The coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an Iraqi patient was sequenced for the first-time using Illumina MiSeq technology. There was a D614G mutation in the spike protein-coding sequence. This report is valuable for better understanding the spread of the virus in Iraq.

Background Sporulation is a complex cell differentiation programme shared by many members of the Firmicutes, the end result of which is a highly resistant, metabolically inert spore that can survive harsh environmental insults. Clostridioides difficile spores are essential for transmission of disease and are also required for recurrent infection. However, the molecular basis of sporulation is poorly understood, despite parallels with the well-studied Bacillus subtilis system. The spore envelope consists of multiple protective layers, one of which is a specialised layer of peptidoglycan, called the cortex, that is essential for the resistant properties of the spore. We set out to identify the enzymes required for synthesis of cortex peptidoglycan in C. difficile . Methods Bioinformatic analysis of the C. difficile genome to identify putative homologues of Bacillus subtilis spoVD was combined with directed mutagenesis and microscopy to identify and characterise cortex-specific PBP activity. Results Deletion of CDR20291_2544 (SpoVD Cd ) abrogated spore formation and this phenotype was completely restored by complementation in cis . Analysis of SpoVD Cd revealed a three domain structure, consisting of dimerization, transpeptidase and PASTA domains, very similar to B. subtilis SpoVD. Complementation with SpoVD Cd domain mutants demonstrated that the PASTA domain was dispensable for formation of morphologically normal spores. SpoVD Cd was also seen to localise to the developing spore by super-resolution confocal microscopy. Conclusions We have identified and characterised a cortex specific PBP in C. difficile . This is the first characterisation of a cortex-specific PBP in C. difficile and begins the process of unravelling cortex biogenesis in this important pathogen.

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21Sporulation is a complex cell differentiation programme shared by many members of the 22 Firmicutes, the end result of which is a highly resistant, metabolically inert spore that can 23 survive harsh environmental insults. Clostridium difficile spores are essential for transmission 24 of disease and are also required for recurrent infection. However, the molecular basis of 25 sporulation is poorly understood, despite parallels with the well-studied Bacillus subtilis 26 system. The spore envelope consists of multiple protective layers, one which is a specialised 27 layer of peptidoglycan, called the cortex, that is essential for the resistant properties of the 28 spore. We have identified and characterised a penicillin binding protein (PBP) that is required 29 for cortex synthesis in C. difficile. Surprisingly this PBP was also found to contribute to 30 cephalosporin resistance, indicating an additional role in the synthesis of vegetative cell wall. 31 This is the first description of a cortex-specific PBP in C. difficile and begins the process of 32 unravelling cortex biogenesis in this important pathogen. 33 34 35C. difficile is the most common cause of nosocomial antibiotic-associated diarrhea, with an 36 estimated 453,000 infections and 29,300 deaths per year in the USA alone (Lessa et al., 2015). 37 C. difficile infection (CDI) requires prior disruption to the gut microbiota, most commonly due 38 to an administered antibiotic (Smits et al., 2016). As current treatments largely rely on 39 antibiotic therapy, with further consequent damage to the microbiota, recurrent disease is 40 common and is associated with worse patient prognosis (Rupnik et al., 2009). In recent years 41 there have been dramatic changes in C. difficile epidemiology, in particular due to the 42 emergence of the epidemic ribotype 027 lineage, a previously rare ribotype that was 43 responsible for a series of large hospital outbreaks in North America in the early years of this 44 century before spreading worldwide (He et al., 2013). 45 The spore is an absolute requirement for transmission of disease (Deakin et al., 2012), it allows 46 the organism to transit the lethal aerobic environment while also providing significant 47 resistance to desiccation, heat and common disinfectants (Dyer et al., 2019). As a result, the 48 spores shed by an infected individual can survive in the environment for an extended period of 49 time, a particular problem in hospital environments where large numbers of susceptible 50 individuals are housed in close proximity. The process of sporulation is still relatively poorly 51 understood, despite significant advances in recent years (Zhu et al., 2018). We have previously 52 used high-density transposon mutagenesis and TraDIS to identify a subset of C. difficile genes 53 required for formation of mature heat-resistance spores (Dembek et al., 2015). In total, 54 transposon insertions in 798 genes were found to significantly impact sporulation, many with 55 no clear homology to previously...