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.

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West Nile virus (WNV) is a mosquito-borne virus belonging to the genus Flavivirus, related to the Japanese encephalitis antigenic complex of Flaviviridae family. It is transmitted by the bite of infected mosquitoes. The virus is maintained in a mosquito–bird–mosquito transmission cycle. WNV has recently dramatically expanded its geographical range and is now considered the most widespread arbovirus in the world, including the Americas, Europe and countries facing the Mediterranean Basin. In Algeria, West Nile disease (WND) infections with human meningoencephalitis cases have been reported in 1994 in Tinerkouk (southwest Sahara. In autumn 2012, one fatal clinical case of WNV neuroinvasive infection was reported in Jijel (coastal east). During the same year, a retrospective serosurvey performed in Algiers and bordering areas highlighted specific anti-WNV IgG in local population. Between 2013 and 2014 two clinical cases were reported, in Timimoune (south) and Guelma (northeast) respectively. Although no case was reported in equids, serosurveys demonstrated its presence: an animal serosurvey was conducted in Djanet (south) in 1975, and in 2014 a seroprevalence of equids in the northeast part of Algeria highlighted a virus circulation. This review aims to evaluate the global epidemiologic situation of West Nile disease in Algeria, with an updated situation based on human cases, equine reports and entomologic investigations. Our study reinforces the need for building the capacity for surveillance in this region to prevent future emergence of WNV and other arboviruses.

Sindbis virus (SINV) is a zoonotic alphavirus (family Togaviridae, genus Alphavirus) that causes human diseases in Africa, Europe, Asia, and Australia. Occasionally, SINV outbreaks were reported in South Africa and northern Europe. Birds are the main amplifying hosts of SINV, while mosquitoes play the role of the primary vector. Culex mosquitoes were collected in Algeria and subsequently tested for SINV. SINV RNA was detected in 10 pools out of 40, from a total of 922 mosquitoes tested. A strain of SINV was isolated from a pool displaying high viral load. Whole-genome sequencing and phylogenetic analysis showed that the SINV Algeria isolate was most closely related to a Kenyan strain. This was the first record of SINV in Algeria and more broadly in northwestern Africa, which can be a potential risk for human health in the circulating area. Further studies are needed to measure the impact on public health through seroprevalence studies in Algeria.

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.

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In the last decade, several phleboviruses transmitted by sand flies were detected in the Mediterranean countries, with the health impact of some of them being unknown. From September to October 2020, a total of 3351 sand flies were captured in Kherrata (Bejaia, northern Algeria) and identified by sex, grouped in 62 pools, which were tested for the presence of phlebovirus RNA using endpoint RT-PCR. Two pools (male and female, respectively) were positive. The genome sequencing and phylogenetic analysis showed that the two phleboviruses detected were closely related to the Punique virus (PUNV) isolated in Tunisia and detected in Algeria. Both PUNV strains were isolated on VERO cells from positive pools. Morphological identification of 300 sand flies randomly selected, showed a clear dominance of Phlebotomus perniciosus (98.67%). The dominance of this species in the study area was confirmed by PCR targeting the mitochondrial DNA. Our result represents the first isolation of PUNV and the second report in Algeria from two distinct regions which confirm its large circulation in the country and more broadly in North Africa. Further studies are needed to measure the impact on public health through seroprevalence studies in humans as well as animals and to investigate its potential involvement in neurological viral diseases.

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