Characterization of the SARS-CoV-2 genomes in Egypt in first and second waves of infection
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ABSTRACT:
SUBMITTER: Zekri A
PROVIDER: S-EPMC8566477 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We assessed the relation between COVID-19 waves in Italy, which was severely affected during the pandemic. We evaluated the hypothesis that a larger impact from the first wave (February-May 2020) predicts a smaller peak during the second wave (September-October 2020), in the absence of local changes in public health interventions and area-specific differences in time trends of environmental parameters. Based on publicly available data on province-specific SARS-CoV-2 infections and both crude and multivariable cubic spline regression models, we found that for provinces with the lowest incidence rates in the first wave, the incidence in the second wave increased roughly in proportion with the incidence in the first wave until an incidence of about 500-600 cases/100,000 in the first wave. Above that value, provinces with higher incidences in the first wave experienced lower incidences in the second wave. It appears that a comparatively high cumulative incidence of infection, even if far below theoretical thresholds required for herd immunity, may provide noticeable protection during the second wave. We speculate that, if real, the mechanism for this pattern could be depletion of most susceptible individuals and of superspreaders in the first wave. A population learning effect regarding cautious behavior could have also contributed. Since no area-specific variation of the national policy against the SARS-CoV-2 outbreak was allowed until early November 2020, neither individual behaviors nor established or purported environmental risk factors of COVID-19, such as air pollution and meteorological factors, are likely to have confounded the inverse trends we observed in infection incidence over time.
| S-EPMC8012166 | biostudies-literature
Project description:BackgroundIn Italy, the incidence of SARS-CoV-2 infection peaked in April and November 2020, defining two pandemic waves of coronavirus disease 2019 (COVID-19). This study compared the characteristics and outcomes of patients with inflammatory bowel disease (IBD) and SARS-CoV-2 infections between pandemic waves.MethodsObservational longitudinal study of IBD patients with SARS-CoV-2 infection. Patients with established diagnoses of IBD and of SARS-CoV-2 infection were consecutively enrolled in two periods: (i) first wave, from 1 March 2020 to 31 May 2020; and (ii) second wave, from 15 September to 15 December 2020.ResultsWe enrolled 937 IBD patients (219 in the first wave, 718 in the second wave). Patients of the first wave were older (mean ± SD: 46.3 ± 16.2 vs. 44.1 ± 15.4 years, p = 0.06), more likely to have ulcerative colitis (58.0% vs. 44.4%, p < 0.001) and comorbidities (48.9% vs. 38.9%; p < 0.01), and more frequently residing in Northern Italy (73.1% vs. 46.0%, p < 0.001) than patients of the second wave. There were no significant differences between pandemic waves in sex (male: 54.3% vs. 53.3%, p = 0.82) or frequency of active IBD (44.3% vs. 39.0%, p = 0.18). The rates of negative outcomes were significantly higher in the first than second wave: pneumonia (27.8% vs. 11.7%, p < 0.001), hospital admission (27.4% vs. 9.7%, p < 0.001), ventilatory support (11.9% vs. 5.4%, p < 0.003) and death (5.5% vs. 1.8%, p < 0.007).ConclusionBetween the first and second SARS-CoV-2 pandemic waves, demographic, clinical and geographical features of IBD patients were different as were the symptoms and outcomes of infection. These differences are likely due to the different epidemiological situations and diagnostic possibilities between the two waves.
