Genomic Surveillance of SARS-CoV-2 in Mozambique Using Pandemic-Scale Phylogenies

Martínez-Martínez, Francisco José; Massinga, Arsénia J.; Jesus, Áuria De; Ernesto, Rita M.; Cano-Jiménez, Pablo; Chiner‐Oms, Álvaro; Gómez-Díaz, Elena; Guillot-Fernández, Marina; Guinovart, Caterina; Sitoe, António; Vubil, Delfino; Bila, Rubão; Gujamo, Rufino; Viegas, Sofía; Ismael, Nália; Jiménez-Serrano, Santiago; Enosse, Sónia; Torres-Puente, Manuela; Comas, Iñaki; Mandomando, Inácio; López, Mariana G.; Mayor, Alfredo

doi:10.2139/ssrn.4231245

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“…To better determine the likely origin and introduction period of the Equatorial Guinea sequenced samples, we performed a genome-based epidemiological analysis using pandemic-scale phylogenies (53). The results are summarized in Fig 4 and Table S6 , our script identifies 17 unique introductions and 7 transmission groups or clusters, whereas 11 out of 43 samples remain unclassified.…”

Section: Resultsmentioning

confidence: 99%

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Circulation of SARS-CoV-2 and co-infection withPlasmodium falciparumin Equatorial Guinea

López-Farfán,

Ncogo,

Oki

et al. 2023

Preprint

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The impact of COVID-19 in Africa has been a big concern since the beginning of the pandemic. However, low incidence of COVID-19 case severity and mortality has been reported in many African countries, although data are highly heterogeneous and, in some regions, like Sub-Saharan Africa, very scarce. Many of these regions are also the cradle of endemic infectious diseases like malaria. The aim of this study was to determine the prevalence of SARS-CoV-2, the diversity and origin of circulating variants as well as the frequency of co-infections with malaria in Equatorial Guinea. For this purpose, we conducted antigen diagnostic tests for SARS-CoV-2, and microscopy examinations for malaria of 1,556 volunteers at six health centres in Bioko and Bata from June to October 2021. Nasopharyngeal swab samples were also taken for molecular detection of SARS-COV-2 by RT-qPCR and whole genome viral sequencing. We report 3.0% of SARS-CoV-2 and 24.4% of malaria prevalence over the sampling in Equatorial Guinea. SARS-CoV-2 cases were found at a similar frequency in all age groups, whereas the age groups most frequently affected by malaria were children (36.8% [95% CI 30.9-42.7]) and teenagers (34.7% [95% CI 29.5-39.9]). We found six cases of confirmed co-infection of malaria and SARS-CoV-2 distributed among all age groups, representing a 0.4% frequency of co-infection in the whole sampled population. Interestingly, the majority of malaria and SARS-CoV-2 co-infections were mild. We obtained the genome sequences of 43 SARS-CoV-2 isolates, most of which belong to the lineage Delta (AY.43) and that according to our pandemic-scale phylogenies were introduced from Europe in multiple occasions (7 transmission groups and 17 unique introductions). This study is relevant in providing first-time estimates of the actual prevalence of SARS-CoV-2 in this malaria-endemic country, with the identification of circulating variants, their origin, and the occurrence of SARS-CoV-2 and malaria co-infection.

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Section: Resultsmentioning

confidence: 99%

“…A genome-based epidemiological analysis was performed on the sequenced Guinea Equatorial samples following the pipeline described in Martínez-Martínez et al (39). We used a pandemic-scale phylogenomics analysis tool called UShER (40) to place the newly-sequenced samples in a prebuilt phylogeny.…”

Section: Genome-based Epidemiological Analysismentioning

confidence: 99%

Circulation of SARS-CoV-2 and co-infection withPlasmodium falciparumin Equatorial Guinea

López-Farfán,

Ncogo,

Oki

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Genomic Surveillance of SARS-CoV-2 in Mozambique Using Pandemic-Scale Phylogenies

Cited by 1 publication

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Circulation of SARS-CoV-2 and co-infection withPlasmodium falciparumin Equatorial Guinea

Circulation of SARS-CoV-2 and co-infection withPlasmodium falciparumin Equatorial Guinea

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