Multiple introduced lineages and the single native lineage co-driving the four waves of the COVID-19 pandemic in West Africa.

Coronavirus disease 2019 (COVID-19) has become a vast burden on public health and socioeconomics in West Africa, but the epidemic situation is unclear. Therefore, we conducted a retrospective analysis of the positive rate, death rate, and diversity of SARS-CoV-2. As of March 31, 2022, a total of 894,813 cases of COVID-19 have been recorded, with 12,028 deaths, both of which were distributed in all 16 countries. There were four waves of COVID-19 during this period. Most cases were recorded in the second wave, accounting for 34.50% of total cases. These data suggest that although West Africa seems to have experienced a low and relatively slow spread of COVID-19, the epidemic was ongoing, evolving with each COVID-19 global pandemic wave. Most cases and most deaths were both recorded in Nigeria. In contrast, the fewest cases and fewest deaths were reported, respectively, in Liberia and Sierra Leone. However, high death rates were found in countries with low incidence rates. These data suggest that the pandemic in West Africa has so far been heterogeneous, which is closely related to the infrastructure of public health and socioeconomic development (e.g., extreme poverty, GDP per capita, and human development index). At least eight SARS-CoV-2 variants were found, namely, Delta, Omicron, Eta, Alpha, Beta, Kappa, Iota, and Gamma, which showed high diversity, implicating that multiple-lineages from different origins were introduced. Moreover, the Eta variant was initially identified in Nigeria and distributed widely. These data reveal that the COVID-19 pandemic in the continent was co-driven by both multiple introduced lineages and a single native lineage. We suggest enhancing the quarantine measures upon entry at the borders and implementing a genome surveillance strategy to better understand the transmission dynamics of the COVID-19 pandemic in West Africa.

Epidemiological Trends of Coronavirus Disease 2019 in Sierra Leone From March 2020 to October 2021.

Coronavirus disease 2019 (COVID-19), a serious public health challenge the world over, has led to significant health concerns in Sierra Leone. In the present study, epidemic indices, such as the number of cases, positivity rate, reproduction rate (R0), case fatality rate (CFR), age, and sex, were used to characterize the epidemiological trends of COVID-19. As of October 31, 2021, a total of 6,398 cases and 121 related deaths had been confirmed. The total number of COVID-19 reverse transcription polymerase chain reaction (RT-PCR) tests conducted to October 31, 2021, was 249,534, and the average positivity rate was 2.56%. Three waves of COVID-19 were recorded, occurring during weeks 15-46 in 2020 (2,369 cases), week 47 in 2020 to week 16 in 2021 (1,665 cases), and weeks 17-43 in 2021 (2,364 cases), respectively. Remarkably, there was no increase in the numbers of confirmed COVID-19 cases despite rising test numbers throughout the three waves. Moreover, three high R0 values were observed before each wave. The number of positive cases significantly correlated with positive numbers of international arrivals (P < 0.01), deaths (P < 0.01), and the positivity rate of tested samples (P < 0.01). Moreover, all of the deaths occurred during the peak of the three waves. Our results indicate that there was a low level of COVID-19 epidemic in Sierra Leone and that COVID-19's introduction led to local transmission. It is vital to fight against the spread of SARS-CoV-2 from the source of origin by strengthening testing and management of people entering the country. Our findings will provide important clues for expanding sample screening and will contribute to the reasonable allocation of medical resources.

Dissemination of Antibiotic Resistance Genes Among Patients with Diarrhea - Freetown, Sierra Leone, 2018.

What is already known about this topic?: Antibiotic resistance (AR) is a serious public health threat worldwide. However, the AR and antibiotic resistance genes (ARGs) data from West Africa, especially from Sierra Leone, are limited. What is added by this report?: The study revealed ARGs' common dissemination, and multiplex antibiotic resistance genes in one sample. Genes bla NDM and bla OXA -48-like were first discovered in Sierra Leone. What are the implications for public health practice?: Basic information is provided for AR research and surveillance and highlights that effective AR surveillance among diarrhea patients is necessary for Sierra Leone and West Africa.

Soil-transmitted helminth infection in school age children in Sierra Leone after a decade of preventive chemotherapy interventions.

