generation sequencing of whole-genome sequencing of two representing samples from the country's early beginning of the fourth pandemic wave. The samples were sequenced using Illumina Miseq system, and the reference sequences were retrieved from GISAID database. Phylogenetic analysis was performed through Mega software. This study provides an initial sequence analysis and molecular characterization of the first Omicron variant cases recorded in the country. Our analysis revealed many mutations on the spike glycoprotein, especially on the receptor binding domain, with potential impact on immune escape and infectivity. The study findings suggest considering the highly mutated immunogenic epitope of the Omicron variant as a reference for developing a new vaccine for combating the ongoing pandemic.

OMICRON-THE VARIANT OF CONCERN (VoC): A RAPID REVIEW

A new variant of coronavirus B.1.1.529. appeared on the scene, when discovered by the researchers in South Africa on Nov 24.2021. It is a heavily mutated variant of coronavirus discovered thus far with over 50+ mutations with 32 mutations over the spike protein itself. Spike proteins help the virus to bind to the bodily receptors of humans to gain entry inside. In comparison to the delta variant, which had nine mutations, it means that Omicron has better chances of evading the host immunity and is also more transmissible. And rightly so, it has been declared as a variant of concern(VoC) by the WHO. The presence of S- gene is of the determinants for the detection of the virus. But omicron seems to have missed this gene- being called as S-gene dropout or S-gene target failure (S- spike glycoprotein)

Variante Ómicron SARS-CoV-2: una nueva variante de preocupación / Ómicron SARS-CoV-2 variant: anew variant of concern

Ha surgido una nueva variante de preocupación de SARS-CoV-2, cuyos efectos en la evolución de la pandemia parecen inciertos. Sin embargo, ha comenzado a surgir evidencia con respecto al comportamiento viral en cuanto a su transmisibilidad, unión a receptor de la célula hospedadora y escape del sistema inmune. Presentamos una revisión actualizada de los datos existentes en la literatura respecto a los aspectos microbiológicos y epidemiológicos que pueden ayudarnos a comprender las futuras investigaciones en esta variante.(AU)

A new variant of concern for SARS-CoV-2 has emerged, the effects of which on the evolution of the pandemic appear uncertain. However, evidence has begun to emerge regarding viral behavior in terms of its transmissibility, receptor binding on the host cell, and escape from the immune system. We present an updated review of the existing data in the literature regarding the microbiological and epidemiological aspects that can help us understand future research on this variant.(AU)

Genomic characteristics of 2019 novel coronavirus from imported cases of coronavirus disease 2019 in Henan Province / 中华传染病杂志

Objective:To analyze the evolutionary characteristics and variations of 2019 novel coronavirus (2019-nCoV) strains imported from abroad in Henan Province.Methods:A total of 16 imported cases of coronavirus disease 2019 (COVID-19) reported in Henan Province from May to December 2020 were enrolled. The throat swab specimens from the patients were collected and sent to the Henan Provincial Center for Disease Control and Prevention for whole genome sequencing. Taking SARS-CoV-2 Wuhan-Hu-1 published in Global Initiative on Sharing All Influenza Data (GISAID) as the reference sequence, the sequences were aligned and analyzed by MEGA X, and the phylogenetic tree was constructed by the maximum likelihood method.Results:Among 16 cases, 13 cases were imported from Russia, two cases were imported from Myanmar, and one case was imported from Ukraine. A total of 16 strains of 2019-nCoV genomes with the lengths of 29 804 bp to 29 882 bp were obtained. A total of 145 nucleotide mutations and 80 amino acid mutations were detected. Nucleotide variations of C241T, C3037T, C14408T, A23403G and the amino acid variation of D614G in spike protein were detected in all sequences. Meanwhile, insertion A at the site of 29704 was found in BetaCov/HEN02/Human/2020, BetaCov/HEN04/Human/2020 and BetaCov/HEN05/Human/2020. Deletion variation was not found. Phylogenetic analysis showed that there was no correlation between the 16 strains and currently epidemic variants of concern (VOC) .Conclusion:From May to December 2020, the detection of viral genome mutations in the imported cases of Henan Province shows randomness and diversity, while the strains are not VOC.

Characteristics and control measures of 2019 novel coronavirus Delta variant of concern / 中华危重病急救医学

2019 novel coronavirus (2019-nCoV) Delta variant of concern (VOC) is one of the variants of 2019-nCoV, which has the characteristics of strong transmission, high pathogenicity, and rapid progression. 2019-nCoV Delta VOC has caused a global pandemic. Understanding the characteristics of 2019-nCoV Delta VOC and implementing targeted control measures are important aspects of controlling the pandemic. In this paper, the characteristics and control measures of 2019-nCoV Delta VOC were reviewed.