Anal swab as a potentially optimal specimen for SARS-CoV-2 detection to evaluate hospital discharge of COVID-19 patients.

Since December 2019, an outbreak of SARS coronavirus 2 (SARS-CoV-2) began in Wuhan, and has rapidly spread worldwide. Previously, discharged patients with coronavirus disease 2019 (COVID-19) patients met the criteria of China's pneumonia diagnosis and treatment program of novel coronavirus infection (trial version 7) for cure of viral infection. Nevertheless, positive detection of SARS-CoV-2 has been found again in several cured COVID-19 patients, leading to conflicts with current criteria. Here, we report clinically cured cases with positive results only in anal swabs, and investigate the clinical value of anal swabs for SARS-CoV-2 detection.

Since December 2019, an outbreak of atypical pneumonia caused by SARS coronavirus 2 (SARS-CoV-2) has led to a serious epidemic in China and other countries. Phylogenetic analyses of the coronavirus genomes revealed that SARS-CoV-2 belongs to the Betacoronavirus genus, a class of positive-sense, ssRNA viruses that can cause respiratory, intestinal, liver and nervous system infections in animals and humans [1]. SARS-CoV-2 is composed of four structural proteins, known as the S (spike), E (envelope), M (membrane) and N (nucleocapsid) proteins, and possesses 82% identity to SARS-CoV and 50% identity to Middle East respiratory syndrome coronavirus (MERS-CoV) based on genome sequencing [2]. Moreover, it spreads by human-to-human transmission via droplets or direct contact, and infection has been estimated to have a mean incubation period of 6.4 days and a basic reproduction number of 2.24–3.58 [3].

Numerous retrospective studies have indicated that prevalent clinical manifestations of COVID-19 patients are fever, dry cough and dyspnea [4]; less common symptoms present as the production of sputum, headache and some gastrointestinal symptoms; moreover, an increasing number of patients with asymptomatic infection patients have been discovered [5-7]. According to the latest guidelines of the diagnosis and treatment of pneumonitis caused by 2019-nCoV (trial version 7) published by the National Health Commission of the People’s Republic of China [8], the diagnosis of COVID-19 must be confirmed by reverse transcriptase-PCR (RT-PCR) or gene sequencing. At present, various biological samples of COVID-19 are used in the detection of SARS-CoV-2, and upper respiratory tract nasopharyngeal swabs are the most common sample type. However, growing evidence has revealed positive detection of nucleic acids in anal swabs of patients with COVID-19, although the positive rate is low [9,10].

A previous study showed a positive RT-PCR test on throat swabs of patients recovered from COVID-19 [11], leading to conflicts with current criteria [8]. Here, we reported clinically cured cases with only positive results in anal swabs, which conflicts with current criteria for releasing people from quarantine, and further investigated the clinical value of anal swabs for SARS-CoV-2 detection. We propose anal swabs as the potentially optimal specimen for SARS-CoV-2 detection for evaluation of hospital discharge of COVID-19 patients.

Materials & methods

Sample collection

Throat swab and anal swab samples were collected using the standard process as previously described [9], and sputum swab samples were induced by inhalation of isotonic saline with salbutamol [12]. All swabs were immediately placed into a sterile tube containing 2–3 ml of transport media [13] and transported to the laboratory within 30 min.

SARS-CoV-2 nucleic acid detection by RT-PCR

RNA was extracted with protease K-magnetic beads (BioPerfectus Technologies, Jiangsu, China). Then, the sequences of SARS-CoV-2 were amplified by targeting three genes (ORF1ab, N and E genes) (Liferiver Bio-Tech, China). The RT-PCR assay was performed on a 7500 thermal cycler (ABI, US) under the following conditions: 50°C for 10 min for the reverse transcription reaction, initial denaturation at 95°C for 5 min, followed by 45 cycles of denaturation at 95°C for 10 s, followed by extension and capture of the fluorescence signal at 55°C for 40 s. Both internal and negative controls were routinely performed with each batch of tests.

Demographic information, laboratory findings and radiological features were collected from electronic medical records. This study was approved by the Weihai Municipal Hospital review board, and the need for informed consent was waived.

Case presentation

Four patients presented to the local fever clinic with fever, cough or both occurring at onset from 2 February 2020 to 20 February 2020. There were three adults and one child, and the age ranged from 3 to 45 years. SARS-CoV-2 detection was positive in throat swab samples, and CT manifestations showed single or multiple patchy areas of ground-glass opacity (Figure 1A). Combined with laboratory examination, these patients were diagnosed with mild COVID-19 infection according to the criteria of China’s pneumonia diagnosis and treatment program of novel coronavirus infection. Noticeably, the 3-year old boy was diagnosed with mild COVID-19 based on both clinical criteria and radiological criteria according to the clinically based classification of disease severity forpediatric COVID-19 [14].

