Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions.

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers

Prevalence of clinically relevant non-tuberculous mycobacteria and detection of antimicrobial resistance at vilnius university hospital santaros klinikos in 2015 – 2018

Master’s degree thesis: Prevalence of clinically relevant non-tuberculous mycobacterium and antimicrobial resistance detection at Vilnius University Hospital Santaros Klinikos in 2015 – 2018. Aim of the study: evaluate the prevalence of clinically relevant nontuberculous mycobacteria, species diversity and to investigate their resistance to antibacterial drugs at Vilnius University Hospital Santaros Klinikos during 2015-2018 period. Materials and methods. The study was conducted at Vilnius University Hospital Santaros Klinikos Center of Laboratory Medicine Tuberculosis Laboratory. A retrospective analysis of 166 nontuberculous mycobacteria was performed. Macrolides and aminoglycosides resistance for M. avium complex, M. abscessus complex and M. chelonae was determined by using GenoType® NTM-DR VER 1.0 commercial kit, a total of 51 cultures were tested. Results. During the retrospective analysis, the most isolated nontuberculous mycobacteria were M. avium – 51.2% (N = 85), M. gordonae - 19.9% (N = 33) and M. fortuitum 7.2% (N = 12), and less commonly found were M. abscessus complex of 1.8% (N = 3), M. chelonae 4.2% (N = 7), M. kansasii 3% (N = 5), M. xenopi 2.4% (N = 4), M. intracellulare 1.8% (N = 3), M. celatum 1.8% (N = 3). None of the investigated nontuberculous mycobacteria had mutations in rrl and rrs genes, indicating macrolides and aminoglycoside resistance respectively. However, a T nucleotide was determined at 28 position of erm(41) gene of M. abscessus subsp. abscessus and M. abscessus subsp. bolletii, associated with resistance to macrolides. Conclusions. The most frequently isolated nontuberculous mycobacteria at Vilnius University Hospital Santaros Klinikos were M. avium, M. gordonae and M. fortuitum during 2015 – 2018 year period. None of the analyzed nontuberculous mycobacteria exhibited mutations showing acquired resistance to macrolides and aminoglycosides. However, an erm(41) gene polymorphism was identified for two isolates - M. abscessus subsp. abscessus and M. abscessus subsp. bolletii showing resistance to macrolides. Detection of common gene mutations of nontuberculous mycobacteria, associated with resistance to macrolides and aminoglycosides, using PCR method is reasonably good, although results should be interpreted in consideration with other clinical tests

Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions

Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers