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An ever growing number of species of Cy CVs have been described in mammals (human, chimpanzee, goat, cattle, bat, pig, sheep, and camel), birds (chicken and duck) and insects (dragonflies and wood cockroach).

The presence of the virus was demonstrated in serum, stool or cerebrospinal fluid (CSF) of patients with acute flaccid paralysis, paraplegia or suspected central nervous system infections from Pakistan, Tunisia, Malawi and southern and central Vietnam.

Cycloviruses, small ss DNA viruses of the Circoviridae family, have been identified in the cerebrospinal fluid from symptomatic human patients.

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Vietnamese VN strains are colored in grey, Malawian VS5700009 in light yellow and Tunisian TN25 and TN18 appear in orange Table 2: Sequence identity matrix for the Capsid protein sequence (%).

Cameroonian swine (KM392284–KM392286) and Madagascan human cycloviruses (KM392287–KM392289) described in this study are bolded. All authors were involved in reviewing and editing of the manuscript.

Cap protein was less conserved compared to that of Madagascan and Vietnamese Cy CV strains (≈84–85% identity), but was much closer to Cy CV-VN Cap proteins than to that of Malawian VS5700009 and Tunisian TN25 Cy CV species (≈34% and ≈48%, respectively) (Table 2).

Overall, Madagascan human-derived Cy Cv strains appeared as typical Cy CV-VN strains, highly conserved, while Cameroonian swine strains belonged to the same species but were less conserved, especially in the Cap protein sequence.

To assess the circulation of Cy CV-VN in Africa, we tested, using a Cy CV species-specific PCR, 410 human stool samples from Madagascar, 1337 human stool samples from Ghana and 520 pig stool samples from Cameroon. Ten swine samples from Cameroon were positive (1 from Bamenda, 9 from Douala). All human samples from (cases and controls) Ghana remained negative for Cy CV-VN.

Out of the 410 human samples from Madagascar, three were positive for Cy CV-VN-like species and the full genome was amplified, sequenced and characterized (Genbank acc. The full genome of three positive samples from Douala was obtained (Genbank acc. The genomic sequences of human Cy CV strains from Madagascar were highly similar (98% identity) to that of human Cy CV-VN species.

Cap protein of Madagascan Cy CV was 222 aa long like typical Cy CV-VN and equally conserved (≈98–99% identity when compared to Cy CV-VN) but more divergent compared to Malawian VS5700009 (≈35% identity) and Tunisian TN25 (≈48%) Cy CV species (Table 2).

In contrast, the swine-derived Cy CV strains from Cameroon exhibited a less conserved genome (86% identity to Cy CV-VN).

Taxon information includes the name, source of isolation, Gen Bank accession number, and country of origin.

The cyclovirus strains generated during this study are bolded.

Phylogenetic analysis based on the complete Rep and Cap protein sequences showed that the Cy CVs from Cameroon, Madagascar and Vietnam clustered together forming a distinct and highly supported clade/group (Cy CV-VN) within the cyclovirus phylogeny (Figure 2).

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