SARS-CoV-2 Circulation, Guinea, March 2020-July 2021.
Ontology highlight
ABSTRACT:
SUBMITTER: Grayo S
PROVIDER: S-EPMC8798712 | biostudies-literature | 2022 Feb
REPOSITORIES: biostudies-literature
Publications
SARS-CoV-2 Circulation, Guinea, March 2020-July 2021.
Grayo Solène S Troupin Cécile C Diagne Moussa Moïse MM Sagno Houlou H Ellis Isabelle I Doukouré Bakary B Diallo Amadou A Bart Jean-Mathieu JM Kaba Mohamed Lamine ML Henry Benoit B Muyisa Billy Sivahera BS Sow Mamadou Saliou MS Dia Ndongo N Faye Ousmane O Keita Sakoba S Tordo Noël N
Emerging infectious diseases 20211214 2
This overview of severe acute respiratory syndrome coronavirus 2 circulation over 1.5 years in Guinea demonstrates that virus clades and variants of interest and concern were progressively introduced, mostly by travellers through Conakry, before spreading through the country. Sequencing is key to following virus evolution and establishing efficient control strategies. ...[more]
Similar Datasets
Project description:We report mean severe acute respiratory syndrome coronavirus 2 serial intervals for Montana, USA, from 583 transmission pairs; infectors' symptom onset dates occurred during March 1-July 31, 2020. Our estimate was 5.68 (95% CI 5.27-6.08) days, SD 4.77 (95% CI 4.33-5.19) days. Subperiod estimates varied temporally by nonpharmaceutical intervention type and fluctuating incidence.
| S-EPMC8084495 | biostudies-literature
Project description:A growing number of emerging SARS-CoV-2 variants is being identified worldwide, potentially impacting the effectiveness of current vaccines. We report the data obtained in several Italian regions involved in the SARS-CoV-2 variant monitoring from the beginning of the epidemic and spanning the period from October 2020 to March 2021.
| S-EPMC8364297 | biostudies-literature
Project description:BackgroundSARS-CoV-2 infection during pregnancy has been linked to preterm birth, but this association is not well understood.ObjectivesTo examine the association between SARS-CoV-2 infection and spontaneous and provider-initiated preterm birth (PTB), and how timing of infection, and race/ethnicity as a marker of structural inequality, may modify this association.MethodsWe conducted a retrospective cohort study among pregnant people who delivered singleton, liveborn infants (22-44 weeks gestation) from 1 March 2020 to 31 March 2021 (n = 68,288). We used Cox proportional hazards models to compare the hazard of PTB between pregnant people with and without laboratory-confirmed SARS-CoV-2 infection during pregnancy. We evaluated this association according to the trimester of infection, timing from infection to birth, and timing of PTB. We also examined the joint associations of SARS-CoV-2 infection and race/ethnicity with PTB using the relative excess risk due to interaction (RERI).ResultsPositive SARS-CoV-2 tests were identified for 2195 pregnant people (3.2%). The prevalence of PTB was 7.2% (3.8% spontaneous, 3.6% provider-initiated). SARS-CoV-2 infection during pregnancy was associated with an increased risk of PTB overall (adjusted hazard ratio [HR] 1.53, 95% confidence interval [CI] 1.34, 1.74), and provider-initiated PTB (HR 1.79, 95% CI 1.50, 2.12) but not spontaneous PTB (HR 1.09, 95% CI 0.89, 1.36). Second trimester infections were associated with an increased risk of provider-initiated PTB, and third trimester infections were associated with an increased risk of both PTB subtypes. A joint inverse association between White non-Hispanic race/ethnicity and SARS-CoV-2 infection and spontaneous PTB (HR 0.56, 95% CI 0.34, 0.94; RERI -0.6, 95% CI -1.0, -0.2) was also observed.ConclusionsSARS-CoV-2 infections were primarily associated with an increased risk for provider-initiated PTB in this study. These findings highlight the importance of promoting infection-prevention strategies among pregnant people.
