Dataset Information

The dynamic change of SARS-CoV-2 variants in Sierra Leone.

ABSTRACT: Since the beginning of the SARS-CoV-2 pandemic, the emergence of multiple new variants posed an increased risk to global public health. The aim of this study is to investigate SARS-CoV-2 variants and possible transmission of variants of concern (VOCs) in Sierra Leone. A total of 65 nasal swab samples were collected from COVID-19 cases in Sierra Leone, among which 24 samples were collected during the second wave and 41 samples were collected during the third wave. Nanopore sequencing generated 54 SARS-CoV-2 whole genomes. The second COVID-19 wave was mainly caused by R.1 lineage while the third COVID-19 wave was dominated by B.1.617.2 lineage (Delta variant). The phylogenetic analysis suggested multiple introductions of SARS-CoV-2 Delta variant into Sierra Leone and subsequent local transmission in this country. Our findings highlight the importance of genomic surveillance of SARS-CoV-2 variants and the urgent need for implementation of strengthened public health and social measures (PHSM) to control the spread of virus variants.

SUBMITTER: Lin L

PROVIDER: S-EPMC8734169 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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The dynamic change of SARS-CoV-2 variants in Sierra Leone.

Lin Lei L Zhang Juling J Rogers James J Campbell Allan A Zhao Jianjun J Harding Doris D Sahr Foday F Liu Yongjian Y Wurie Isata I

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 20220106

Since the beginning of the SARS-CoV-2 pandemic, the emergence of multiple new variants posed an increased risk to global public health. The aim of this study is to investigate SARS-CoV-2 variants and possible transmission of variants of concern (VOCs) in Sierra Leone. A total of 65 nasal swab samples were collected from COVID-19 cases in Sierra Leone, among which 24 samples were collected during the second wave and 41 samples were collected during the third wave. Nanopore sequencing generated 54 ...[more]

PMID: 34999288

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Project description:BackgroundLassa fever (LF), an often-fatal hemorrhagic disease caused by Lassa virus (LASV), is a major public health threat in West Africa. When the violent civil conflict in Sierra Leone (1991 to 2002) ended, an international consortium assisted in restoration of the LF program at Kenema Government Hospital (KGH) in an area with the world's highest incidence of the disease.Methodology/principal findingsClinical and laboratory records of patients presenting to the KGH Lassa Ward in the post-conflict period were organized electronically. Recombinant antigen-based LF immunoassays were used to assess LASV antigenemia and LASV-specific antibodies in patients who met criteria for suspected LF. KGH has been reestablished as a center for LF treatment and research, with over 500 suspected cases now presenting yearly. Higher case fatality rates (CFRs) in LF patients were observed compared to studies conducted prior to the civil conflict. Different criteria for defining LF stages and differences in sensitivity of assays likely account for these differences. The highest incidence of LF in Sierra Leone was observed during the dry season. LF cases were observed in ten of Sierra Leone's thirteen districts, with numerous cases from outside the traditional endemic zone. Deaths in patients presenting with LASV antigenemia were skewed towards individuals less than 29 years of age. Women self-reporting as pregnant were significantly overrepresented among LASV antigenemic patients. The CFR of ribavirin-treated patients presenting early in acute infection was lower than in untreated subjects.Conclusions/significanceLassa fever remains a major public health threat in Sierra Leone. Outreach activities should expand because LF may be more widespread in Sierra Leone than previously recognized. Enhanced case finding to ensure rapid diagnosis and treatment is imperative to reduce mortality. Even with ribavirin treatment, there was a high rate of fatalities underscoring the need to develop more effective and/or supplemental treatments for LF.

Project description:BackgroundThe quality of contraceptive counseling information received by prospective clients of family planning services can greatly influence both the uptake and continued use of contraceptives. Therefore, an understanding of the level and determinants of quality contraception information among young women in Sierra Leon could inform family programs, with the aim of reducing the high unmet need in the country.MethodsWe analyzed secondary data from the 2019 Sierra Leone Demographic Health Survey (SLDHS). Participants were young women aged 15-24 years, who were using a family planning method (n = 1,506). Good quality family planning counselling was defined a composite variable that included; a woman being told about side effects, how to deal with side effects, and the availability of other family planning methods/options. Logistic regression was performed using SPSS software version 25.ResultsOut of 1,506 young women, 955 (63.4%, 95% CI: 60.5-65.3) received good quality family planning counselling services. Of the 36.6% that received inadequate counselling, 17.1% received no counselling at all. Good quality family planning counselling services was positively associated with receiving family planning services from government health facilities (aOR: 2.50, 95% CI: 1.83-3.41), having no major challenges with distance to access healthcare (aOR: 1.45, 95% CI: 1.10-1.90), having visited a health facility (AOR: 1.93, 95% CI: 1.45-2.58), and having been visited by a health field worker within the last 12 months (aOR: 1.67, 95% CI: 1.24-2.26) while residing in the southern region ( aOR: 0.39, 95% CI: 0.22-0.69) and belonging to the richest wealth quintile (aOR: 0.49, 95% CI: 0.24-0.98) were associated with less odds of receiving good quality family planning counselling services.ConclusionAbout 37% of the young women in Sierra Leone do not receive good quality family planning counselling services of which 17.1% received none. Based on the study's findings, it is important to emphasize the need to ensure that all young women have access to proper counselling services especially for those receiving these services from private health units, from the southern region and richest wealth quintile. Ensuring easier access through increasing affordable and friendly access points and strengthening field health workers' capacity in providing family planning services could also help improve access to good quality family planning services.

Dataset Information

The dynamic change of SARS-CoV-2 variants in Sierra Leone.

Publications

The dynamic change of SARS-CoV-2 variants in Sierra Leone.

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