Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction.
Mathematical modelling of SARS-CoV-2 variant outbreaks reveals their probability of extinction.
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DOI：
10.1038/s41598-021-04108-8
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发表时间：
2021-12-30
影响因子：
4.6
通讯作者：
Bøgsted M
中科院分区：
文献类型：
--
作者：
Schiøler H;Knudsen T;Brøndum RF;Stoustrup J;Bøgsted M
当病毒传播时，它可能会变异成，疫苗耐药或快速传播的谱系，如SARS-CoV-2病毒的丹麦Cluster-5水貂变体（属于B.1.1.298谱系）、英国B.1.1.7谱系和南非B.1.351谱系的情况。处理这种传播的一种方法是通过遏制战略，即受影响地区的人口被隔离，直到传播停止。在这种情况下，重要的是通过对病毒亚型的大规模检测来监测突变病毒是否已经灭绝。如果成功的话，这种策略会导致子类型的数量越来越少，最终会灭绝。一个重要的问题是，我们应该等待多久才能确定这种亚型已经灭绝？我们使用隐马尔可夫模型的感染传播和近似的两阶段抽样方案来推断灭绝的概率。该方法的潜力是通过模拟研究说明。最后，该模型用于评估2020年夏季SARS-CoV-2从貂传播到人时丹麦的遏制策略，包括Cluster-5亚型。为了避免进一步传播，以及水貂是一个大型动物病毒储存库，这种情况导致该国北方的七个城市被隔离，整个丹麦1700万大水貂种群被扑杀，并通过了一项法案，临时禁止丹麦水貂生产，直到2021年底。
When a virus spreads, it may mutate into, e.g., vaccine resistant or fast spreading lineages, as was the case for the Danish Cluster-5 mink variant (belonging to the B.1.1.298 lineage), the British B.1.1.7 lineage, and the South African B.1.351 lineage of the SARS-CoV-2 virus. A way to handle such spreads is through a containment strategy, where the population in the affected area is isolated until the spread has been stopped. Under such circumstances, it is important to monitor whether the mutated virus is extinct via massive testing for the virus sub-type. If successful, the strategy will lead to lower and lower numbers of the sub-type, and it will eventually die out. An important question is, for how long time one should wait to be sure the sub-type is extinct? We use a hidden Markov model for infection spread and an approximation of a two stage sampling scheme to infer the probability of extinction. The potential of the method is illustrated via a simulation study. Finally, the model is used to assess the Danish containment strategy when SARS-CoV-2 spread from mink to man during the summer of 2020, including the Cluster-5 sub-type. In order to avoid further spread and mink being a large animal virus reservoir, this situation led to the isolation of seven municipalities in the Northern part of the country, the culling of the entire Danish 17 million large mink population, and a bill to interim ban Danish mink production until the end of 2021.
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影响因子：
10.7
作者：
Kühnert D;Stadler T;Vaughan TG;Drummond AJ
通讯作者：
Drummond AJ
影响因子：
4.6
作者：
Algaissi A;Alfaleh MA;Hala S;Abujamel TS;Alamri SS;Almahboub SA;Alluhaybi KA;Hobani HI;Alsulaiman RM;AlHarbi RH;ElAssouli MA;Alhabbab RY;AlSaieedi AA;Abdulaal WH;Al-Somali AA;Alofi FS;Khogeer AA;Alkayyal AA;Mahmoud AB;Almontashiri NAM;Pain A;Hashem AM
通讯作者：
Hashem AM
DOI：
10.3390/ani11010164
发表时间：
2021-01-12
期刊：
Animals : an open access journal from MDPI
影响因子：
--
作者：
Boklund A;Hammer AS;Quaade ML;Rasmussen TB;Lohse L;Strandbygaard B;Jørgensen CS;Olesen AS;Hjerpe FB;Petersen HH;Jensen TK;Mortensen S;Calvo-Artavia FF;Lefèvre SK;Nielsen SS;Halasa T;Belsham GJ;Bøtner A
通讯作者：
Bøtner A
影响因子：
5.2
作者：
Lassaunière R;Fonager J;Rasmussen M;Frische A;Polacek C;Rasmussen TB;Lohse L;Belsham GJ;Underwood A;Winckelmann AA;Bollerup S;Bukh J;Weis N;Sækmose SG;Aagaard B;Alfaro-Núñez A;Mølbak K;Bøtner A;Fomsgaard A
通讯作者：
Fomsgaard A
DOI：
10.1098/rspa.1932.0171
发表时间：
1932-10-01
期刊：
PROCEEDINGS OF THE ROYAL SOCIETY OF LONDON SERIES A-CONTAINING PAPERS OF A MATHEMATICAL AND PHYSICAL CHARACTER
影响因子：
--
作者：
Kermack, WO;McKendrick, AG
通讯作者：
McKendrick, AG