ABSTRACT
The genetic evolution of SARS-CoV-2 began in February 2020, with G614 spike protein strains superseding D614 strains globally. Since then with each subsequent mutations, the SARS-CoV-2 variants of concern, namely Alpha, Beta, Gamma, Delta and Omicron, superseded the previous one to become the dominant strain during the pandemic. By the end of November 2022, the Omicron variant and its descendent lineages account for 99.9% of sequences reported globally. All five VOCs have mutations located in the RBD of the spike protein, resulting in increased affinity of the spike protein to the ACE2 receptors resulting in enhanced viral attachment and its subsequent entry into the host cells. In vitro studies showed the mutations in spike protein help increase the viral fitness, enhancing both transmissibility and replication. In general, Alpha, Beta, Gamma, and Delta variants, were reported with higher transmissibility of 43-90%, around 50%, 170-240%, or 130-170% than their co-circulating VOCs, respectively. The Omicron however was found to be 2.38 times and 3.20 times more transmissible than Delta among the fully-vaccinated and booster-vaccinated households. Even the SARS-Cov-2 Omicron subvariants appear to be inherently more transmissible than the ones before. With the broader distribution, enhanced evasion, and improved transmissibility, SARS-CoV-2 variants infection cause severe diseases due to immune escape from host immunity and faster replication. Reports have shown that each subsequent VOC, except Omicron, cause increased disease severity compared with those infected with other circulating variants. The Omicron variant infection however, appears to be largely associated with a lower risk of hospitalisation, ICU admission, mechanical ventilation, and even a shorter length of hospital stay. It has been shown that the relatively much slower replication of the Omicron variants in the lung, resulted in a less severe disease.Copyright © 2022, Malaysian Society of Pathologists. All rights reserved.
ABSTRACT
Purpose : Coronavirus-19 (COVID-19) has been associated with ophthalmic manifestations. The relationship between tear film SARS-CoV-2 RNA, timing of illness and eye disease are unknown. We evaluated hospitalized COVID-19 inpatients for retinopathy and tear film viral RNA. Methods : Hospitalized COVID-19 inpatients were offered enrollment from January-June 2021. Full dilated ophthalmic examination and conjunctival swabs were taken for triplex RT-PCR for SARS-CoV-2 RNA targeting N2, E and RNAse P. Demographic, clinical outcomes and laboratory data were collected. Univariate and multivariate analyses of systemic disease and laboratory risk factors for retinopathy and SARS-CoV-2 RNA detection were assessed. Results : Sixty patients were prospectively enrolled in this cross-sectional, observational study. The mean age was 58.8 years (Standard deviation [SD] 15.2 years) and 29 (48%) were female. Retinopathy associated with COVID-19 in 12 of 60 patients (20%). Univariate analyses revealed that younger age, greater body mass index (BMI) and extracorporeal membrane (ECMO) requirement were associated with increased odds of COVID-19 retinopathy. The mean age (SD) of patients with COVID-19 retinopathy was 49.0. (11.6) compared to 61.2 (15.1) years in individuals without retinopathy (p=0.01). The mean BMI was 38.8 (9.8) in patients with retinopathy compared to 31.8 (9.0) in those without retinal disease findings (p=0.04). ECMO requirement was observed in 33% of patients with retinopathy compared to 8% in those without retinopathy (p=0.04). Multivariate analyses trended towards increased risk of retinopathy with younger age (aOR 0.95 (95% CI 0.90- 1.01, p=0.095) and with increased BMI (aOR. 1.08, 95% CI 1.00-1.18, p=0.056). Fifteen of 60 patients (25%) tested positive in their tear film for SARS-CoV-2 RNA with a trend towards a shorter length of illness and hospitalization in patients who were positive. The N2 gene was particularly sensitive with 18 of 19 eyes (94.7%) showing N2-positivity (with or without E gene detection), including 2 patients in whom the B.117 / B.1.525 alpha or ?United Kingdom? variant was detected. Conclusions : A 20% rate of retinopathy was observed and SARS-CoV-2 RNA within tear film was detected in 25% of hospitalized COVID-19 patients. Continued infection control precautions are required given the risk of viral RNA in tear film, which may also be sensitive for the detection of COVID-19 variants.
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Introduction/ Background: In Senegal, SARS-CoV-2 incidence evolved with three successive epidemic waves. The first wave started on March 2020 with low virus variability whilst the second outbreak started in December was dominated by the Alpha variant. With the third taking place in June 2021, we investigated the involvement of other variants. Methods: During three waves of the pandemic, 163,788 nasopharyngeal swabs have been analysed at the Institut de Recherche en Santé, de Surveillance Epidémiologique et de Formations (IRESSEF). From those, 10,189 positive samples were screened with Seegene Real-time reverse-transcription polymerase chain reaction RT-PCR new variant. From the screened samples, 972 positives were sequenced and 10% of the negatives for detection of new variants. The ARTIC Network methodology with Oxford Nanopore Technologies (ONT) has been used for sequencing. Results: Our data have overall shown that the Senegalese strains are very similar to each other or closely related to other. During the first wave, the most common clade found was 19A (70.27%) and majority of the samples were of the B.1 (54.05) lineage. We noted more diversity during the second wave where clade 20B (40.82%) was more frequent, followed by clade 20A (28.91%), 20I (10.54%). At the level of lineages, we identified variants of interest as B.1.1.7 (10.54%), B.1.525 (6.12%), and B.1.617.2 (0.68%). In the third wave, we observed at the clade level with mainly 21D (47.69%) and 21A (20%). Impact: SARS-CoV-2 diversity may affect the virus's properties, such as it spreads, disease severity, performance of vaccines, tools, or other public health and social measures. Therefore, such tracking of SARS-CoV-2 variants highlight the role some African institutes like IRESSEF surveillance capabilities through real-time sequencing of SARS-CoV-2 genomes in the local context. Conclusion: In Senegal, the SARS-CoV-2 pandemic has disrupted the organization of the health system. IRESSEF contributed to put in place strategies to respond effectively to the expectations of medical authorities by providing them with data on the strains circulating in Senegal at each moment of the epidemic.
