A pre-vaccine exploratory survey of SARS-CoV-2 humoral immunity among Egyptian general population

Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020-2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality

BACKGROUND

The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed millions of people and caused widespread concern around the world. Multiple genetic variants of SARS-CoV-2 have been identified as the pandemic continues. Concerns have been raised about high transmissibility and lower vaccine efficacy against omicron. There is an urgent need to better describe how omicron will impact clinical presentation and vaccine efficacy. This study aims at comparing the epidemiologic, clinical, and genomic characteristics of the omicron variant prevalent during the fifth wave with those of other VOCs between May 2020 and April 2022.

METHODS

Epidemiological data were obtained from the National Electronic Diseases Surveillance System. Secondary data analysis was performed on all confirmed COVID-19 patients. Descriptive data analysis was performed for demographics and patient outcome and the incidence of COVID-19 was calculated as the proportion of SARS-CoV-2 confirmed patients out of the total population of Egypt. Incidence and characteristics of the omicron cohort from January- April 2022, were compared to those confirmed from May 2020-December 2021. We performed the whole-genome sequencing of SARS-CoV-2 on 1590 specimens using Illumina sequencing to describe the circulation of the virus lineages in Egypt.

RESULTS

A total of 502,629 patients enrolled, including 60,665 (12.1%) reported in the fifth wave. The incidence rate of omicron was significantly lower than the mean of incidences in the previous subperiod (60.1 vs. 86.3/100,000 population, p < 0.001). Symptoms were reported less often in the omicron cohort than in patients with other variants, with omicron having a lower hospitalization rate and overall case fatality rate as well. The omicron cohort tended to stay fewer days at the hospital than did those with other variants. We analyzed sequences of 2433 (1590 in this study and 843 were obtained from GISAID platform) Egyptian SARS-CoV-2 full genomes. The first wave that occurred before the emergence of global variants of concern belonged to the B.1 clade. The second and third waves were associated with C.36. Waves 4 and 5 included B.1.617.2 and BA.1 clades, respectively.

CONCLUSIONS

The study indicated that Omicron-infected patients had milder symptoms and were less likely to be hospitalized; however, patients hospitalized with omicron had a more severe course and higher fatality rates than those hospitalized with other variants. Our findings demonstrate the importance of combining epidemiological data and genomic analysis to generate actionable information for public health decision-making.

COVID-19 vaccine acceptance rates and predictors among the Egyptian general population and Healthcare workers, the intersectionality of age and other factors

The promise of COVID-19 vaccines in ending the pandemic can only be achieved by overcoming the challenge of vaccine refusal. Healthcare workers (HCWs) are the trusted advisors of vaccination decisions. Recommendations for vaccinating children against COVID-19 are recently gaining more public health attention due to the role of children in disease transmission and associated morbidities. Vaccination is one of the first medical decisions parents or guardians make on behalf of their children. To investigate the determinants associated with vaccine acceptability among the general population through a direct interview questionnaire and assess guardians' views towards childhood COVID-19 vaccinations. This cross-sectional study included 2919 participants A pre-designed structured questionnaire about COVID-19 vaccination acceptability was completed by trained interviewers and interviewing the participants or their guardians (for those below 18 years old). Nearly two-thirds of participants (66.5%) accepted vaccination, 20.2% were refusing and 13.3% were hesitant. Most participants who were guardians of children below 12 years and from 13 to 17 years reported that they would accept vaccination of their children (72.5% and 70.5%, respectively). The acceptance rate among HCWs was 58.2%. The main reasons beyond vaccine refusal were mistrust of vaccine efficacy (39.5%) and having concerns regarding vaccine safety (38.8%). In a multivariable regression model, being male (OR 1.362, 95% CI 1.082-1.714, p = 0.008) resident in rural area (OR 1.796, 95% CI 1.435-2.247, p = 0.000), and lower education (OR 1.245, 95% CI 1.018-1.523, p = 0.033) were associated with an increased acceptance to be vaccinated. The acceptance rate for vaccinating children reported among their guardians was higher than adults for themselves. Extremes of age showed higher vaccine acceptance compared to young adults. Upper Egypt governorates (Faiyum and Giza) were outpacing Lower Egypt governorates in vaccination acceptance rates.

Determining the SARS-CoV-2 Anti-Spike Cutoff Level Denoting Neutralizing Activity Using Two Commercial Kits

BACKGROUND

The viral neutralization assay is the gold standard to estimate the level of immunity against SARS-CoV-2. This study analyzes the correlation between the quantitative Anti-SARS-CoV-2 QuantiVac ELISA (IgG) and the NeutraLISA neutralization assay.

METHODS

650 serum samples were tested for both SARS-CoV-2 anti-spike (anti-S) immunoglobulin G (IgG) and neutralizing antibodies (nAbs) using kits by EUROIMMUN, Germany.

RESULTS

There was a significant correlation between levels of anti-S and nAbs (Spearman's rho = 0.913). Among the positive samples for anti-S, 77.0% (n = 345) were positive for nAbs. There was a substantial agreement between anti-S and nAbs (Cohen's kappa coefficient = 0.658; agreement of 83.38%). Considering NeutraLISA as a gold standard, anti-S had a sensitivity of 98.57%, specificity of 65.66%, NPV of 97.5%, and PPV of 77.0%. When the anti-S titer was greater than 18.1 RU/mL (57.9 BAU/mL), nAbs were positive, with a sensitivity of 90.0% and specificity of 91%.

CONCLUSIONS

A titer of SARS-CoV-2 anti-S IgG can be correlated with levels of nAbs.