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.

Monkeypox is a rare viral zoonotic disease; primary infections are reported from remote forest areas of Central and West Africa. We report an investigation of a monkeypox outbreak in Lobaye, southwest Central African Republic, in October 2018.

Monkeypox is an emerging and neglected zoonotic disease whose number of reported cases has been gradually increasing in Central Africa since 1980. This disease is caused by the monkeypox virus (MPXV), which belongs to the genus Orthopoxvirus in the family Poxviridae. Obtaining molecular data is particularly useful for establishing the relationships between the viral strains involved in outbreaks in countries affected by this disease. In this study, we evaluated the use of the MinION real-time sequencer as well as different polishing tools on MinION-sequenced genome for sequencing the MPXV genome originating from a pustular lesion in the context of an epidemic in a remote area of the Central African Republic. The reads corresponding to the MPXV genome were identified using two taxonomic classifiers, Kraken2 and Kaiju. Assembly of these reads led to a complete sequence of 196,956 bases, which is 6322 bases longer than the sequence previously obtained with Illumina sequencing from the same sample. The comparison of the two sequences showed mainly indels at the homopolymeric regions. However, the combined use of Canu with specific polishing tools such as Medaka and Homopolish was the best combination that reduced their numbers without adding mismatches. Although MinION sequencing is known to introduce a number of characteristic errors compared to Illumina sequencing, the new polishing tools allow a better-quality MinION-sequenced genome, thus to be used to help determine strain origin through phylogenetic analysis.

Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), in which outbreaks mainly occurred in West and Central Africa, with only sporadic spillovers to countries outside Africa due to international travel or close contact with wildlife. During May 2022, multiple countries in Europe, North and South America, Australia, Asia, and Africa reported near-simultaneous outbreaks of MPXV, the first time that patient clusters were reported over such a large geographical area. Cases have no known epidemiological links to MPXV-endemic countries in West or Central Africa. Real-time PCR is currently the gold standard for MPXV diagnostics, but it requires trained laboratory personnel and specialized equipment, and results can only be obtained after several hours. A rapid and simple-to-operate point-of-care diagnostic test for MPXV is crucial for limiting its spread and controlling outbreaks. Here, three recombinase-based isothermal amplification assays (RPA/RAA) for the rapid detection of MPXV isolates were developed. These three assays target the MPXV G2R gene, and the limit of detection for these systems is approximately 100 copies of DNA per reaction. The assays were found to be specific and non-cross reactive against other pox viruses, such as vaccinia virus, and the results can be visualized within 20–30 min. The assays were validated with DNA extracted from 19 clinical samples from suspected or confirmed MPXV patients from Central Africa, and found to be consistent with findings from traditional qPCR. These results provide a solid platform for the early diagnosis of potential MPXV cases, and will help with the control and prevention of current and future outbreaks.

M onkeypox, caused by monkeypox virus (MPXV), a member of the Orthopoxvirus genus, was considered a rare emerging disease before a multinational outbreak was identified in May 2022 (1).After global smallpox eradication in 1977, monkeypox became the most concerning human Orthopoxvirus infection. Clinical manifestations of monkeypox typically resemble those of smallpox, including a febrile prodrome and subsequent disseminated maculopapular rash, including vesicles and pustules, that occurs in successive stages (2). Lymphadenopathy is a prominent feature of monkeypox and usually does not occur for smallpox and chickenpox (3). Illness is less severe and death less likely among monkeypox cases than smallpox cases, but monkeypox mortality rates vary and are higher for clade I (formerly the Congo Basin clade) than for clade II (formerly the West African clade) viruses (2). Prior smallpox vaccination can confer cross-immunity for monkeypox, but smallpox vaccination programs worldwide ended in the early 1980s (4).In 1970, a human monkeypox case was reported from Basankusu, Equateur Province, Democratic Republic of the Congo (DRC) (5). Subsequent sporadic monkeypox cases were reported among human and animal populations from remote areas of Central Africa during the 1970s and 1980s (6,7). Since 1990, increases in the frequency and scale of epidemics in Africa have been reported for clade I and, to a lesser extent, since 2000 for clade II. Since 2016, confirmed monkeypox cases have been reported in DRC, Central African Republic (CAR), Republic of Congo (hereafter Congo), Nigeria, Sierra Leone, Liberia, and Cameroon (6). The true burden, circulation rates, and geographic range of this emerging disease remain unknown because many countries lack systematic routine monkeypox surveillance and affected areas often are remote (8,9).An outbreak of human monkeypox disease occurred outside Africa in 2003, after infected animals from Ghana were imported into the United States