SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study.

A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient's samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulins using chemiluminescence immunoassay and its correlation with neutralizing antibodies.

BACKGROUND: Neutralizing antibodies (NAbs) against SARS-CoV-2 infection have a pivotal role in protective immune response; however, their measurement requires specialized facilities. We evaluated the degree of correlation between NAbs and anti-SARS-CoV-2 IgG/total Ig antibodies detected by chemiluminescent immunoassay in asymptomatic and previously symptomatic SARS-CoV-2 patients. METHODS: A total of 1241 participants (previously symptomatic patients and asymptomatic individuals), who were screened for SARS-CoV-2 infection by RT-PCR or serology, were enrolled in our study. Sera were analyzed for the presence of anti-spike-1(S1)-SARS-CoV-2 IgG/total Ig antibodies, using Ortho Clinical Diagnostics, USA. A signal/cut-off value (S/CO) ≥ 1 was considered reactive. NAbs were measured in 103 random samples from groups using microneutralization assay, with titer ≥ 1:10 being considered positive. RESULTS: Asymptomatic (n = 229) and 261 previously symptomatic individuals with positive serology and negative RT-PCR were finally included. Significant higher anti-S1-IgG titers were seen in asymptomatic individuals (P < 0.0001). Conversely, anti-S1-total Ig titers were significantly higher in previously symptomatic (P < 0.0001). NAbs were detected in both groups, however, higher titers were seen in previously symptomatic patients. There is a correlation between NAbs and both IgG/total anti-S1-SARS-CoV-2 antibodies (r = 0.47, P < 0.0001 and r = 0.49, P < 0.0001, respectively). IgG and total Ig could predict a neutralization titer of ≥ 1:160 at S/CO >4.44 and >65 with AUC 0.69 and 0.67, respectively. CONCLUSION: Asymptomatic SARS-CoV-2 infection can produce comparable antibodies response to previously symptomatic individuals, however higher neutralization activity was seen in the previously symptomatic. Anti-S1-SARS-CoV-2 IgG/total Ig antibodies showed a correlation with neutralization activity and can be used to estimate the presence of protective immunity.

Safety and immunogenicity evaluation of inactivated whole-virus-SARS-COV-2 as emerging vaccine development in Egypt.

BACKGROUND: Current worldwide pandemic coronavirus disease 2019 (COVID-19) with high numbers of mortality rates and huge economic problems require an urgent demand for safe and effective vaccine development. Inactivated SARS-CoV2 vaccine with alum. Hydroxide can play an important role in reducing the impacts of the COVID-19 pandemic. In this study, vaccine efficacy was evaluated through the detection of the neutralizing antibodies that protect mice from challenge with SARS-CoV 2 3 weeks after the second dose. We conclude that the vaccine described here has safety and desirable properties, and our data support further development and plans for clinical trials. METHODS: Characterized SARS-COV-2 strain, severe acute respiratory syndrome coronavirus 2 isolates (SARS-CoV-2/human/EGY/Egy-SERVAC/2020) with accession numbers; MT981440; MT981439; MT981441; MT974071; MT974069; and MW250352 at GenBank were isolated from Egyptian patients SARS-CoV-2-positive. Development of inactivated vaccine was carried out in a BSL-3 facilities and the immunogenicity was determined in mice at two doses (55 and 100 µg per dose). RESULTS: The distinct cytopathic effect induced by SARS-COV-2 propagation on Vero cell monolayers and the viral particles were identified as Coronaviridae by transmission electron microscopy and RT-PCR on infected cells cultures. Immunogenicity of the developed vaccine indicated the high antigen-binding and neutralizing antibody titers, regardless of the dose concentration, with excellent safety profiles and no deaths or clinical symptoms in mice groups. The efficacy of the inactivated vaccine formulation was tested by the wild virus challenge of the vaccinated mice and viral replication detection in lung tissues. CONCLUSIONS: Vaccinated mice recorded complete protection from challenge infection via inhibition of SARS-COV-2 replication in the lung tissues of mice following virus challenge, regardless of the level of serum neutralizing antibodies. This finding will support future trials for the evaluation of an applicable SARS-CoV-2 vaccine candidate.

Prevalence of SARS-CoV-2 infection and dynamics of antibodies response among previously undiagnosed healthcare workers in a university hospital: A prospective cohort study.