| S-EPMC10324268 | biostudies-literature
Project description:Background: The Grand Hôpital de Charleroi is a large non-academic Belgian hospital that treated a large number of COVID-19 inpatients. In the context of this pandemic, all professions-combined healthcare workers (HCWs), and not only direct caregivers, are a frontline workforce in contact with suspected and confirmed COVID-19 cases and seem to be a high-risk group for exposure. The aim of our study was to estimate the prevalence of anti-SARS-CoV-2 antibodies in HCWs in our hospital after the first and second pandemic waves and to characterize the distribution of this seroprevalence in relation to various criteria. Methods: At the end of the two recruitment periods, a total of 4008 serological tests were performed in this single-center cross-sectional study. After completing a questionnaire including demographic and personal data, possible previous COVID-19 diagnostic test results and/or the presence of symptoms potentially related to COVID-19, the study participants underwent blood sampling and serological testing using DiaSorin's LIAISON® SARS-CoV-2 S1/S2 IgG test for the first phase and LIAISON® SARS-CoV-2 TrimericS IgG test for the second phase of this study. Results: In total, 302 study participants (10.72%) in the first round of the study and 404 (33.92%) in the second round were positive for SARS-CoV-2-IgG antibodies. The prevalence of seropositivity observed after the second wave was 3.16 times higher than after the first wave. We confirmed that direct, prolonged, and repeated contact with patients or their environment was a predominant seroconversion factor, but more unexpectedly, that this was the case for all HCWs and not only caregivers. Finally, the notion of high-risk contact seemed more readily identifiable in one's workplace than in one's private life. Conclusions: Our study confirmed that HCWs are at a significantly higher risk of contracting COVID-19 than the general population, and suggests that repeated contacts with at-risk patients, regardless of the HCWs' professions, represents the most important risk factor for seroconversion (Clinicaltrials.gov number, NCT04723290).
| S-EPMC9322964 | biostudies-literature
Project description:BackgroundA description of individuals with SARS-CoV-2 infection comparing the first and second waves could help adapt health services to manage this highly transmissible infection.ObjectiveWe aimed to describe the epidemiology of individuals with suspected SARS-CoV-2 infection, and the characteristics of patients with a positive test comparing the first and second waves in Catalonia, Spain.MethodsThis study had 2 stages. First, we analyzed daily updated data on SARS-CoV-2 infection in individuals from Girona (Catalonia). Second, we compared 2 retrospective cohorts of patients with a positive reverse-transcription polymerase chain reaction or rapid antigen test for SARS-CoV-2. The severity of patients with a positive test was defined by their admission to hospital, admission to intermediate respiratory care, admission to the intensive care unit, or death. The first wave was from March 1, 2020, to June 24, 2020, and the second wave was from June 25, 2020, to December 8, 2020.ResultsThe numbers of tests and cases were lower in the first wave than in the second wave (26,096 tests and 3140 cases in the first wave versus 140,332 tests and 11,800 cases in the second wave), but the percentage of positive results was higher in the first wave than in the second wave (12.0% versus 8.4%). Among individuals with a positive diagnostic test, 818 needed hospitalization in the first wave and 680 in the second; however, the percentage of hospitalized individuals was higher in the first wave than in the second wave (26.1% versus 5.8%). The group that was not admitted to hospital included older people and those with a higher percentage of comorbidities in the first wave, whereas the characteristics of the groups admitted to hospital were more alike.ConclusionsScreening systems for SARS-CoV-2 infection were scarce during the first wave, but were more adequate during the second wave, reflecting the usefulness of surveillance systems to detect a high number of asymptomatic infected individuals and their contacts, to help control this pandemic. The characteristics of individuals with SARS-CoV-2 infection in the first and second waves differed substantially; individuals in the first wave were older and had a worse health condition.
