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Full genomes sequences of six Tunisian SARS-CoV-2 strains were obtained from imported and locally transmission cases during the COVID-19 outbreak. Reported sequences were non-identical with 0.1% nucleotide divergence rate and clustered into 6 different clades with worldwide sequences. SNPs results favor the distribution of the reported Tunisian sequences into 3 major genotypes. These results indicate multiple introductions of the virus in Tunisia and add new genomic data on SARS-CoV-2 at the international level. Hosted file Main_text.doc available at https://authorea.com/users/330423/articles/457189-first-wholegenome-sequences-and-phylogenetic-analysis-of-sars-cov-2-virus-isolates-during-covid-19outbreak-in-tunisia-north-africa Hosted file Figure_1.ppt available at https://authorea.com/users/330423/articles/457189-first-wholegenome-sequences-and-phylogenetic-analysis-of-sars-cov-2-virus-isolates-during-covid-19outbreak-in-tunisia-north-africa

Introduction Routine laboratory screening is based on the detection of WNV specific IgM and IgG in blood and cerebrospinal fluid. Confirmation is then classically applied RT-PCR in CSF, which often give negative results due to too short virorachia and late sampling.RT-PCR was applied-for the first time for routine diagnosis purpose-on urine samples.Methods During 2018 outbreak in Tunisia, 107 patients presented WNV neurologic symptoms and were positive for WNV serology. Of them, 95 patients were sampled for urine and 35 were sampled for CSF. Qualitative RT-PCR was performed on both type of samples. Results WNV RNA was detected in 50,5% of urine samples (48/95) and in 2,8% of CSF samples (1/35). WNV RNA was detectable from 1 to 41 day from symptom onset, however, positive urine rate was 53,1% during the first 10 days from symptom onset. The proportions of urine-positive and urine-negative samples, based on day of collection, showed no statistical difference ( p >0,005). Cycle threshold values ranged from 12 to 39, with no correlation with the day of collection. The lowest Ct value was detected for urine sampled on day 5 after symptom onset. A statistically significant difference was found between age groups of confirmed and non confirmed cases ( p <0,001). Discussion/Conclusion Our study reports the use of RT-PCR on urine samples as a confirmatory diagnostic tool for WNV probable cases during an outbreak. Our findings underline the reliability, and rapidity of this confirmatory tool, even late and show its superiority on CSF investigation.