Identification, propagation and molecular characterization of SARS-CoV-2 delta variant isolated from Egyptian COVID-19 patients

Alotaibi, Badriyah; El‐Masry, Thanaa A.; Seadawy, Mohamed G.; Elharty, Bassem; Saleh, Asmaa; Gad, Ahmed F.; El-Hosseny, Mostafa F.; Mahran, Yasmen F.; El‐Bouseary, Maisra M.

doi:10.1016/j.meegid.2022.105278

Cited by 4 publications

(5 citation statements)

References 43 publications

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“…We worked with local distributors who imported them for us based on their availability. Overall, as shown by other studies, Real-Time RT-PCR assays are an efficient tool for rapid detection and surveillance of VOC [24][25][26].…”

Section: Plos Global Public Healthsupporting

confidence: 63%

Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings

Nasir

Aamir

Kanji

et al. 2023

PLOS Glob Public Health

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COVID-19 resulted in extensive morbidity and mortality worldwide. SARS-CoV-2 evolved rapidly, with increasing transmission due to Variants of Concern (VOC). Identifying VOC became important but genome submissions from low-middle income countries (LMIC) remained low leading to gaps in genomic epidemiology. We demonstrate the use of a specific mutation RT-PCR based approach to identify VOC in SARS-CoV-2 positive samples through the pandemic in Pakistan. We selected 2150 SARS-CoV-2 PCR positive respiratory specimens tested between April 2021 and February 2022, at the Aga Khan University Hospital Clinical Laboratories, Karachi, Pakistan. Commercially available RT-PCR assays were used as required for mutations in Spike protein (N501Y, A570D, E484K, K417N, L452R, P681R and deletion69_70) to identify Alpha, Beta, Gamma, Delta, and Omicron variants respectively. Three pandemic waves associated with Alpha, Delta and Omicron occurred during the study period. Of the samples screened, VOC were identified in 81.7% of cases comprising mainly; Delta (37.2%), Alpha (29.8%) and Omicron (17.1%) variants. During 2021, Alpha variants were predominant in April and May; Beta and Gamma variants emerged in May and peaked in June; the Delta variant peaked in July and remained predominant until November. Omicron (BA.1) emerged in December 2021 and remained predominant until February 2022. The CT values of Alpha, Beta, Gamma and Delta were all significantly higher than that of Omicron variants (p<0.0001). We observed VOC through the pandemic waves using spike mutation specific RT-PCR assays. We show the spike mutation specific RT-PCR assay is a rapid, low-cost and adaptable for the identification of VOC as an adjunct approach to NGS to effectively inform the public health response. Further, by associating the VOC with CT values of its diagnostic PCR we gain information regarding the viral load of samples and therefore the level of transmission and disease severity in the population.

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Section: Plos Global Public Healthsupporting

confidence: 63%

Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings

Nasir

Aamir

Kanji

et al. 2023

PLOS Glob Public Health

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Section: Discussionsupporting

confidence: 92%

“…The clade 20A with the S_D614G mutation was reported in 17 samples. Our findings regarding the prevalence of different clades during the third wave of the COVID-19 pandemic are consistent with previous studies conducted in Egypt and worldwide (Davies et al, 2021;Doghish et al, 2021;Gravagnuolo et al, 2021;Alotaibi et al, 2022a;Hart et al, 2022;Lambrou et al, 2022;Seadawy et al, 2022). Concerning mutations detected in the SARS-CoV-2 viral genome, the ORF1a, S, ORF1b, N, and ORF3a genes showed high-frequency mutations with 33 nonsynonymous mutations, including A570D, A1708D, D3L, D63G, D377Y, D614G, D950N, D1118H, G204R, G662S, I82T, I2230T, L452R, N501Y, P314L, P681H, P681R, P1000L, Q27*, R203K, R203M, S26L, S235F, S982A, T19R, T60A, T120I, T478K, T716I, T1001I, T3646A, and Y73C.…”

Section: Discussionsupporting

confidence: 92%

The Mutational Landscape of SARS-CoV-2 Variants of Concern Recovered From Egyptian Patients in 2021

Seadawy¹,

Binsuwaidan

Alotaibi

et al. 2022

Front. Microbiol.