| S-EPMC9877646 | biostudies-literature
Project description:Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may be underestimated because of limited access to testing. We measured SARS-CoV-2 seroprevalence in South Africa every 2 months during July 2020-March 2021 in randomly selected household cohorts in 2 communities. We compared seroprevalence to reported laboratory-confirmed infections, hospitalizations, and deaths to calculate infection-case, infection-hospitalization, and infection-fatality ratios in 2 waves of infection. Post-second wave seroprevalence ranged from 18% in the rural community children <5 years of age, to 59% in urban community adults 35-59 years of age. The second wave saw a shift in age distribution of case-patients in the urban community (from persons 35-59 years of age to persons at the extremes of age), higher attack rates in the rural community, and a higher infection-fatality ratio in the urban community. Approximately 95% of SARS-CoV-2 infections were not reported to national surveillance.
| S-EPMC8632160 | biostudies-literature
Project description:The emergence and rapid spread of SARS-CoV-2 variants of concern (VOC) have been linked to new waves of COVID-19 epidemics occurring in different regions of the world. The VOC have acquired adaptive mutations that have enhanced virus transmissibility, increased virulence, and reduced response to neutralizing antibodies. Kenya has experienced six waves of COVID-19 epidemics. In this study, we analyzed 64 genome sequences of SARS-CoV-2 strains that circulated in Nairobi and neighboring counties, Kenya between March 2021 and July 2021. Viral RNA was extracted from RT-PCR confirmed COVID-19 cases, followed by sequencing using the ARTIC network protocol and Oxford Nanopore Technologies. Analysis of the sequence data was performed using different bioinformatics methods. Our analyses revealed that during the study period, three SARS-CoV-2 variants of concern (VOC) circulated in Nairobi and nearby counties in Kenya. The Alpha (B.1.1.7) lineage predominated (62.7%), followed by Delta (B.1.617.2, 35.8%) and Beta (B.1.351, 1.5%). Notably, the Alpha (B.1.1.7) VOC were most frequent from March 2021 to May 2021, while the Delta (B.1.617.2) dominated beginning June 2021 through July 2021. Sequence comparisons revealed that all the Kenyan viruses were genetically similar to those that circulated in other regions. Although the majority of Kenyan viruses clustered together in their respective phylogenetic lineages/clades, a significant number were interspersed among foreign strains. Between March and July 2021, our study's findings indicate the prevalence of multiple lineages of SAR-CoV-2 VOC in Nairobi and nearby counties in Kenya. The data suggest that the recent increase in SARS-CoV-2 infection, particularly in Nairobi and Kenya as a whole, is attributable to the introduction and community transmission of SARS-CoV-2 VOC among the populace. In conclusion, the findings provide a snapshot of the SARS-CoV-2 variants that circulated in Kenya during the study period.
| S-EPMC9640859 | biostudies-literature
Project description:BackgroundSeveral SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains.AimWe aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility.MethodsWe conducted two genomic surveillance surveys on 18 February and 18 March 2021 across the whole Italian territory covering 3,243 clinical samples and developed a mathematical model that describes the dynamics of co-circulating strains.ResultsThe Alpha variant was already dominant on 18 February in a majority of regions/autonomous provinces (national prevalence: 54%) and almost completely replaced historical lineages by 18 March (dominant across Italy, national prevalence: 86%). We found a substantial proportion of the Gamma variant on 18 February, almost exclusively in central Italy (prevalence: 19%), which remained similar on 18 March. Nationally, the mean relative transmissibility of Alpha ranged at 1.55-1.57 times the level of historical lineages (95% CrI: 1.45-1.66). The relative transmissibility of Gamma varied according to the assumed degree of cross-protection from infection with other lineages and ranged from 1.12 (95% CrI: 1.03-1.23) with complete immune evasion to 1.39 (95% CrI: 1.26-1.56) for complete cross-protection.ConclusionWe assessed the relative advantage of competing viral strains, using a mathematical model assuming different degrees of cross-protection. We found substantial co-circulation of Alpha and Gamma in Italy. Gamma was not able to outcompete Alpha, probably because of its lower transmissibility.
