Bousali Maria, Dimadi Aristea, Kostaki Evangelia-Georgia, Tsiodras Sotirios, Nikolopoulos Georgios K, Sgouras Dionyssios N, Magiorkinis Gkikas, Papatheodoridis George, Pogka Vasiliki, Lourida Giota, Argyraki Aikaterini, Angelakis Emmanouil, Sourvinos George, Beloukas Apostolos, Paraskevis Dimitrios, Karamitros Timokratis
Bioinformatics and Applied Genomics Unit, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece.
Department of Hygiene Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, 15772 Athens, Greece.
Life (Basel). 2021 Mar 9;11(3):219. doi: 10.3390/life11030219.
The spatiotemporal profiling of molecular transmission clusters (MTCs) using viral genomic data can effectively identify transmission networks in order to inform public health actions targeting SARS-CoV-2 spread.
We used whole genome SARS-CoV-2 sequences derived from ten European regions belonging to eight countries to perform phylogenetic and phylodynamic analysis. We developed dedicated bioinformatics pipelines to identify regional MTCs and to assess demographic factors potentially associated with their formation.
The total number and the scale of MTCs varied from small household clusters identified in all regions, to a super-spreading event found in Uusimaa-FI. Specific age groups were more likely to belong to MTCs in different regions. The clustered sequences referring to the age groups 50-100 years old (y.o.) were increased in all regions two weeks after the establishment of the lockdown, while those referring to the age group 0-19 y.o. decreased only in those regions where schools' closure was combined with a lockdown.
The spatiotemporal profiling of the SARS-CoV-2 MTCs can be a useful tool to monitor the effectiveness of the interventions and to reveal cryptic transmissions that have not been identified through contact tracing.
利用病毒基因组数据对分子传播簇（MTC）进行时空分析，可有效识别传播网络，为针对严重急性呼吸综合征冠状病毒2（SARS-CoV-2）传播的公共卫生行动提供依据。
我们使用来自八个国家十个欧洲地区的SARS-CoV-2全基因组序列进行系统发育和系统动力学分析。我们开发了专门的生物信息学流程，以识别区域MTC，并评估可能与其形成相关的人口统计学因素。
MTC的总数和规模各不相同，从所有地区发现的小家庭聚集，到在芬兰新地区发现的超级传播事件。特定年龄组在不同地区更有可能属于MTC。在封锁措施实施两周后，所有地区50至100岁年龄组的聚集序列增加，而0至19岁年龄组的聚集序列仅在学校关闭并实施封锁的地区减少。
SARS-CoV-2 MTC的时空分析可作为监测干预措施有效性和揭示通过接触者追踪未发现的隐匿传播的有用工具。
