Undetectable SARS-CoV-2 in a nasopharyngeal swab but persistent viral RNA from deep lung swabs: findings from an autopsy

Abstract

During the global pandemic of COVID-19 accurate diagnosis of the infection by demonstrating SARS-CoV-2 viral RNA by PCR in specimens is crucial for therapeutic and preventative interventions. There have been instances where nasal and throat swabs have been negative despite the patient having typical clinical and radiological findings compatible with the disease. We report a case of a man in his late 50s, brought to the hospital following a cardiac arrest and prolonged unsuccessful resuscitation. The history was typical for COVID-19 with fever for 10 days and worsening shortness of breath. His throat and nasal swabs (after death) were negative for SARS-CoV-2. A limited diagnostic autopsy was performed after 27 days, and lung swabs confirmed presence of SARS-CoV-2. This case highlights the importance of lung swabs when initial upper respiratory tract swabs are negative and proves that the virus can be detected from dead human tissue almost a month later.

Survey on postmortem screening and management of COVID-19 related deaths

“…The oropharyngeal swab also had a very high rate of positivity except for one case where this sample was negative but the swab from cut surface of lung had been positive. This is similar to a recent case report where a nasopharyngeal swab taken at the time of death had been negative but a swab taken at autopsy 27 days later had been positive 7 .…”

Viral mapping in COVID-19 deceased in the Augsburg autopsy series of the first wave: A multiorgan and multimethodological approach

“…Despite the fact of viral spreading from the upper to lower airway, the virus or at least parts of the virus remain detectable in the upper airway at the time of death. Skok et al reported almost identical results [34] relativizing the opposing results of some case and small series reports in this regard [35][36][37]. Our cohort's lower airways showed less often a positive ISH signal for negative-sense RNA in correlation to positive-sense RNA (3 vs. 13, 23%), indicating that not all detectable virus by RT-qPCR remains active.…”

Died with or Died of? Development and Testing of a SARS CoV-2 Significance Score to Assess the Role of COVID-19 in the Deaths of Affected Patients

“…By performing rhino-pharyngeal, tracheal and lung swabs in 12 autopsy cases of patients with a clinical diagnosis of Sars-CoV-2 related pneumonia, 9 out of 12 cases had at least one post-mortem swab positive for Sars-CoV-2, with the virus found in samples up to 310 h from the post mortem sampling [ 71 ]. Moreover, a paper by Prema Seetulsingh et al described the case of a patient who died of respiratory failure during transport to the hospital, with a negative upper airway swab, but with SARS CoV-2 found in the lung at an analysis performed 27 days following the death [ 74 ]. However, a correlation between the negativity of the lung swabs and the number of days elapsed from the ante mortem swabs was also found, as well as a negative correlation between the positivity of the other swabs and the number of days passed from the ante mortem swabs [ 71 ].…”