Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal

Ahouidi, Ambroise D.; Rodgers, Mary A.; Padane, Abdou; Leye, Nafissatou; Olivo, Ana; Mbow, Moustapha; Mboup, Aminata; Diaw, Papa Alassane; Dia, Aminata; Harris, Barbara J.; Padane, Yacine Amet Dia; Lô, Gora; Meyer, Todd; Diédhiou, Cyrille K.; Diagne, Diabou; Kâne, Ndèye Coumba Touré; Cloherty, Gavin; Mboup, Souleymane

doi:10.1038/s41598-021-02874-z

Cited by 7 publications

(10 citation statements)

References 21 publications

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“…In several west African countries, the VOC Alpha and the VOI Eta constituted the two main competing variants. 31 – 34 These data were confirmed by the analysis of west African sequences deposited in GISAID. From November 2020 to May 2021, 1,901 complete and high-coverage genomes were deposited by the 16 west African countries ( Supplemental Table 5 ).…”

Section: Resultssupporting

confidence: 53%

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COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

Ndiaye,

Beye,

Sow

et al. 2023

The American Journal of Tropical Medicine and Hygiene

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ABSTRACT. West Africa faced the COVID-19 pandemic in early March 2020 and, as of March 31, 2022, had more than 900,000 confirmed cases and more than 12,000 deaths. During this period, SARS-CoV-2 genomes evolved genetically, resulting in the emergence of distinct lineages. This review was conducted to provide the epidemiological profile of COVID-19, the mutational profile of SARS-CoV-2, and the dynamics of its lineages in the 16 west African countries by analyzing data from 33 studies and seven situation reports. For a more complete representation of the epidemiology and genetic diversity of SARS-CoV-2, we used reliable public data in addition to eligible studies. As of March 31, 2022, the 16 west African countries experienced four epidemic waves with variable intensities. Higher mortality was noted during the third wave with a case fatality rate (CFR) of 1.9%. After these four epidemic waves, Liberia recorded the highest CFR (4.0%), whereas Benin had the lowest CFR (0.6%). Through mutational analysis, a high genetic heterogeneity of the genomes was observed, with a predominance of mutations in the spike protein. From this high mutational rate, different lineages emerged. Our analysis of the evolutionary diversity allowed us to count 205 lineages circulating in west Africa. This study has provided a good representation of the mutational profile and the prevalence of SARS CoV-2 lineages beyond the knowledge of the global epidemiology of the 16 African countries.

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Section: Resultssupporting

confidence: 53%

“…In Senegal, lineage B.1.416 represented 59.4% of sequenced strains. 31 No lineage corresponding to a SARS-CoV-2 VOC circulated during this first epidemic wave in west Africa.…”

Section: Resultsmentioning

confidence: 99%

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

Ndiaye,

Beye,

Sow

et al. 2023

The American Journal of Tropical Medicine and Hygiene

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“…reported the emergence of L452M in clade 20A during the second wave of COVID-19 on December 2020 to March 2021 in Senegal. 17 In Pt 5, we detected S-E484Q on Day 3 after RDV treatment and N501Y before treatment, whereas it was reverted to N501I after treatment. Our findings showed that S-E484Q could appear during treatment with RDV in the absence of mAbs therapies.…”

Section: Sars-cov-2 Genome Analysismentioning

confidence: 82%

“…It seems that S‐L452M in Pt 4 might be a transient variation that was triggered after using three courses of RDV in long‐term infection independently. In addition, Ahouidi et al reported the emergence of L452M in clade 20A during the second wave of COVID‐19 on December 2020 to March 2021 in Senegal 17 …”

Section: Discussionmentioning

confidence: 99%

SARS‐CoV‐2 intrahost evolution in immunocompromised patients in comparison with immunocompetent populations after treatment

