Summary Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb) and a few related mycobacteria, is a devastating disease, killing more than a million individuals per year worldwide. However, its pathogenesis remains largely elusive, as only a small proportion of infected individuals develop clinical disease either during primary infection or during reactivation from latency or secondary infection. Subacute, hematogenous, and extrapulmonary disease tends to be more frequent in infants, children, and teenagers than in adults. Life-threatening primary TB of childhood can result from known acquired or inherited immunodeficiencies, although the vast majority of cases remain unexplained. We review here the conditions conferring a predisposition to childhood clinical diseases caused by mycobacteria, including not only M.tb but also weakly virulent mycobacteria, such as BCG vaccines and environmental mycobacteria. Infections with weakly virulent mycobacteria are much rarer than TB, but the inherited and acquired immunodeficiencies underlying these infections are much better known. Their study has also provided genetic and immunological insights into childhood TB, as illustrated by the discovery of single-gene inborn errors of IFN-γ immunity underlying severe cases of TB. Novel findings are expected from ongoing and future human genetic studies of childhood TB in countries that combine a high proportion of consanguineous marriages, a high incidence of TB, and an excellent clinical care, such as Iran, Morocco, and Turkey.

Background and ObjectivesIn the last decade, autosomal recessive IL-12Rβ1 deficiency has been diagnosed in four children with severe tuberculosis from three unrelated families from Morocco, Spain, and Turkey, providing proof-of-principle that tuberculosis in otherwise healthy children may result from single-gene inborn errors of immunity. We aimed to estimate the fraction of children developing severe tuberculosis due to IL-12Rβ1 deficiency in areas endemic for tuberculosis and where parental consanguinity is common.Methods and Principal FindingsWe searched for IL12RB1 mutations in a series of 50 children from Iran, Morocco, and Turkey. All children had established severe pulmonary and/or disseminated tuberculosis requiring hospitalization and were otherwise normally resistant to weakly virulent BCG vaccines and environmental mycobacteria. In one child from Iran and another from Morocco, homozygosity for loss-of-function IL12RB1 alleles was documented, resulting in complete IL-12Rβ1 deficiency. Despite the small sample studied, our findings suggest that IL-12Rβ1 deficiency is not a very rare cause of pediatric tuberculosis in these countries, where it should be considered in selected children with severe disease.SignificanceThis finding may have important medical implications, as recombinant IFN-γ is an effective treatment for mycobacterial infections in IL-12Rβ1-deficient patients. It also provides additional support for the view that severe tuberculosis in childhood may result from a collection of single-gene inborn errors of immunity.

Large scale genomic analysis of 3067 SARS-1 CoV-2 genomes reveals a clonal geo-distribution 2 and a rich genetic variations of hotspots 3 mutations 4 Abstract 33In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, 34China, and became a global pandemic. Characterization of the genetic variants of SARS-35CoV-2 is crucial in following and evaluating it spread across countries. In this study, we 36 collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the 37 first three months after the onset of this virus. Using comparative genomics analysis, we 38 traced the profiles of the whole-genome mutations and compared the frequency of each 39 mutation in the studied population. The accumulation of mutations during the epidemic 40 period with their geographic locations was also monitored. The results showed 782 variant 41 sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles 42 revealed the presence of 38 recurrent non-synonymous mutations, including ten hotspot 43 mutations with a prevalence higher than 0.10 in this population and distributed in six 44 SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map 45 revealed certain genotypes specific to the geographic location. We also found co-occurring 46 mutations resulting in the presence of several haplotypes. Moreover, evolution over time 47We have also created an inclusive unified database (http://genoma.ma/covid-19/) that lists 52 all of the genetic variants of the SARS-CoV-2 genomes found in this study with 53 phylogeographic analysis around the world. 54 55 56

The observed prevalence of PID was 0.81/100,000 inhabitants, suggesting considerable underdiagnosis and a need to increase awareness of these conditions in Morocco. The distribution of PIDs was different from that reported in Western countries, with a particularly high proportion of SCID, MHC II deficiencies, hyper-IgE syndrome and autosomal recessive agammaglobulinemia. However, we have now organized a national network, which should improve diagnosis rates in remote regions.

In late December 2019, an emerging viral infection COVID-19 was identified in Wuhan, China, and became a global pandemic. Characterization of the genetic variants of SARS-CoV-2 is crucial in following and evaluating it spread across countries. In this study, we collected and analyzed 3,067 SARS-CoV-2 genomes isolated from 55 countries during the first three months after the onset of this virus. Using comparative genomics analysis, we traced the profiles of the whole-genome mutations and compared the frequency of each mutation in the studied population. The accumulation of mutations during the epidemic period with their geographic locations was also monitored. The results showed 782 variants sites, of which 512 (65.47%) had a non-synonymous effect. Frequencies of mutated alleles revealed the presence of 68 recurrent mutations, including ten hotspot non-synonymous mutations with a prevalence higher than 0.10 in this population and distributed in six SARS-CoV-2 genes. The distribution of these recurrent mutations on the world map revealed that certain genotypes are specific to geographic locations. We also identified co-occurring mutations resulting in the presence of several haplotypes. Moreover, evolution over time has shown a mechanism of mutation co-accumulation which might affect the severity and spread of the SARS-CoV-2. The phylogentic analysis identified two major Clades C1 and C2 harboring mutations L3606F and G614D, respectively and both emerging for the first time in China. On the other hand, analysis of the selective pressure revealed the presence of negatively selected residues that could be taken into considerations as therapeutic targets. We have also created an inclusive unified database (http://covid-19.medbiotech.ma) that lists all of the genetic variants of the SARS-CoV-2 genomes found in this study with phylogeographic analysis around the world.