The potential of fibre optic UV-Vis-NIR spectroscopy to distinguish vital and devitalised forms of microbial contamination of paper substrates

Abstract Microorganisms, especially microscopic filamentous fungi, represent one of the most significant factors influencing the degradation of cultural heritage cellulosic objects. Early detection, identification and characterisation of microbial communities can help select a suitable conservation intervention and, in addition, allow possible control of its effectiveness. A combination of spectral methods and statistical data processing appears to be a suitable alternative to conventional methods for monitoring microbial contamination. The main goal of the presented research was the investigation of the spectral properties of vital and devitalised filamentous fungi Alternaria alternata, Aspergillus niger, Cladosporium herbarum, Penicillium chrysogenum, and Trichoderma atroviride, inoculated on a paper substrate Whatman in two phases—dormant (conidia) and active (mycelium). The combination of the UV-Vis-NIR and NIR Fibre Optics Reflection Spectroscopy (FORS) with the Principal Component Analysis (PCA) was set to determine whether the spectra of vital and devitalised forms of studied samples differ. The obtained results prove differences between the spectra of vital and devitalised forms of filamentous fungi, at least in one studied spectral region. Therefore, UV-Vis-NIR and NIR FORS combined with PCA seems to be a promising tool for monitoring paper-based objects' microbial contamination

Systematic Genomic Surveillance of SARS-CoV-2 Virus on Illumina Sequencing Platforms in the Slovak Republic—One Year Experience

To explore a genomic pool of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the pandemic, the Ministry of Health of the Slovak Republic formed a genomics surveillance workgroup, and the Public Health Authority of the Slovak Republic launched a systematic national epidemiological surveillance using whole-genome sequencing (WGS). Six out of seven genomic centers implementing Illumina sequencing technology were involved in the national SARS-CoV-2 virus sequencing program. Here we analyze a total of 33,024 SARS-CoV-2 isolates collected from the Slovak population from 1 March 2021, to 31 March 2022, that were sequenced and analyzed in a consistent manner. Overall, 28,005 out of 30,793 successfully sequenced samples met the criteria to be deposited in the global GISAID database. During this period, we identified four variants of concern (VOC)—Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529). In detail, we observed 165 lineages in our dataset, with dominating Alpha, Delta and Omicron in three major consecutive incidence waves. This study aims to describe the results of a routine but high-level SARS-CoV-2 genomic surveillance program. Our study of SARS-CoV-2 genomes in collaboration with the Public Health Authority of the Slovak Republic also helped to inform the public about the epidemiological situation during the pandemic