Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Viral diarrhea remains a major cause of childhood morbidity and mortality worldwide. In Tunisia, no comprehensive studies of all viral agents related to diarrhea in children have yet been conducted. The present study was performed to investigate the role of enteric viruses in acute diarrhea in the country. Six hundred thirty-eight stool samples were collected from children under 5 years of age seeking medical care for acute diarrhea between October 2003 and September 2005 in hospitals from the Eastern-Center Tunisia. All samples were tested for rotavirus, astrovirus, and adenovirus using commercial antigen enzyme immunoassays (EIAs). Positive samples for rotavirus and astrovirus were confirmed by an "in-house" reverse transcriptase-polymerase chain reaction (RT-PCR). Samples positive for adenovirus antigen were subjected to further EIA screening for species F enteric adenovirus types 40 and 41. At least one viral agent was found in 30% of the specimens. The frequency of rotavirus, astrovirus, and adenovirus was 20%, 7%, and 6%, respectively. Of the stool samples containing adenovirus, 57% (20/35) were found to be positive for species F adenovirus types 40/41. Dual infections were found in 9% (17/191) of the positive samples. Enteric viruses appear to play an important role in pediatric diarrhea in Tunisia. The introduction of affordable viral diagnosis in pediatric hospitals will improve patient care by reducing the unnecessary use of antibiotics.

An epidemiological survey investigating rotavirus infections in children was undertaken in the Eastern Center of Tunisia between January 1995 and December 2004. A total of 982 faecal specimens collected from children less than 5 years in age were screened by enzyme-linked immunosorbent assay (ELISA) or latex agglutination assay for the presence of group A rotavirus antigen. Rotavirus-positive samples were used for G and P typing by multiplex semi-nested reverse transcription-PCR. Rotaviruses were detected in 22% (n = 220) of stools. Of these, 164 were typed for VP7: G genotypes found were G1 (59%), G2 (2%), G3 (9%), G4 (10%), G8 (1%), and G9 (1%). Sixteen specimens (9%) showed mixed G profiles. A total of 119 specimens were typed for VP4. P genotypes detected were P[8] (32%), P[6] (15%), and P[4] (13%). Mixed P profiles were also detected (6%). Although the distribution of the detected genotypes appeared to change annually, G1P[8] rotavirus strains always predominated during the 10-year period of study. This is the first report of rotaviruses in Tunisia with unconventional VP7 serotypes such as G8 and G9, highlighting the need for continual surveillance of emerging strains in Northern Africa. Indeed, the new commercial vaccines only contain the VP7 genes that dictate G1 or G1 to G4 specificities. These vaccines may protect less well against unusual strains circulating in countries planning to implement a rotavirus vaccine strategy.