| S-EPMC8815098 | biostudies-literature
Project description:Accurate estimates of the total burden of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to inform policy, planning, and response. We sought to quantify SARS-CoV-2 cases, hospitalizations, and deaths by age in Michigan. Coronavirus disease 2019 cases reported to the Michigan Disease Surveillance System were multiplied by age and time-specific adjustment factors to correct for under-detection. Adjustment factors were estimated in a model fit to incidence data and seroprevalence estimates. Age-specific incidence of SARS-CoV-2 hospitalization, death, vaccination, and variant proportions were estimated from publicly available data. We estimated substantial under-detection of infection that varied by age and time. Accounting for under-detection, we estimate the cumulative incidence of infection in Michigan reached 75% by mid-November 2021, and over 87% of Michigan residents were estimated to have had ≥1 vaccination dose and/or previous infection. Comparing pandemic waves, the relative burden among children increased over time. In general, the proportion of cases who were hospitalized or who died decreased over time. Our results highlight the ongoing risk of periods of high SARS-CoV-2 incidence despite widespread prior infection and vaccination. This underscores the need for long-term planning for surveillance, vaccination, and other mitigation measures amidst continued response to the acute pandemic.
| S-EPMC9350192 | biostudies-literature
Project description: Not available
| S-EPMC9348424 | biostudies-literature
Project description:Estimating the actual extent of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is challenging because virus test positivity data undercount the actual number and proportion of persons infected. SARS-CoV-2 seroprevalence is a marker of past SARS-CoV-2 infection regardless of presence or severity of symptoms and therefore is a robust biomarker of infection period prevalence. We estimated SARS-CoV-2 seroprevalence among residents of Hillsborough County, Florida, USA, to determine factors independently associated with SARS-CoV-2 antibody status overall and among asymptomatic antibody-positive persons. Among 867 participants, SARS-CoV-2 period prevalence (October 2020-March 2021) was 19.5% (asymptomatic seroprevalence was 8%). Seroprevalence was 2-fold higher than reported SARS-CoV-2 virus test positivity. Factors related to social distancing (e.g., essential worker status, not practicing social distancing, contact with a virus-positive person, and length of contact exposure time) were consistently associated with seroprevalence but did not differ by time since suspected or known infection (<6 months vs. >6 months).
| S-EPMC8888241 | biostudies-literature
Project description:Estimating an infectious disease attack rate requires inference on the number of reported symptomatic cases of a disease, the number of unreported symptomatic cases, and the number of asymptomatic infections. Population-level immunity can then be estimated as the attack rate plus the number of vaccine recipients who had not been previously infected; this requires an estimate of the fraction of vaccines that were distributed to seropositive individuals. To estimate attack rates and population immunity in southern New England, we fit a validated dynamic epidemiological model to case, clinical, and death data streams reported by Rhode Island, Massachusetts, and Connecticut for the first 15 months of the COVID-19 pandemic, from March 1 2020 to May 31 2021. This period includes the initial spring 2020 wave, the major winter wave of 2020-2021, and the lagging wave of lineage B.1.1.7(Alpha) infections during March-April 2021. In autumn 2020, SARS-CoV-2 population immunity (equal to the attack rate at that point) in southern New England was still below 15%, setting the stage for a large winter wave. After the roll-out of vaccines in early 2021, population immunity in many states was expected to approach 70% by spring 2021, with more than half of this immune population coming from vaccinations. Our population immunity estimates for May 31 2021 are 73.4% (95% CrI: 72.9% - 74.1%) for Rhode Island, 64.1% (95% CrI: 64.0% - 64.4%) for Connecticut, and 66.3% (95% CrI: 65.9% - 66.9%) for Massachusetts, indicating that >33% of southern Englanders were still susceptible to infection when the Delta variant began spreading in July 2021. Despite high vaccine coverage in these states, population immunity in summer 2021 was lower than planned due to 34% (Rhode Island), 25% (Connecticut), and 28% (Massachusetts) of vaccine distribution going to seropositive individuals. Future emergency-setting vaccination planning will likely have to consider over-vaccination as a strategy to ensure that high levels of population immunity are reached during the course of an ongoing epidemic.
| S-EPMC8669856 | biostudies-literature