Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy

被引：87

作者：

Alteri, Claudia ^{[1
]}

Cento, Valeria ^{[1
]}

Piralla, Antonio ^{[2
]}

Costabile, Valentino ^{[3
]}

Tallarita, Monica ^{[2
]}

Colagrossi, Luna ^{[4
]}

Renica, Silvia ^{[1
]}

Giardina, Federica ^{[2
]}

Novazzi, Federica ^{[2
]}

Gaiarsa, Stefano ^{[2
]}

Matarazzo, Elisa ^{[5
]}

Antonello, Maria ^{[1
]}

Vismara, Chiara ^{[6
]}

Fumagalli, Roberto ^{[7
]}

Epis, Oscar Massimiliano ^{[8
]}

Puoti, Massimo ^{[9
]}

Perno, Carlo Federico ^{[4
]}

Baldanti, Fausto ^{[2
,10
]}

机构：

[1] Univ Milan, Dept Oncol & Hematooncol, Milan, Italy

[2] Fdn IRCCS Policlin San Matteo, Microbiol & Virol Dept, Mol Virol Unit, Pavia, Italy

[3] Univ Milan, Dept Pathophysiol & Transplantat, Milan, Italy

[4] Bambino Gesu Pediat Hosp, IRCCS, Microbiol & Diagnost Immunol Unit, Rome, Italy

[5] Univ Milan, Residency Microbiol & Virol, Milan, Italy

[6] ASST Grande Osped Metropolitano Niguarda, Chemicoclin & Microbiol Anal, Milan, Italy

[7] ASST Grande Osped Metropolitano Niguarda, Dept Anesthesiol Crit Care & Pain Med, Milan, Italy

[8] ASST Grande Osped Metropolitano Niguarda, Rheumatol Unit, Milan, Italy

[9] ASST Grande Osped Metropolitano Niguarda, Infect Dis, Milan, Italy

[10] Univ Pavia, Dept Clin Surg Diagnost & Paediat Sci, Pavia, Italy

来源：

NATURE COMMUNICATIONS | 2021年 / 12卷 / 01期

关键词：

NUCLEOCAPSID PROTEIN; RICH MOTIF; COVID-19;

D O I：

10.1038/s41467-020-20688-x

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

From February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy. The Lombardy region of Italy was heavily affected early in the SARS-CoV-2 pandemic. Here, the authors use whole genome sequencing and show that there were multiple introductions into the region, with transmission occurring before the first case was detected.

引用

页数：13

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