Molecular Evidence for SARS-CoV-2 in Samples Collected From Patients With Morbilliform Eruptions Since Late Summer 2019 in Lombardy, Northern Italy

Background: Skin manifestations have been reported in patients with SARS-CoV-2 infection. As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like symptomatology while providing evidence for undetected early circulation of SARS-CoV-2. Methods: Overall, 435 samples from 156 cases were investigated. RNA isolated from oropharyngeal swabs (N=148) and urine (N=141) was screened by hemi-nested PCRs targeting key sites for viral typing. After Sanger sequencing, detected mutations were used to estimate the time of emergence of the progenitor SARS-CoV-2 using a previously calibrated molecular clock. Sera (N=146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA, and the titre of neutralizing antibodies was assessed. Findings: Molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two patients were from the pandemic period (2/12, 16·7%, March 2020-March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019-February 2020). Five of the positive individuals showed the simultaneous presence of anti-SARS-CoV-2 antibodies. No clear evidence of infection was found in 281 samples collected between August 2018 and July 2019 from 100 patients. The first positivity for SARS-CoV-2 RNA was found in a sample collected on September 12, 2019. Mutations typical of B.1 (PANGOLIN classification) strains, previously reported to have emerged in January 2020, had already been circulating in October 2019. Hence, we estimate SARS-CoV-2 progenitor of known human infections to have emerged in late June-late August 2019. Interpretations: We find evidence that SARS-CoV-2 was circulating in Lombardy during the late summer of 2019. This finding highlights the importance of retrospective surveillance studies to understand the early dynamics of COVID-19 spread and improve national-level preparedness.