BACKGROUND: Healthcare workers (HCWs) are a presumed high-risk population for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Identifying factors associated with seroprevalence can help establish better practices in healthcare settings. In this study, we evaluate prevalence of SARS-CoV-2 infection among previously undiagnosed HCWs and describe profiling of antibody responses against SARS-CoV-2, including neutralizing antibodies (NAbs). METHODS: We analyzed a cohort of 386 HCWs in a university hospital in Egypt and 725 volunteers not affiliated to any healthcare facility (non-healthcare workers - NHCWs). Participants provided a nasopharyngeal swab and serum samples for SARS-CoV-2 nucleic acid and SARS-CoV-2-specific antibodies, respectively. HCWs who tested positive by either test were sequentially monitored. RESULTS: At baseline, point prevalence of viral carriage was 11.4% in HCWs (n = 44/386) and 11.9% in NHCWs (86/725). The cumulative prevalence of SARS-CoV-2 infection among HCWs considering all studies was 25.6%, which was statistically lower than in NHCWs (41.0%). Prevalence was greatest among janitorial staff (45.9%) and the most affected departments were gastroenterology (31.1%), and emergency medicine (30.0%). Prior anosmia, fever or headache were associated with higher odds of positivity for SARS-CoV-2 infection. Regarding serial antibody measurements, RT-PCR-positive HCWs displayed IgG detection rates of 29.5%, 70% and 60% at visit 1, visit 2 and visit 3, respectively with slow decline of median IgG antibody titers, whereas, corresponding detection rates for total Ig antibodies were 50%, 90.3%, and 88.9%, respectively with increasing median titers. NAbs measured at each time point were positively correlated with total Ig levels, whereas IgG levels were positively correlated with NAbs at visit 1 and visit 3. CONCLUSION: Our results demonstrate lower cumulative prevalence of SARS-CoV-2 infection in HCWs than general population and suggest that asymptomatic HCWs exhibit considerable IgG and total Ig antibodies response as well as NAbs for up to 120 days, with positive correlation in between.

SARS-CoV-2 infection among asymptomatic healthcare workers of the emergency department in a tertiary care facility.

BACKGROUND: Healthcare workers (HCWs) represent a high-risk category during the coronavirus disease 2019 (COVID-19) pandemic crisis, with frontline HCWs at emergency departments (EDs) may be at an even higher risk. Determining the spread of infection among HCWs may have implications for infection control policies in hospitals. This study aimed to detect severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection among asymptomatic HCWs of the ED of a large tertiary center in Cairo, Egypt. METHODS: The study was conducted from June 1st to June 14th, 2020. All the recommended national and international indications on infection control measures were followed. Two hundred and three HCWs were included in the study and tested by nasopharyngeal swab (NPS) and rapid serological test (RST). Descriptive statistical analyses were used to summarize the data. RESULTS: Of the 203 HCWs, 29 (14.3 %) tested positive by real-time reverse transcription polymerase chain reaction (RT-PCR). Thirty-seven (18.2 %) HCWs tested positive with RST: 20 with both IgM and IgG; 14 with IgM only, and 3 with IgG only. Age, gender, and/or occupation were not risk factors for SARS-CoV-2 infection. CONCLUSIONS: Point prevalence of COVID-19 in asymptomatic HCWs in ED of tertiary care facility is 14.3 % by RT-PCR. This illustrates the importance of screening all HCWs regardless of symptoms, and the need for strict measures in securing HCWs to reduce transmission from healthcare facilities to the community during the current pandemic.

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.

SARS-CoV-2 infection among healthcare workers of a gastroenterological service in a tertiary care facility.

BACKGROUND AND STUDY AIMS: Frontlines healthcare workers (HCWs) during the coronavirus disease 2019 (COVID-19) pandemic are at increased risk of infection by SARS-CoV-2, but there are limited data on the prevalence of COVID-19 among HCWs in Egypt. This study aimed to assess SARS-CoV-2 infection among HCWs providing gastroenterological services. SUBJECTS AND METHODS: Seventy-four HCWs at the gastroenterological service of Al-Manial University Hospital, the main hospital of the largest tertiary university hospitals complex in Egypt (Kasr Al-Ainy Faculty of Medicine, Cairo University) were tested using real-time reverse transcription-polymerase chain reaction (RT-PCR) on nasopharyngeal samples, and rapid serological IgM/IgG tests (RST). A questionnaire was used to collect demographic, occupational and clinical data. RESULTS: Of the 74 HCWs, 10 tested positive by RT-PCR (13.5%). In 9/74 (12.2%) HCWs, antibodies could be detected by RST: three with both IgM and IgG lines; six with IgM line only and none with IgG line only. Frequency of positive tests was more among subjects with minor symptoms compared to completely asymptomatic HCWs (50% vs 16.1%, respectively). Neither age, gender or occupation was a risk factor for SARS-CoV-2 infection. CONCLUSIONS: Point prevalence of COVID-19 in gastroenterology HCWs is 13.5% by RT-PCR. Continued measures are warranted to assure HCWs safety and reduce transmission from healthcare settings to the community during COVID-19 pandemic. Presence of positive test results among asymptomatic HCWs illustrates the importance of screening all HCWs irrespective of symptoms.