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.

Investment in Africa over the past year with regards to SARS-CoV-2 genotyping has led to a massive increase in the number of sequences, exceeding 100,000 genomes generated to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence within their own borders, coupled with a decrease in sequencing turnaround time. Findings from this genomic surveillance underscores the heterogeneous nature of the pandemic but we observe repeated dissemination of SARS-CoV-2 variants within the continent. Sustained investment for genomic surveillance in Africa is needed as the virus continues to evolve, particularly in the low vaccination landscape. These investments are very crucial for preparedness and response for future pathogen outbreaks.One-Sentence SummaryExpanding Africa SARS-CoV-2 sequencing capacity in a fast evolving pandemic.

Our data indicate the predominance of HBV subgenotype D7 and a low prevalence of HDV infection.

The geographic and evolutionary origins of the SARS-CoV-2 Omicron variant (BA.1), which was first detected mid-November 2021 in Southern Africa, remain unknown. We tested 13,097 COVID-19 patients sampled between mid-2021 to early 2022 from 22 African countries for BA.1 by real-time RT-PCR. By November-December 2021, BA.1 had replaced the Delta variant in all African sub-regions following a South-North gradient, with a peak Rt of 4.1. Polymerase chain reaction and near-full genome sequencing data revealed genetically diverse Omicron ancestors already existed across Africa by August 2021. Mutations, altering viral tropism, replication and immune escape, gradually accumulated in the spike gene. Omicron ancestors were therefore present in several African countries months before Omicron dominated transmission. These data also indicate that travel bans are ineffective in the face of undetected and widespread infection.

West Nile Virus (WNV) is the most widely distributed flavivirus worldwide. It is a mosquito-borne virus, and birds constitute its natural reservoir. Humans and equines are considered accidental hosts. Human WNV infections are usually asymptomatic or express as a mild febrile syndrome; however, in around 1% of cases they are responsible for more serious neurological diseases with a potentially lethal outcome. In the Mediterranean basin the virus circulation is regarded as endemic. Outbreaks of WNV meningoencephalitis are regularly notified, especially during summer and autumn seasons. In Algeria, although some surveys have reported WNV activity in the Sahara, to date few data are available about virus circulation in the northern part of the country. We conducted this study to detect possible WNV activity in this part of Algeria. For this purpose, in 2010 a total of 164 human sera were collected from native patients of the Algiers district and surrounding areas, then tested retrospectively for IgG anti-WNV by ELISA. Plaque reduction neutralization technique (PRNT) was used for result confirmation. In this cohort, 9.8% of the 164 collected sera returned positive for anti-WNV IgG; after confirmation by PRNT; 6.7% had specific neutralizing antibodies. No statistically significant difference was observed according to the sex or transfusion status of the patients. In conclusion, these data show for the first time serological evidence of WNV circulation in Algiers and its surrounding areas. They also highlight the need for implementing an integrated surveillance programme covering all aspects of WNV disease in order to better understand the circulation dynamics of WNV in this region. Other flaviviruses antigenically related to WNV should be investigated, given the evidence of serological cross-reaction, as specific IgG antibodies decrease after PRNT confirmation.