Unique SARS-CoV-2 variant found in public sequence data of Antarctic soil samples collected in 2018-2019

The COVID-19 pandemic has been going on for two years now and although many hypotheses have been put forward, its origin remain obscure. We investigated whether the huge public sequencing data archives’ samples collected earlier than the earliest known cases of the pandemic might contain traces of SARS-CoV-2. Here we report the bioinformatic analysis of a metagenome sample set collected from soil on King George Island, Antarctica between 2018-12-24 and 2019-01-13. It contains sequence fragments matching the SARS-CoV-2 reference genome with altogether more than half million nucleotides, covering the complete genome on average 17×. Preliminary phylogeny analysis places the sample close to the known earliest cases. The high sequence coverage rules out chance alignments from other species but possible laboratory contamination cannot be excluded. The sequence harbours a unique combination of mutations, unseen in other samples, so whatever its origin, it can add important piece of information to the puzzle of the ongoing pandemic.

DNA extraction from concrete v2

This is a protocol for extracting DNA from concrete, based on the protocol developed by L. S. Weyrich, et al. for extraction of DNA from ancient calcified dental plaque. We have scaled it up for larger sample sizes and made some additional modifications for the chemistry of concrete. DNA extracted using this method is suitable for metagenomic sequencing by Illumina MiSeq and NextSeq, as well as amplicon sequencing. This protocol should yield 10 ng to 5 μg DNA per 10 g of concrete, depending on the age and integrity of the sample. Reference: L. S. Weyrich et al., Laboratory contamination over time during low-biomass sample analysis. Mol. Ecol. Resour. 19, 982–996 (2019).

A 5-Years (2015–2019) Control Activity of an EU Laboratory: Contamination of Histamine in Fish Products and Exposure Assessment

Histamine contamination was evaluated on 474 batches (3130 determinations) of fish products collected in Puglia and Basilicata (southern part of Italy) during the years 2015–2019, using a high-throughput two-tier approach involving a screening (ELISA test) and confirmatory method (HPLC/FLD with o-phthalaldehyde derivatization). Histamine concentration >2.5 mg kg−1 was detected in 51% of total batches with the 2.5% of non-compliance. Except for two samples of fresh anchovies, all non-compliant samples were frozen, defrosted and canned tuna. Among 111 fresh tuna batches, 9 had a content of histamine between 393 and 5542 mg kg−1, and scombroid poisoning cases were observed after their consumption. Good quality canned tuna and ripened anchovies sold in Italy was observed. Furthermore, the analysis of the processing technology and storage practice critical points were reported in this study, with useful considerations to minimize the histamine risk for consumers. Finally, based on these results, several considerations about risk exposure were reported.

Identifying and Eliminating Laboratory Contamination by Topical Testosterone Therapeutics

Many prescription and over-the-counter drugs are available as topical formulations. Contamination of clinical laboratory workspaces by topical drugs may increase the risk of potential interference with diagnostic testing. An example of localized workspace contamination attributed to a topical hormonal drug (testosterone, T) is presented to highlight significant challenges in identifying and resolving this potential problem. Investigation included precision studies, instrument service and parts replacement, instrument replacement, airflow analysis, environmental dust sampling, and the development of customized methods for workspace monitoring and cleaning. Laboratory policies and procedures were also revised to minimize future risk.

Laboratory contamination over time during low-biomass sample analysis

Bacteria are not only ubiquitous on earth but can also be incredibly diverse within clean laboratories and reagents. The presence of both living and dead bacteria in laboratory environments and reagents is especially problematic when examining samples with low endogenous content (e.g.skin swabs, tissue biopsies, ice, water, degraded forensic samples, or ancient material), where contaminants can outnumber endogenous microorganisms within samples. The contribution of contaminants within high-throughput studies remains poorly understood because of the relatively low number of contaminant surveys. Here, we examined 144 negative control samples (extraction blank and no-template amplification controls) collected in both typical molecular laboratories and an ultraclean ancient DNA laboratory over five years to characterize long-term contaminant diversity. We additionally compared the contaminant content within a homemade silica-based extraction method, commonly used to analyse low-endogenous samples, with a widely used commercial DNA extraction kit. The contaminant taxonomic profile of the ultraclean ancient DNA laboratory was unique compared to the modern molecular biology laboratories, and changed over time according to researchers, month, and season. The commercial kit contained higher microbial diversity and several human-associated taxa in comparison to the homemade silica extraction protocol. We recommend a minimum of two strategies to reduce the impacts of laboratory contaminants within low-biomass metagenomic studies: 1) extraction blank controls should be included and sequenced with every batch of extractions and 2) the contributions of laboratory contamination should be assessed and reported in each high-throughput metagenomic study.