Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection.

At Wuhan, in December 2019, the SRAS-CoV-2 outbreak was detected and it has been the pandemic worldwide. This study aims to investigate the mutations in sequence of the SARS-CoV-2 genome and characterize the mutation patterns in Egyptian COVID-19 patients during different waves of infection. The samples were collected from 250 COVID-19 patients and the whole genome sequencing was conducted using Next Generation Sequencing. The viral sequence analysis showed 1115 different genome from all Egyptian samples in the second wave mutations including 613 missense mutations, 431 synonymous mutations, 25 upstream gene mutations, 24 downstream gene mutations, 10 frame-shift deletions, and 6 stop gained mutation. The Egyptian genomic strains sequenced in second wave of infection are different to that of the first wave. We observe a shift of lineage prevalence from the strain B.1 to B.1.1.1. Only one case was of the new English B.1.1.7. Few samples have one or two mutations of interest from the Brazil and South Africa isolates. New clade 20B appear by March 2020 and 20D appear by May 2020 till January 2021.

Clinical presentation of COVID-19-positive and -negative patients in Lagos Nigeria: A comparative study.

BACKGROUND: A lot has been documented about the pathophysiology and clinical presentation of coronavirus disease 2019 (COVID-19). We compared the clinical features of real-time reverse transcriptase polymerase-chain-reaction (RT-PCR) confirmed COVID-19 positive and negative patients admitted in Lagos State. METHODS: Medical records of all patients admitted in 15 isolation centres across Lagos state between 27th February 2020 and 30th September 2020, were abstracted and reviewed. We compared the clinical features, co-morbidities and clinical outcomes of COVID-19 positive and negative patients. RESULTS: A total of 3157 records of patients admitted in 15 isolation centres in Lagos State were reviewed of which 302 (9.6%) tested negative to RT-PCR COVID-19. There was no gender difference between COVID-19 positive and negative patients (P = 0.687). The average age of the negative patients was higher (46.8 ± 18.3 years) than positive patients (41.9 ± 15.5 years) (P < 0.001). A higher proportion of the COVID-19 negative patients had co-morbidity (38.1% vs. 27.8%), were symptomatic (67.5% vs. 44.6%) and higher mortality (21.9% vs. 6.6%) than positive patients (P < 0.001). The percentages with hypertension (26.2% vs. 21.0%, P = 0.038), diabetes (17.2% vs. 9.4%, P < 0.001), cardiovascular disease (2.3% vs. 0.9%, P < 0.029) and cancer (2.3% vs. 0.5%, P < 0.002) were more among patients without COVID-19. More patients without COVID-19 presented with fever (36.1% vs. 18.8%), cough (33.7% vs. 23.1%) and breathlessness (40.8% vs. 16.1%) than the positive patients (P < 0.001). CONCLUSION: Anosmia and dysgeusia were strongly associated with COVID-19. Clinical decision-making should only be used to prioritise testing and isolation of patients suspected to have COVID-19, especially in settings with limited access to diagnostic kits.

Genome sequencing of SARS-CoV-2 in a cohort of Egyptian patients revealed mutation hotspots that are related to clinical outcomes.

BACKGROUND: Severe acute respiratory syndrome-2 (SARS-CoV-2) exhibits a broad spectrum of clinical manifestations. Despite the fact that SARS-CoV-2 has slower evolutionary rate than other coronaviruses, different mutational hotspots have been identified along the SARS-CoV-2 genome. METHODS: We performed whole-genome high throughput sequencing on isolates from 50 Egyptian patients to see if the variation in clinical symptoms was related to mutations in the SARS-CoV-2 genome. Then, we investigated the relationship between the observed mutations and the clinical characteristics of the patients. RESULTS: Among the 36 most common mutations, we found two frameshift deletions linked to an increased risk of shortness of breath, a V6 deletion in the spike glycoprotein's signal peptide region linked to an increased risk of fever, longer fever duration and nasal congestion, and L3606-nsp6 deletion linked to a higher prevalence of cough and conjunctival congestion. S5398L nsp13-helicase was linked to an increased risk of fever duration and progression. The most common mutations (241, 3037, 14,408, and 23,403) were not linked to clinical variability. However, the E3909G-nsp7 variant was more common in children (2-13 years old) and was associated with a shorter duration of symptoms. The duration of fever was significantly reduced with E1363D-nsp3 and E3073A-nsp4. CONCLUSIONS: The most common mutations, D614G/spike-glycoprotein and P4715L/RNA-dependent-RNA-polymerase, were linked to transmissibility regardless of symptom variability. E3909G-nsp7 could explain why children recover so quickly. Nsp6-L3606fs, spike-glycoprotein-V6fs, and nsp13-S5398L variants may be linked to clinical symptom worsening. These variations related to host-virus interactions might open new therapeutic avenues for symptom relief and disease containment.

Genomic characterization of SARS-CoV-2 in Egypt.

Introduction: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread throughout the globe, causing a pandemic. In Egypt over 115,000 individuals were infected so far. Objective: In the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients. Methods: Nasopharyngeal swabs were collected from 61 COVID-19 patients who attended at National Cancer Institute, Kasr Al-Aini Hospital and the army hospital. Viral RNA was extracted and whole genomic sequencing was conducted using Next Generation Sequencing. Results: In all cases, the sequenced virus has at least 99% identity to the reference Wuhan 1. The sequence analysis showed 204 distinct genome variations including 114 missense mutations, 72 synonymous mutations, 1 disruptive in-frame deletion, 7 downstream gene mutations, 6 upstream gene mutations, 3 frame-shift deletions, and 1 in-frame deletion. The most dominant clades were G/GH/GR/O and the dominant type is B. Conclusion: The whole genomic sequence of SARS-CoV2 showed 204 variations in the genomes of the Egyptian isolates, where the Asp614Gly (D614G) substitution is the most common among the samples (60/61). So far, there were no strikingly variations specific to the Egyptian population, at least for this set of samples.

Organ donation during the COVID-19 pandemic.

The coronavirus disease 2019 (COVID-19) pandemic is a rapidly changing circumstance with dramatic policy changes and universal efforts to deal with the initial crisis and minimize its consequences. To identify changes to organ donation and transplantation during this time, an anonymous web-based survey was distributed to 19 select organ procurement organizations (OPOs) throughout the United States comparing 90-day activity during March-May 2020 and March-May 2019. Seventeen OPOs responded to the survey (response rate of 89.5%). Organ authorization decreased by 11% during the current pandemic (n = 1379 vs n = 1552, P = .0001). Organ recovery for transplantation fell by 17% (P = .0001) with a further 18% decrease in the number of organs transplanted (P = .0001). Donor cause of death demonstrated a 4.5% decline in trauma but a 35% increase in substance abuse cases during the COVID-19 period. All OPOs reported significant modifications in response to the pandemic, limiting the onsite presence of staff and transitioning to telephonic approaches for donor family correspondence. Organ donation during the current climate has seen significant changes and the long-term implications of such shifts remain unclear. These trends during the COVID-19 era warrant further investigation to address unmet needs, plan for a proportionate response to the virus and mitigate the collateral impact.