ABSTRACT
We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on March 2, 2020. Since whole genome sequencing (WGS) data is very crucial to understand the spreading dynamics of the ongoing pandemic, but only limited sequencing data is available from the Sahel region to date, we have focused our efforts on generating the first Malian sequencing data available. Screening 217 Malian patient samples for the presence of SARS-CoV-2 resulted in 38 positive isolates, from which 21 whole genome sequences were generated. Our analysis shows that both the early A (19B) and the later observed B (20A/C) clade are present in Mali, indicating multiple and independent introductions of SARS-CoV-2 to the Sahel region.
Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Genome, Viral/genetics , Pneumonia, Viral/epidemiology , RNA, Viral/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Betacoronavirus/isolation & purification , COVID-19 , Child , Child, Preschool , Female , Genetic Variation/genetics , Genomics , Humans , Male , Mali/epidemiology , Middle Aged , Pandemics , Phylogeny , SARS-CoV-2 , Whole Genome Sequencing , Young AdultABSTRACT
Background. We performed 2 cross-sectional studies in Ménaka in the Northeastern Mali across 9 sites in different ecological settings: 4 sites have permanent ponds, 4 without ponds, and one (City of Ménaka) has a semipermanent pond. We enrolled 1328 subjects in May 2004 (hot dry season) and 1422 in February 2005 (cold dry season) after the rainy season. Objective. To examine the seasonality of malaria parasite prevalence in this dry northern part of Mali at the edge of the Sahara desert. Results. Slide prevalence was lower in hot dry than cold dry season (4.94 versus 6.85%, P = 0.025). Gametocyte rate increased to 0.91% in February. Four species were identified. Plasmodium falciparum was most prevalent (74.13 and 63.72%). P. malariae increased from 9.38% to 22.54% in February. In contrast, prevalence of P. vivax was higher (10.31%) without seasonal variation. Smear positivity was associated with splenomegaly (P = 0.007). Malaria remained stable in the villages with ponds (P = 0.221); in contrast, prevalence varied between the 2 seasons in the villages without ponds (P = 0.004). Conclusion. Malaria was mesoendemic; 4 species circulates with a seasonal fluctuation for Plasmodium falciparum.