BACKGROUND: Baseline mapping of soil-transmitted helminth (STH) infections among school age children (SAC) in 2008-2009 found high or moderate prevalence in 13 of the 14 districts in Sierra Leone. Following these surveys, mass drug administration (MDA) of mebendazole/albendazole was conducted biannually at national level targeting pre-school children (PSC) aged 12-59 months and intermittently at sub-national level targeting SAC. In addition, MDA with ivermectin and albendazole for eliminating lymphatic filariasis (LF) has been conducted nationwide since 2010 targeting individuals over 5 years of age. Each MDA achieved high coverage, except in 2014 when all but one round of MDA for PSC was cancelled due to the Ebola emergency. The objective of the current study was to determine the prevalence and intensity of STH infections among SAC after a decade of these deworming campaigns. METHODS: Seventy-three schools in 14 districts were purposefully selected, including 39 schools from the baseline surveys, with approximately two sites from each of low, moderate and high prevalence categories at baseline per district. Fresh stool samples were collected from 3632 children aged 9-14 years (male 51%, female 49%) and examined using the Kato Katz technique. RESULTS: The prevalence of STH infections in Sierra Leone decreased in 2016 compared to 2008: Ascaris lumbricoides 4.4% (95% confidence interval [CI]: 3.7-5.1%) versus 6.6% (95% CI: 0-25%), Trichuris trichiura 0.7% (95% CI: 0.5-1.1%) versus 1.8% (95% CI: 0-30.2%), hookworm 14.9% (95% CI: 13.8-16.1) versus 38.5% (95% CI: 5.4-95.1%), and any STH 18.3% (95% CI:17.0-19.5%) versus 48.3% (CI: 5.4-96.3%), respectively. In 2016, no district had high hookworm prevalence and four districts had moderate prevalence, compared with eight and four districts respectively in 2008. In 2016, the arithmetic mean hookworm egg count in all children examined was light: 45.5 eggs per gram (EPG) of faeces, (95% CI:\ 35.96-55.07 EPG); three (0.08%) children had heavy infections and nine (0.25%) children had moderate infections. CONCLUSIONS: Sierra Leone has made considerable progress toward controlling STH as a public health problem among SAC. As LF MDA phases out (between 2017 and 2021), transition of deworming to other platforms and water and sanitation strategies need to be strengthened to maintain STH control and ultimately interrupt transmission.

Schistosomiasis in School Age Children in Sierra Leone After 6 Years of Mass Drug Administration With Praziquantel.

Historic data and baseline surveys showed schistosomiasis as highly/moderately endemic in 7 of 14 districts in Sierra Leone, justifying annual/biennial mass drug administration (MDA) with praziquantel. MDA commenced in 2009 and reported treatment coverage had been above the World Health Organization recommended 75% of target population. Assessment in 2012 showed significant reduction in infection. In 2016, another national school-based survey was conducted to evaluate the progress. Two schools from each category (high, moderate or low) of endemic communities in each MDA district and five schools in non-MDA districts were selected. Fifty children (25 boys and 25 girls) aged 9-14 years were randomly selected per school. Parasitological examination of 1,980 stool and 1,382 urine samples were conducted. Overall Schistosoma mansoni prevalence in the seven MDA districts decreased to 20.4% (95% CI: 18.7-22.3%) in 2016 from 42.2% (95% CI: 39.8-44.5%) at baseline (p < 0.0001). Mean overall S. mansoni intensity of infection reduced to 52.8 epg (95% CI: 43.2-62.4 epg) in 2016 from 100.5 epg (95% CI: 88.7-112.3 epg) at baseline (p < 0.001). The prevalence of Schistosoma haematobium in the five MDA districts that had baseline prevalence data decreased to 2.2% (95% CI: 1.5-3.1%) in 2016 from 18.3% (95% CI: 16.3-20.5%) at baseline (p < 0.0001). Mean overall intensity of infection increased to 1.12 e/10 ml (95% CI: 0.55-0.1.70 e/10 ml) in 2016 compared to 0.47 e/10 ml (95% CI: 0.16-0.78 e/10 ml) in 2012 (p < 0.05) (no baseline data). No district was highly endemic in 2016 compared to three at baseline and there was no significant difference in prevalence or intensity of infection by sex for both species. This survey illustrated the significant progress made in controlling schistosomiasis in Sierra Leone. The fact that prevalence and intensity of infection showed an increase from the 2010 level suggested a detrimental effect of missing MDA due to the Ebola toward schistosomiasis control. The national program needs to continue the treatment and adopt a comprehensive approach including water, hygiene, and sanitation measures to achieve control and elimination of schistosomiasis.

Serological Investigation of Laboratory-Confirmed and Suspected Ebola Virus Disease Patients During the Late Phase of the Ebola Outbreak in Sierra Leone.

This study aimed to investigate the serological characteristics of Ebola virus (EBOV) infection during the late phase of the Ebola outbreak in Sierra Leone. In total, 877 blood samples from 694 suspected Ebola virus disease (EVD) cases assessed from March to December 2015, were analyzed via real-time reverse transcription polymerase chain reaction (RT-PCR) for viral RNA and enzyme-linked immunosorbent assay (ELISA) and Luminex to detect antibodies against EBOV. Viral load and EBOV-specific IgM/IgG titers displayed a declining trend during March to December 2015. Viral RNA load decreased rapidly at earlier stages after disease onset, while EBOV-specific IgM and IgG still persisted in 58.1% (18/31) and 93.5% (29/31) of the confirmed EVD patients and in 3.8% (25/663) and 17.8% (118/663) of the RNA-negative suspected patients in the later phase, respectively. Dynamic analysis of longitudinally collected samples from eight EVD patients revealed typically reversed trends of declining viral load and increasing IgM and/or IgG titers in response to the EBOV infection. The present results indicate that certain populations of Sierra Leone developed immunity to an EBOV infection in the late phase of the outbreak, providing novel insights into the risk assessment of EBOV infections among human populations.