Genomic history of human monkey pox infections in the Central African Republic between 2001 and 2018

Abstract

Monkeypox is an emerging infectious disease, which has a clinical presentation similar to smallpox. In the two past decades, Central Africa has seen an increase in the frequency of cases, with many monkeypox virus (MPXV) isolates detected in the Democratic Republic of Congo (DRC) and the Central African Republic (CAR). To date, no complete MPXV viral genome has been published from the human cases identified in the CAR. The objective of this study was to sequence the full genome of 10 MPXV isolates collected during the CAR epidemics between 2001 and 2018 in order to determine their phylogenetic relationships among MPXV lineages previously described in Central Africa and West Africa. Our phylogenetic results indicate that the 10 CAR isolates belong to three lineages closely related to those found in DRC. The phylogenetic pattern shows that all of them emerged in the rainforest block of the Congo Basin. Since most human index cases in CAR occurred at the northern edge of western and eastern rainforests, transmissions from wild animals living in the rainforest is the most probable hypothesis. In addition, molecular dating estimates suggest that periods of intense political instability resulting in population movements within the country often associated also with increased poverty may have led to more frequent contact with host wild animals. The CAR socio-economic situation, armed conflicts and ecological disturbances will likely incite populations to interact more and more with wild animals and thus increase the risk of zoonotic spillover.

Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic

“…However, despite the presence of these differences in the MPXV-M sequence compared with the MPXV-I sequence, phylogenetic analyses showed that the MPXV-M sequence is positioned in the CAR1 lineage of group II strains belonging to the Central African clade. The position of the MPXV-M sequence, along with the Bao (A4 and A5) and Bangassou (B2) sequences of 2016 and 2017, respectively, is identical to the phylogenetic analyses previously performed in a previous study using all CAR MPXV sequences obtained with Illumina sequencing 19 (Fig. 5 ).…”

“…Although TGS is not the most suitable tool for rapid differential diagnosis of MPXV to distinguish it from Varicella-Zoster virus, its main advantage resides in the very fast identification of the origin of the strain. Our phylogenetic analysis showed that the MPXV-M sequence was sufficiently precise to position it correctly in the CAR1 lineage 19 . Molecular data obtained with TGS makes it possible to identify the relationships between detected cases more rapidly, especially those identified in the same city within a very short timeframe.…”

“…Although the reasons are not clear, there has been a gradual increase in the number of monkeypox cases since 1980 in Central Africa (mainly in the DRC) and the Central African Republic (CAR) 10 – 13 ), but also more recently in West Africa, particularly in Nigeria since 2017–2018 14 , 15 where the previous case was reported several decades ago.Unlike the strains belonging to the West African clade, in particular that of the last epidemic in Nigeria, which have already spread in several countries outside the African continent and to Cameroon 16 – 18 , the strains belonging to the Congo Basin clade (Central Africa) have never been identified outside their geographical region of origin. Indeed, genomic analyses of the main MPXV strains detected in the CAR between 2001 and 2018 confirmed that they belonged to three lineages closely related to those found in DRC 19 . Finally, molecular data obtained from viral genomes can trace the origin of strains and establish relationships between strains isolated from different outbreaks in the countries affected by this disease.…”

“…Molecular data obtained with TGS makes it possible to identify the relationships between detected cases more rapidly, especially those identified in the same city within a very short timeframe. For instance, in the city of Rafai, several cases had been reported in the space of a few weeks between March and April 2018 67 , but only phylogenetic analyses were able to resolve the specific relationship between them 19 . Similarly, early differential diagnosis of MPXV, distinguishing it from Varicella-Zoster virus, and as close as possible to the index case can help limit its spread to the immediate environment.…”

The never-ending global emergence of viral zoonoses after COVID-19? The rising concern of monkeypox in Europe, North America and beyond

“…Amid the COVID-19 pandemic, the increasing reporting of cases of monkeypox virus infection in humans spreading through many countries outside Africa is a major reason for concern [ [5] , [6] , [7] , [8] , [9] , [10] , [11] , [12] ]. Monkeypox virus is a double-stranded DNA virus of the Poxviridae family which also includes the variola virus, the causative agent of smallpox [ 14 , 15 ].…”