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In December 2019, a mysterious viral pneumonia first developed in Wuhan, China, resulting in a huge number of fatal cases. This pneumonia, which was named COVID-19, was attributed to a novel coronavirus, SARS-CoV-2. The emerging SARS-CoV-2 mutations pose the greatest risk to human health because they could result in an increase in the COVID-19 severity or the failure of current vaccines. One of these notable mutations is the SARS-CoV-2 Delta variant (B.1.617) that was first detected in India and has rapidly expanded to 115 countries worldwide. Consequently, in this study, we performed next-generation sequencing and phylogenetic analysis of SARS-CoV-2 during the third wave of the pandemic to determine the SARS-CoV-2 variants of concern (VOC) prevalence in Egypt. We observed several mutational patterns, revealing that SARS-CoV-2 evolution has expanded in Egypt with a considerable increase in the number of VOC. Therefore, the Egyptian authorities should take an appropriate approach to investigate the compatibility of already employed vaccines with this VOC and to examine the efficacy of the existing therapeutic regimen against new SARS-CoV-2 variants.

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“…The entire country was enlisted on the list of international high-risk areas [ 38 ]. The situation was in line with reports that SARS-CoV-2 genomes from Israeli, Lebanese, and Egyptian patients were dominated by the Delta Variant during July to December 2021 [ 41 , 42 ]. Our study detected 45 cases of the Delta Variant who were Palestinian travelers arriving mainly from Turkey through the border bridge with Jordan and tested for COVID-19 directly upon arrival.…”

Section: Discussionsupporting

confidence: 89%

Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine

Ereqat,

Alikhan,

Al-Jawabreh

et al. 2024

Pathogens

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The emergence of new SARS-CoV-2 variants in Palestine highlights the need for continuous genetic surveillance and accurate screening strategies. This case series study aimed to investigate the geographic distribution and genetic variation of the SARS-CoV-2 Delta Variant in Palestine in August 2021. Samples were collected at random in August 2021 (n = 571) from eight districts in the West Bank, Palestine. All samples were confirmed as positive for COVID-19 by RT-PCR. The samples passed the quality control test and were successfully sequenced using the ARTIC protocol. The Delta Variant was revealed to have four dominant lineages: B.1.617 (19%), AY.122 (18%), AY.106 (17%), and AY.121 (13%). The study revealed eight significant purely spatial clusters (p < 0.005) distributed in the northern and southern parts of Palestine. Phylogenetic analysis of SARS-CoV-2 genomes (n = 552) showed no geographically specific clades. The haplotype network revealed three haplogroups without any geographic distribution. Chronologically, the Delta Variant peak in Palestine was shortly preceded by the one in the neighboring Israeli community and shortly followed by the peak in Jordan. In addition, the study revealed an extremely intense transmission network of the Delta Variant circulating between the Palestinian districts as hubs (SHR ≈ 0.5), with Al-Khalil, the district with the highest prevalence of COVID-19, witnessing the highest frequency of transitions. Genetic diversity analysis indicated closely related haplogroups, as haplotype diversity (Hd) is high but has low nucleotide diversity (π). However, nucleotide diversity (π) in Palestine is still higher than the global figures. Neutrality tests were significantly (p < 0.05) low, including Tajima’s D, Fu-Li’s F, and Fu-Li’s D, suggesting one or more of the following: population expansion, selective sweep, and natural negative selection. Wright’s F-statistic (Fst) showed genetic differentiation (Fst > 0.25) with low to medium gene flow (Nm). Recombination events were minimal between clusters (Rm) and between adjacent sites (Rs). The study confirms the utility of the whole genome sequence as a surveillance system to track the emergence of new SARS-CoV-2 variants for any possible geographical association and the use of genetic variation analysis and haplotype networking to delineate any minimal change or slight deviation in the viral genome from a reference strain.

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Identification, propagation and molecular characterization of SARS-CoV-2 delta variant isolated from Egyptian COVID-19 patients

Cited by 4 publications

References 43 publications

Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings

Tracking SARS-CoV-2 variants through pandemic waves using RT-PCR testing in low-resource settings

The Mutational Landscape of SARS-CoV-2 Variants of Concern Recovered From Egyptian Patients in 2021

Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine

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