| S-EPMC8734611 | biostudies-literature
Project description:BackgroundSARS-CoV-2 infection during pregnancy is associated with adverse pregnancy outcomes, including fetal death and preterm birth. It is not known whether that risk occurs only during the time of acute infection or whether the risk persists later in pregnancy.ObjectiveThis study aimed to evaluate whether the risk of SARS-CoV-2 infection during pregnancy persists after an acute maternal illness.Study designA retrospective cohort study of pregnant patients with and without SARS-CoV-2 infection delivering at 17 hospitals in the United States between March 2020 and December 2020. Patients experiencing a SARS-CoV-2-positive test at or before 28 weeks of gestation with a subsequent delivery hospitalization were compared with those without a positive SAR-CoV-2 test at the same hospitals with randomly selected delivery days during the same period. Deliveries occurring at <20 weeks of gestation in both groups were excluded. The study outcomes included fetal or neonatal death, preterm birth at <37 weeks of gestation and <34 weeks of gestation, hypertensive disorders of pregnancy (HDP), any major congenital malformation, and size for gestational age of <5th or <10th percentiles at birth based on published standards. HDP that were collected included HDP and preeclampsia with severe features, both overall and with delivery at <37 weeks of gestation.ResultsOf 2326 patients who tested positive for SARS-CoV-2 during pregnancy and were at least 20 weeks of gestation at delivery from March 2020 to December 2020, 402 patients (delivering 414 fetuses or neonates) were SARS-CoV-2 positive before 28 weeks of gestation and before their admission for delivery; they were compared with 11,705 patients without a positive SARS-CoV-2 test. In adjusted analyses, those with SARS-CoV-2 before 28 weeks of gestation had a subsequent increased risk of fetal or neonatal death (2.9% vs 1.5%; adjusted relative risk, 1.97; 95% confidence interval, 1.01-3.85), preterm birth at <37 weeks of gestation (19.6% vs 13.8%; adjusted relative risk, 1.29; 95% confidence interval, 1.02-1.63), and HDP with delivery at <37 weeks of gestation (7.2% vs 4.1%; adjusted relative risk, 1.74; 95% confidence interval, 1.19-2.55). There was no difference in the rates of preterm birth at <34 weeks of gestation, any major congenital malformation, and size for gestational age of <5th or <10th percentiles. In addition, there was no significant difference in the rate of gestational hypertension overall or preeclampsia with severe features.ConclusionThere was a modest increase in the risk of adverse pregnancy outcomes after SARS-CoV-2 infection.
| S-EPMC9374493 | biostudies-literature
Project description:IntroductionThe 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.ObjectiveIn the present study, the objective is to perform a complete genome sequence of SAR-CoV2 isolated from Egyptian coronavirus disease (COVID-19) patients.MethodsNasopharyngeal 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.ResultsIn 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.ConclusionThe 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.
| S-EPMC7688418 | biostudies-literature
Project description:Aim: The aim of this study was to investigate the SARS-CoV-2 spike protein evolution during the first and second wave of COVID-19 infections in India. Materials & Methods: Detailed mutation analysis was done in 763 samples taken from GISAID for the ten most affected Indian states between March 2020 to August 2021. Results: The study revealed 242 mutations corresponding to 207 sites. Fifty one novel mutations emerged during the assessment period, including many with higher transmissibility and immune evasion functions. Highest number of mutations per spike protein also rose from 5 (first wave) to 13 (second wave). Conclusion: The study identified mutation-rich and no mutation regions in the spike protein. The conserved spike regions can be useful for designing future diagnostics, vaccines and therapeutics.
| S-EPMC9203035 | biostudies-literature
Project description:BackgroundSurfaces and air in healthcare facilities can be contaminated with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Previously, the authors identified SARS-CoV-2 RNA on surfaces and air in their hospital during the first wave of the coronavirus disease 2019 pandemic (April 2020).AimTo explore whether the profile of SARS-CoV-2 surface and air contamination had changed between April 2020 and January 2021.MethodsThis was a prospective, cross-sectional, observational study in a multi-site London hospital. In January 2021, surface and air samples were collected from comparable areas to those sampled in April 2020, comprising six clinical areas and a public area. SARS-CoV-2 was detected using reverse transcription polymerase chain reaction and viral culture. Sampling was also undertaken in two wards with natural ventilation alone. The ability of the prevalent variants at the time of the study to survive on dry surfaces was evaluated.FindingsNo viable virus was recovered from surfaces or air. Five percent (N=14) of 270 surface samples and 4% (N=1) of 27 air samples were positive for SARS-CoV-2, which was significantly lower than in April 2020 [52% (N=114) of 218 surface samples and 48% (N=13) of 27 air samples (P<0.001, Fisher's exact test)]. There was no clear difference in the proportion of surface and air samples positive for SARS-CoV-2 RNA based on the type of ventilation in the ward. All variants tested survived on dry surfaces for >72 h, with a <3-log10 reduction in viable count.ConclusionThis study suggests that enhanced infection prevention measures have reduced the burden of SARS-CoV-2 RNA on surfaces and air in healthcare facilities.