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Introduction/ Background: In this cross-sectional study, we conducted genomic surveillance of SARS-CoV-2 with the aim of identifying emerging variants and tracking the genomic evolution of the virus. Furthermore, we analyzed the trends of SARS-CoV-2 lineages over time in Uganda. Methods: We performed SARS-CoV-2 whole-genome deep sequencing on samples collected between June- August 2021 from 107 patients (RT-PCR Ct values < 26) from 10 Districts in central (Kampala, Wakiso, Mpigi, Kalungu, Kalangala, Kassanda and Mityana) and northern (Dokolo, Amudat, Moroto) Uganda. Sequencing was done using the Illumina Miseq and Oxford Nanopore MinION next generation sequencing platforms. Deep sequence reads were assembled using Genome Detective and Nanopolish/Medaka (ARTIC). Quality control of the sequences was done using Nextclade and Geneious followed by lineage analysis using PANGOLIN (Phylogenetic Assignment of Named Global Outbreak LINeages). Results: 102 (95.3%) of 107 genomes were of the Delta variant (B.1.617.2). Delta AY sub-lineages detected at low prevalence included AY.1, AY.4, AY.16, AY.33 and AY.39. One AY.1 (delta plus) and 2 AY.16 sub-lineages were identified. Additionally, 1 Kappa B.1.617.1 variant was detected. Other minority lineages included A, B and Eta (B.1.525). By 20th September 2021, 712 SARSCoV- 2 sequences from Uganda had been deposited in GISAID (https://www.gisaid.org) and between December 2020 to January 2021, the A.23.1 variant dominated. The first Delta variant (B.1.617.1) sample was collected in March 2021 and by June 2021, Delta accounted for >90% of all detected variants. Impact: This study provides valuable information on the circulating variants and lineages in Uganda and contributes towards the national SARS-CoV-2 genomic surveillance. However, a major limitation of the study is the suboptimal sampling as a result of funding challenges. Conclusion: In Uganda, Delta has largely replaced other variants and is the dominant circulating SARS-CoV-2 variant. Study findings suggest that continued SARS-CoV-2 genomic surveillance from recently collected samples is critical to keep track of the circulating and emerging variants.
ABSTRACT
The SARS-CoV-2 genetic variants emergence doesn't spare the West African continent which has to face vaccination implementation delay. Beside classical qRT-PCR diagnostic testing, strengthening of sequencing capacity is the cornerstone for tracking and fighting the emergence of SARS-CoV-2 variants in real time. From March 12th, 2020 to July 16th, 2021, a panel of 136 full length genomes of SARS-CoV-2 mutants/variants present in human nasopharyngeal swab samples conserved in the Biobank of the Institut Pasteur De Guinée were sequenced using Illumina methodology. The Guinean sequences, originating from the general population, expatriates, and travelers, were distributed into 7 clades. During March- August 2020, the sequences were exclusively distributed into 2 clades, 20A and 20B, most originating from Europe. The 20D and 20C clades were furtively observed in October 2020 and February 2021 respectively. The SARS-CoV-2 variant of concern (VOC) 20I/B.1.1.7/Alpha was first identified in January 2021, increased in incidence up to March 2021, and then decreased from April to June 2021, corresponding to the dynamic described in Africa. The variant of interest (VOI) 21D/B.1.525/Eta originating from Nigeria circulated in February-May 2021. The 21A/B.1.617.2/Delta VOC was detected from May 2021 in Guinea, became dominant in July and persisted behind the present sampling over August and September 2021. A similar dynamic was globally observed in Africa resulting in a clear increase of lethality in the population. In contrast, other variants previously found in Africa, such as the 20H/B.1.351/Beta VOC and variants from the sublineage A (A.23.1 lineage from East Africa and the A.27 lineage), were not detected in this study. This overview of SARS-CoV-2 over 1.5 years in Guinea demonstrates that virus clades, VOC and VOI were progressively introduced, mostly by travelers through the Conakry Airport, before spreading through the country. The tracking of viral evolution by sequencing is a continuous task. Since November 2021, a new wave is related to the emergence of the VOC Omicron. Making countries autonomous in sequencing is a challenge in Africa, not only to fight Covid-19, but also to face the numerous other emerging zoonoses which circulate across the continent.