Broadinstitute/Viral-Ngs: V1.19.2

Park, Daniel; Tomkins-Tinch, Chris; Ye, Simon; Jungreis, Irwin; Metsky, Hayden C.; Shlyakhter, Ilya; Hanna,; Lin, Mike; Le, Vang Quy

doi:10.5281/zenodo.1167849

Cited by 3 publications

(2 citation statements)

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“…We subsequently performed reference based assembly with an in-house pipeline. 51 We mapped reads against a Clade IIb reference genome (NC_063383) with bwa-mem 52 , and called consensus using samtools 53 and iVar. 54 …”

Section: Methodsmentioning

confidence: 99%

Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa

Djuicy,

Omah,

Parker

et al. 2024

Preprint

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Nigeria and Cameroon reported their first mpox cases in over three decades in 2017 and 2018 respectively. The outbreak in Nigeria is recognised as an ongoing human epidemic. However, owing to sparse surveillance and genomic data, it is not known whether the increase in cases in Cameroon is driven by zoonotic or sustained human transmission. Notably, the frequency of zoonotic transmission remains unknown in both Cameroon and Nigeria. To address these uncertainties, we investigated the zoonotic transmission dynamics of the mpox virus (MPXV) in Cameroon and Nigeria, with a particular focus on the border regions. We show that in these regions mpox cases are still driven by zoonotic transmission of a newly identified Clade IIb.1. We identify two distinct zoonotic lineages that circulate across the Nigeria-Cameroon border, with evidence of recent and historic cross border dissemination. Our findings support that the complex cross-border forest ecosystems likely hosts shared animal populations that drive cross-border viral spread, which is likely where extant Clade IIb originated. We identify that the closest zoonotic outgroup to the human epidemic circulated in southern Nigeria in October 2013. We also show that the zoonotic precursor lineage circulated in an animal population in southern Nigeria for more than 45 years. This supports findings that southern Nigeria was the origin of the human epidemic. Our study highlights the ongoing MPXV zoonotic transmission in Cameroon and Nigeria, underscoring the continuous risk of MPXV (re)emergence.

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Section: Methodsmentioning

confidence: 99%

Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa

Djuicy,

Omah,

Parker

et al. 2024

Preprint

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“…We performed initial de novo assembly with the viral-ngs pipeline, followed by reference based assembly with an in-house pipeline. 32 Briefly, we mapped reads against a Clade IIb reference genome (NC_063383, an early hMPXV-1 genome from Nigeria) with bwa-mem 33 , and called consensus using samtools 34 and iVar. 35…”

Section: Methodsmentioning

confidence: 99%

Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans

Parker,

Omah,

Varilly

et al. 2024

Preprint

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Five years before the 2022–2023 global mpox outbreak Nigeria reported its first cases in nearly 40 years, with the ongoing epidemic since driven by sustained human-to-human transmission. However, limited genomic data has left questions about the timing and origin of the mpox virus’ (MPXV) emergence. Here we generated 112 MPXV genomes from Nigeria from 2021-2023. We identify the closest zoonotic outgroup to the human epidemic in southern Nigeria, and estimate that the lineage transmitting from human-to-human emerged around July 2014, circulating cryptically until detected in September 2017. The epidemic originated in Southern Nigeria, particularly Rivers State, which also acted as a persistent and dominant source of viral dissemination to other states. We show that APOBEC3 activity increased MPXV’s evolutionary rate twenty-fold during human-to-human transmission. We also show how Delphy, a tool for near-real-time Bayesian phylogenetics, can aid rapid outbreak analytics. Our study sheds light on MPXV’s establishment in West Africa before the 2022–2023 global outbreak and highlights the need for improved pathogen surveillance and response.

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Genomic investigation of atypical malaria cases in Kanel, northern Senegal

Badiane

Déme

et al. 2021

Malar J

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Background The diagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low is more challenging, in part because of reduced clinical presumption of malaria. The appearance of a cluster of malaria cases with atypical symptoms in Mbounguiel, a village in northern Senegal where malaria transmission is low, in September 2018 exemplifies this scenario. The collaboration between the National Malaria Control Programme (NMCP) at the Senegal Ministry of Health and the Laboratory of Parasitology and Mycology at Cheikh Anta Diop University worked together to evaluate this cluster of malaria cases using molecular and serological tools. Methods Malaria cases were diagnosed primarily by rapid diagnostic test (RDT), and confirmed by photo-induced electron transfer-polymerase chain reaction (PET-PCR). 24 single nucleotide polymorphisms (SNPs) barcoding was used for Plasmodium falciparum genotyping. Unbiased metagenomic sequencing and Luminex-based multi-pathogen antibody and antigen profiling were used to assess exposure to other pathogens. Results Nine patients, of 15 suspected cases, were evaluated, and all nine samples were found to be positive for P. falciparum only. The 24 SNPs molecular barcode showed the predominance of polygenomic infections, with identifiable strains being different from one another. All patients tested positive for the P. falciparum antigens. No other pathogenic infection was detected by either the serological panel or metagenomic sequencing. Conclusions This work, undertaken locally within Senegal as a collaboration between the NMCP and a research laboratory at University of Cheikh Anta Diop (UCAD) revealed that a cluster of malaria cases were caused by different strains of P. falciparum. The public health response in real time demonstrates the value of local molecular and genomics capacity in affected countries for disease control and elimination.

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Broadinstitute/Viral-Ngs: V1.19.2

Cited by 3 publications

References 0 publications

Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa

Molecular epidemiology of recurrent zoonotic transmission of mpox virus in West Africa

Genomic epidemiology uncovers the timing and origin of the emergence of mpox in humans

Genomic investigation of atypical malaria cases in Kanel, northern Senegal

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