| S-EPMC9683853 | biostudies-literature
Project description:COVID-19 is an infectious disease caused by SARS-CoV-2 and has spread globally, resulting in the ongoing coronavirus pandemic. The current study aimed to analyze the clinical and epidemiological features of COVID-19 in Egypt. Oropharyngeal swabs were collected from 197 suspected patients who were admitted to the Army Hospital and confirmation of the positivity was performed by rRT-PCR assay. Whole genomic sequencing was conducted using Illumina iSeq 100® System. The average age of the participants was 48 years, of which 132 (67%) were male. The main clinical symptoms were pneumonia (98%), fever (92%), and dry cough (66%). The results of the laboratory showed that lymphocytopenia (79.2%), decreased levels of haemoglobin (77.7%), increased levels of interleukin 6, C-reactive protein, serum ferritin, and D-dimer (77.2%, 55.3%, 55.3%, and 25.9%, respectively), and leukocytopenia (25.9%) were more common. The CT findings showed that scattered opacities (55.8%) and ground-glass appearance (27.9%) were frequently reported. The recovered validated sequences (n = 144) were submitted to NCBI Virus GenBank. All sequenced viruses have at least 99% identity to Wuhan-Hu-1. All variants were GH clade, B.1 PANGO lineage, and L.GP.YP.HT haplotype. The most predominant subclade was D614G/Q57H/V5F/G823S. Our findings have aided in a deep understanding of COVID-19 evolution and identifying strains with unique mutational patterns in Egypt.
| S-EPMC8801622 | biostudies-literature
Project description:ObjectivesStudies that measure the prevalence of antibodies to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ('seroprevalence') are essential to understand population exposure to SARS-CoV-2 among symptomatic and asymptomatic individuals. We aimed to measure seroprevalence in the Scottish population over the course of the COVID-19 pandemic - from before the first recorded case in Scotland through to the second pandemic wave.Study designThe study design of this study is serial cross sectional.MethodsWe tested 41,477 residual samples retrieved from primary and antenatal care settings across Scotland for SARS-CoV-2 antibodies over a 12-month period from December 2019-December 2020 (before rollout of COVID-19 vaccination). Five-weekly rolling seroprevalence estimates were adjusted for the sensitivity and specificity of the assays and weighted to reference populations. Temporal trends in seroprevalence estimates and weekly SARS-CoV-2 notifications were compared.ResultsFive-weekly rolling seroprevalence rates were 0% until the end of March, when they increased contemporaneously with the first pandemic wave. Seroprevalence rates remained stable through the summer (range: 3%-5%) during a period of social restrictions, after which they increased concurrently with the second wave, reaching 9.6% (95% confidence interval [CI]: 8.4%-10.8%) in the week beginning 28th December in 2020. Seroprevalence rates were lower in rural vs. urban areas (adjusted odds ratio [AOR]: 0.70, 95% CI: 0.61-0.79) and among individuals aged 20-39 years and 60 years and older (AOR: 0.74, 95% CI: 0.64-0.86; AOR: 0.80, 95% CI: 0.69-0.91, respectively) relative to those aged 0-19 years.ConclusionsAfter two waves of the COVID-19 pandemic, less than one in ten individuals in the Scottish population had antibodies to SARS-CoV-2. Seroprevalence may underestimate the true population exposure as a result of waning antibodies among individuals who were infected early in the first wave.
| S-EPMC8289625 | biostudies-literature