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Nature Papers on Environmental Transformation Sequencing, Limited Viral Genomic Surveillance

A strategy for species-specific genome editing in microbial communities is reported in this week's Nature Microbiology. Understanding microbial gene function requires the application of experimental genetics in cultured microorganisms, yet most bacteria and archaea remain uncultured, precluding the use of traditional genetic methods in these organisms. To overcome this, a team led by scientists from the University of California, Berkeley, developed a technique called environmental transformation sequencing, or ET-seq, which involves exposing a microbial community to a randomly integrating mobile genetic element and, in the absence of any selection, extracting total community DNA for sequencing using two protocols. In the first protocol, the junctions between the inserted and host DNA are enriched and sequenced to determine insertion location and quantity in each host. In the second, low-depth metagenomic sequencing is used to quantify the abundance of each community member in a sample. DNA-editing all-in-one RNA-guided CRISPR–Cas transposase (DART) systems for targeted DNA insertion are then used with organisms identified as tractable by ET-seq to enable organism- and locus-specific genetic manipulation in a community context. "Traditionally, the combined steps of culturing an environmental microbe, determining the ideal means to transform it, and implementing targeted editing could take years or might fail altogether," the study's authors write. "ET-seq, together with [DART], can accelerate this process to weeks and move it into the more realistic and information-rich context of communities."

Limited genomic surveillance in many low-income countries could lead to delays in identifying SARS-CoV-2 variants with previously undescribed phenotypic characteristics, according to a review of the emergence, genomic diversity, and global spread of the virus appearing in Nature this week. In the report, a team led by scientists from Shandong First Medical University & Shandong Academy of Medical Sciences provide an overview of the available data on the emergence and spread of SARS-CoV-2 and describe how genomic surveillance has helped track genetic variation in the virus. They also highlight challenges to these surveillance efforts such as the lack of genomic sequencing in nations other than the US and the UK, where around half of all sequenced virus genomes have been generated. "SARS-CoV-2 has led to an increased understanding of coronavirus evolution and the virus has entered a new evolutionary phase characterized by the frequent emergence and spread of variants that affect immune escape and reduce the efficacy of vaccines," the authors write. "To contain the current and future pandemics, we urgently call for closer international cooperation, increased vaccine supply and sharing, rapid information exchange, and the establishment of both the infrastructure and trained personnel required for the effective genomic surveillance of SARS-CoV-2 and other emerging viruses."