严重急性呼吸综合征冠状病毒2（SARS-CoV-2）基因组监测的全球差异

Global disparities in SARS-CoV-2 genomic surveillance.

作者信息

Brito Anderson F, Semenova Elizaveta, Dudas Gytis, Hassler Gabriel W, Kalinich Chaney C, Kraemer Moritz U G, Ho Joses, Tegally Houriiyah, Githinji George, Agoti Charles N, Matkin Lucy E, Whittaker Charles, Howden Benjamin P, Sintchenko Vitali, Zuckerman Neta S, Mor Orna, Blankenship Heather M, de Oliveira Tulio, Lin Raymond T P, Siqueira Marilda Mendonça, Resende Paola Cristina, Vasconcelos Ana Tereza R, Spilki Fernando R, Aguiar Renato Santana, Alexiev Ivailo, Ivanov Ivan N, Philipova Ivva, Carrington Christine V F, Sahadeo Nikita S D, Gurry Céline, Maurer-Stroh Sebastian, Naidoo Dhamari, von Eije Karin J, Perkins Mark D, van Kerkhove Maria, Hill Sarah C, Sabino Ester C, Pybus Oliver G, Dye Christopher, Bhatt Samir, Flaxman Seth, Suchard Marc A, Grubaugh Nathan D, Baele Guy, Faria Nuno R

机构信息

Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA.

Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil.

出版信息

medRxiv. 2021 Dec 9:2021.08.21.21262393. doi: 10.1101/2021.08.21.21262393.

DOI:10.1101/2021.08.21.21262393

PMID:34462754

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8404891/

Abstract

Genomic sequencing provides critical information to track the evolution and spread of SARS-CoV-2, optimize molecular tests, treatments and vaccines, and guide public health responses. To investigate the spatiotemporal heterogeneity in the global SARS-CoV-2 genomic surveillance, we estimated the impact of sequencing intensity and turnaround times (TAT) on variant detection in 167 countries. Most countries submit genomes >21 days after sample collection, and 77% of low and middle income countries sequenced <0.5% of their cases. We found that sequencing at least 0.5% of the cases, with a TAT <21 days, could be a benchmark for SARS-CoV-2 genomic surveillance efforts. Socioeconomic inequalities substantially impact our ability to quickly detect SARS-CoV-2 variants, and undermine the global pandemic preparedness.

摘要

基因组测序为追踪新冠病毒的进化和传播、优化分子检测、治疗方法及疫苗，并指导公共卫生应对措施提供了关键信息。为研究全球新冠病毒基因组监测中的时空异质性，我们估算了测序强度和周转时间（TAT）对167个国家病毒变异株检测的影响。大多数国家在样本采集21天之后才提交基因组，77%的低收入和中等收入国家对其病例的测序比例不到0.5%。我们发现，对至少0.5%的病例进行测序，且周转时间短于21天，可作为新冠病毒基因组监测工作的一个基准。社会经济不平等严重影响我们快速检测新冠病毒变异株的能力，并破坏全球大流行防范工作。