Vaccination-related contamination-induced false positive SARS-CoV-2 specimen from a suspected COVID-19 case in Chengdu city: a gene tracing-based analysis

Abstract

ObjectiveTo conduct a gene tracing-based analysis on a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) positive oropharyngeal swab specimen from a suspected coronavirus disease 2019 (COVID-19) case without epidemiologically-confirmed exposure history and with negative results in confirmation tests in Chengdu city, Sichuan province for providing evidence to the operation of clinics engaged in COVID-19 vaccination.MethodsAn epidemiological investigation was conducted on a suspected COVID-19 case reported by a medical institution providing both COVID-19 vaccination and SARS-CoV-2 nucleic acid screening services in a district of Chengdu city, Sichuan province on February 24, 2021. The information on case′s onset and treatment, travel and close contacts within 14 days before the onset were collected and analyzed. Specimen collection and laboratory nucleic acid testing were conducted for the case, the case′s close contacts and living environment, and the environment and work clothes of medical staff of the reporting medical institution. Second generation gene sequencing and gene tracing analysis were performed for the case′s positive specimen collected for the screening test. ResultsThe suspected case was a 57-year old man seeking medication for cough, throat discomfort, and runny nose at a medical institution provided both COVID-19 vaccination and SARS-CoV-2 nucleic acid screening services and having a oropharyngeal swab test for screening SARS-CoV-2 infection at the medical institution on February 23, 2021. The case reported no history of travelling abroad himself and his close contacts, contacting with confirmed/suspected COVID-19 patients, potential exposure to SARS-CoV-2, and COVID-19 vaccination. No positive results of SARS-CoV-2 nucleic acid were detected for case′s oropharyngeal/nasal and anal swab specimens, close contacts′ oropharyngeal swab specimens, swab specimens of living/working/relevant public place environment, swab specimens of environment and working clothes of the staff of the medical institution for retests performed one day after the case′s screening test. The results of gene sequencing for the case′s positive specimen at the screening test showed a 99.99% sequence homology with the sample of COVID-19 vaccine for inoculation service at the medical institution. The Pangolin type was B for both the case′s specimen and the vaccine sample. ConclusionThe clinical manifestation and laboratory test of the suspected case were not consistent with the diagnosis criterion for COVID-19 patient and asymptomatic SARS-CoV-2 infection. The case′s false SARS-CoV-2 positivity of the suspected specimen at the screening test probably results from vaccination related contamination of the case′s oropharyngeal swab specimen at the medical institution proving both COVID-19 vaccination and SARS-CoV-2 nucleic acid screening services. The result needs to be concerned when conducting SARS-CoV-2 nucleic acid screening.

Keywords

• severe acute respiratory syndrome coronavirus 2
• vaccination site
• vaccination-related specimen contamination
• second generation gene sequencing