Ahmadi

Zadheidar

Sadeghi

et al. 2023

Journal of Medical Virology

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Many evidence suggests that long‐lasting infection can develop with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2). This occurrence has been widely described in immunocompromised individuals. In these patients, ineffective clearance of virus infection provides an opportunity for developing immune escape mutants. This study aimed to characterize SARS‐CoV‐2 intrahost evolution in five immunocompromised in comparison with five immunocompetent COVID‐19 patients during treatment. We performed next‐generation sequencing (NGS) on collected two oropharyngeal samples from immunocompromised and immunocompetent COVID‐19 patients before and after treatment. In this study, we detected alpha and delta variants of SARS‐CoV‐2. The most common substitutions in structural proteins in patients with alpha variant were S‐ΔY143‐144, A570D, D614G and D1118H, and N‐R203K and G204R, and in delta variant S‐T19R, G142D, E156G, 157‐158del, L452R, T478K, D614G, D950N and N‐D63G, R203M and D377Y were dominant. The common variations in nonstructural and accessory proteins including nsp3‐A488S, P1228L, nsp6‐T77A, nsp12‐P323L, G671S, nsp13‐P77L, NS3‐S26L, and NS7a‐T120I were detected. Also some infrequent substitutions were seen in immunocompromised and immunocompetent patients. After treatment, nsp12‐V166A was emerged as a remdesivir resistance and S‐L452M in a patient with common variable immunodeficiency. S‐E484Q was detected in a patient with acute lymphoma leukemia. This study showed the possibility of the genetic diversity and development of some new mutations in immunocompromised patients. Therefore, surveillance of these patients to characterize any new variants is necessary.

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“…Though respiratory, enteric, and opportunistic pathogens are not optimally detected in plasma, SARS-CoV-2 was found once in Bounkiling from a patient (BK247) received in April 2021; despite only recovering 8% of the genome, enough coverage in the spike protein was present to putatively assign it to the Alpha variant (lineage B.1.1.7), which was indeed present in the country at the time ( Ahouidi et al, 2021 ; Perez et al, 2022 ). We also identified human rotavirus A (HRV-A) infections in two adults from Bounkiling (BK080 and BK183); of these two, the patient corresponding to specimen BK183 presented to the clinic with fever and vomiting, consistent with rotavirus infection.…”

Section: Resultsmentioning

confidence: 99%

Next-generation sequencing survey of acute febrile illness in Senegal (2020–2022)

Orf,

Ahouidi,

Mata

et al. 2024

Front. Microbiol.

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IntroductionAcute febrile illnesses (AFI) in developing tropical and sub-tropical nations are challenging to diagnose due to the numerous causes and non-specific symptoms. The proliferation of rapid diagnostic testing and successful control campaigns against malaria have revealed that non-Plasmodium pathogens still contribute significantly to AFI burden. Thus, a more complete understanding of local trends and potential causes is important for selecting the correct treatment course, which in turn will reduce morbidity and mortality. Next-generation sequencing (NGS) in a laboratory setting can be used to identify known and novel pathogens in individuals with AFI.MethodsIn this study, plasma was collected from 228 febrile patients tested negative for malaria at clinics across Senegal from 2020–2022. Total nucleic acids were extracted and converted to metagenomic NGS libraries. To identify viral pathogens, especially those present at low concentration, an aliquot of each library was processed with a viral enrichment panel and sequenced. Corresponding metagenomic libraries were also sequenced to identify non-viral pathogens.Results and DiscussionSequencing reads for pathogens with a possible link to febrile illness were identified in 51/228 specimens, including (but not limited to): Borrelia crocidurae (N = 7), West Nile virus (N = 3), Rickettsia felis (N = 2), Bartonella quintana (N = 1), human herpesvirus 8 (N = 1), and Saffold virus (N = 1). Reads corresponding to Plasmodium falciparum were detected in 19 specimens, though their presence in the cohort was likely due to user error of rapid diagnostic testing or incorrect specimen segregation at the clinics. Mosquito-borne pathogens were typically detected just after the conclusion of the rainy season, while tick-borne pathogens were mostly detected before the rainy season. The three West Nile virus strains were phylogenetically characterized and shown to be related to both European and North American clades. Surveys such as this will increase the understanding of the potential causes of non-malarial AFI, which may help inform diagnostic and treatment options for clinicians who provide care to patients in Senegal.

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Emergence of novel combinations of SARS-CoV-2 spike receptor binding domain variants in Senegal

Cited by 7 publications

References 21 publications

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves

SARS‐CoV‐2 intrahost evolution in immunocompromised patients in comparison with immunocompetent populations after treatment

Next-generation sequencing survey of acute febrile illness in Senegal (2020–2022)

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