Genome sequencing is a key strategy in the surveillance of SARS-CoV-2, the virus responsible for the COVID-19 pandemic. Latin America is the hardest hit region of the world, accumulating almost 20% of COVID-19 cases worldwide. Costa Rica was first exemplary for the region in its pandemic control, declaring a swift state of emergency on March 16th that led to a low quantity of cases, until measures were lifted in early May. From the first detected case in March 6th to December 31st almost 170 000 cases have been reported in Costa Rica, 99.5% of them from May onwards. We analyzed the genomic variability during the SARS-CoV-2 pandemic in Costa Rica using 185 sequences, 52 from the first months of the pandemic, and 133 from the current wave. Three GISAID clades (G, GH, and GR) and three PANGOLIN lineages (B.1, B.1.1, and B.1.291) are predominant, with phylogenetic relationships that are in line with the results of other Latin American countries, suggesting introduction and multiple re-introductions from other regions of the world. The whole-genome variant calling analysis identified a total of 283 distinct nucleotide variants. These correspond mostly to non-synonymous mutations (51.6%, 146) but 45.6% (129) corresponded to synonymous mutations. The 283 variants showed an expected power-law distribution: 190 single nucleotide mutations were identified in single sequences, only 16 single nucleotide mutations were found in >5% sequences, and only two mutations in >50% genomes. These mutations were distributed through the whole genome. However, 63.6% were present in ORF1ab, 11.7% in Spike gene and 10.6% in the Nucleocapsid gene. Additionally, the prevalence of worldwide-found variant D614G in the Spike (98.9% in Costa Rica), ORF8 L84S (1.1%) is similar to what is found elsewhere. Interestingly, the frequency of mutation T1117I in the Spike has increased during the current pandemic wave beginning in May 2020 in Costa Rica, reaching 29.2% detection in the full genome analyses in November 2020. This variant has been observed in less than 1% of the GISAID reported sequences worldwide in all the 2020. Structural modeling of the Spike protein with the T1117I mutation suggest a potential effect on the viral oligomerization needed for cell infection, but no differences with other genomes on transmissibility, severity nor vaccine effectiveness are predicted. Nevertheless, in-vitro experiments are required to support these in-silico findings. In conclusion, genome analyses of the SARS-CoV-2 sequences over the course of COVID-19 pandemic in Costa Rica suggest introduction of lineages from other countries as travel bans and measures were lifted, similar to results found in other studies, as well as an increase in the Spike-T1117I variant that needs to be monitored and studied in further analyses as part of the surveillance program during the pandemic.

中文翻译：

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哥斯达黎加的SARS-CoV-2基因组监测：不同种群的证据和穗型T1117I突变检测增加

基因组测序是监视SARS-CoV-2（一种导致COVID-19大流行的病毒）的关键策略。拉丁美洲是世界上受灾最严重的地区，在全球累积了近20％的COVID-19病例。哥斯达黎加是该地区大流行控制中的首个典范，3月16日宣布紧急状态，导致案件数量减少，直到5月初取消措施为止。从3月6日到12月31日发现的第一例病例，哥斯达黎加已报告了近170 000例病例，其中5月以后报告了99.5％。我们分析了哥斯达黎加SARS-CoV-2大流行期间的基因组变异性，使用了185个序列，大流行最初几个月的52个序列和潮流中的133个序列。三个GISAID进化枝（G，GH和GR）和三个PANGOLIN谱系（B.1，B.1.1和B.1.291）占主导地位，系统发育关系与其他拉丁美洲国家的研究结果相吻合，表明来自世界其他地区的引进和多次再引入。全基因组变异调用分析共鉴定出283个不同的核苷酸变异。这些主要对应于非同义突变（51.6％，146），但45.6％（129）对应于同义突变。283个变体显示出预期的幂律分布：在单个序列中鉴定出190个单核苷酸突变，在> 5％序列中仅发现16个单核苷酸突变，而在> 50％基因组中仅发现两个突变。这些突变分布在整个基因组中。但是，ORF1ab中存在63.6％，Spike基因中存在11.7％，Nucleocapsid基因中存在10.6％。另外，在斯派克地区（哥斯达黎加，全球范围内发现的变体D614G（在哥斯达黎加为98.9％），ORF8 L84S（1.1％）的患病率与其他地方相似。有趣的是，在2020年5月哥斯达黎加爆发的当前大流行波中，Spike突变T1117I的频率有所增加，在2020年11月的全基因组分析中检出率达到29.2％。 GISAID报告了整个2020年的序列。带有T1117I突变的Spike蛋白的结构模型表明，对细胞感染所需的病毒寡聚可能产生潜在影响，但预测与其他基因组在传播性，严重性或疫苗效力方面没有差异。尽管如此，仍需要进行体外实验以支持这些计算机模拟结果。结论，