SynthesisEpidemiology and infection2026
Local genomic epidemiology investigations of SARS-CoV-2 during the early pandemic response: A global systematic review.
Synthesis in Epidemiology and infection, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
0 citing papers in PubMed.
No citing paper in PubMed yet.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomic epidemiology was essential for characterizing SARS-CoV-2 transmission during the early COVID-19 pandemic. This systematic review examined how whole-genome sequencing was used in local outbreak investigations published between March 2020 and March 2021. Searches of PubMed, Scopus, and Web of Science identified 32 studies from 18 countries that integrated genomic and epidemiological data for local outbreak investigations. Most studies were conducted in healthcare settings or in high-income countries. A limited number of studies were conducted in low- and middle-income countries, except for China and Vietnam. Illumina or Oxford Nanopore platforms and tiled-amplicon protocols were the most common sequencing methods. Phylogenetic trees were the most common genomic epidemiology analytical approach. Genomic data enabled confirmation of suspected transmission links, detection of multiple introductions, and identification of asymptomatic or presymptomatic transmission. Important enablers of early implementation included open-access genomics databases, standardized protocols (e.g. ARTIC), open-source tools (e.g. Nextstrain), and cross-sector partnerships and funding. Study quality and adherence to common observational study reporting guidelines varied widely. Familiarity with the STROME-ID guidelines for molecular epidemiology studies would have improved overall quality. These findings highlight the utility of genomic epidemiology in outbreak response and support its continued integration into public health surveillance systems.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.