Figure 1.

CT scans of patients.

(A) CT scans performed on admission to the hospital; (B) CT scans performed after quarantine.

After appropriate supportive care and active treatment with antiviral therapy for less than 9 days, mainly including oral lopinavir and ritonavir tablets, aerosol inhalation of interferon-α2b at a dose of 5 × 106 U/day and oral administration of acetylcysteine tablets and Chinese medicine Lianhua Qingwen capsule. SARS-CoV-2 detection was successively negative twice for these patients, in addition to normal body temperature for 3 days as well as obvious improvement in respiratory symptoms and CT scan. Therefore, the patients were determined to be clinically cured at discharge [8]. One discharged patient was quarantined in a hotel, and the other three patients were quarantined in the hospital for 2 weeks.

To determine whether the abovementioned patients could discontinue quarantine, throat, sputum and anal swab samples were collected for SARS-CoV-2 detection at 2 weeks after quarantine. Intriguingly, SARS-CoV-2 detection was positive in the anal swab of two patients and negative in throat swab and sputum samples. RT-PCR was performed again for all patients the following day, and positive detection was confirmed, including in the 3-year old boy (Figure 2). Further clinical manifestations, laboratory characteristics and chest CT findings (Figure 1B) showed obvious improvement in all patients.

Figure 2.

Chronology of treatment and detection of reverse transcriptase-PCR on throat swabs, sputum swabs and anal swabs.

The box with an internal red cross means admission to the hospital; the box with an internal green cross means quarantined in the hotel or in the hospital for 2 weeks.

+: Positive result; -: Negative result; ND: No detection.

Discussion

Since December 2019, the outbreak of COVID-2019 caused by SARA-CoV-2 has become a global health concern [15]. SARS-CoV-2 has quickly spread across China and all continents except Antarctica [16-19] and caused more than 3.5 million confirmed cases with 24,000 deaths (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/situation-reports). Thus far, the origin of the coronavirus remains unclear. The latest report discovered that the pangolin-CoV genome showed 91.02% nucleotide identity with the SARS-CoV genome, which suggested that pangolin species are a natural reservoir of SARS-CoV-2-like CoVs [20].

Molecular detection remains the gold standard for diagnosis. As a recommended method, RT-PCR is widely used to detect SARS-CoV-2. To date, throat, sputum and anal swabs have been considered applicable for RT-PCR detection. Evidence has shown that sample type plays a critical role in SARS-CoV-2 detection. Viral RNA can be easily detected in nasopharyngeal, sputum and stool specimens [21], and the highest positivity rates were detected in sputum and bronchoalveolar lavage specimens [22]. However, the course of SARS-CoV-2 infection remains unclear.

As the cellular receptor for SARS-CoV-2, angiotensin-converting enzyme 2 (ACE2) is the key for SARS-CoV to enter target cells during the course of viral infection [23-25]. Expression of ACE2 protein in human organs showed that ACE2 is most abundantly expressed on the surface of alveolar epithelial cells and small intestine epithelial cells [26], which are involved in the progression of pneumonia [27]. Intriguingly, a connection may exist between the lungs and GI tract [28], and SARS-CoV-2 may be shed through multiple routes in the different phases of viral infection.

In this study, we found that SARS-CoV-2 detection was positive in anal swabs but negative in other sample types of a few cured patients, which challenges the current standards for discharge and termination of compulsory isolation for COVID-19 patients. Similar to SARS-CoV and MERS-CoV patients [29,30], intestinal infection was observed in the later stages of infection, indicating that the clearance time of SARS-CoV-2 in the digestive tract was later than that in the respiratory tract. In particular, gastrointestinal symptoms were found in children with COVID-19 [31]. However, the burden of novel coronavirus infections is still underestimated; only approximately 1% of all confirmed SARS-CoV-2 cases involve children according to the current estimates [32], so more biological samples and methods (e.g., serologic detection) for SARS-CoV-2 infection in children must be studied. Notably, live SARS-CoV-2 virus was isolated from fecal samples in three of 11 adult patients [33]. Therefore, anal swabs might be the optimal specimen for SARS-CoV-2 detection to evaluate hospital discharge of COVID-19 patients. Patients with positive stool results require further isolation until the virus is completely eliminated.

Based on the knowledge about this specific viral infection and considering the prolonged viral RNA detection in anal swabs [34] and detectable viral RNA in the blood cohort progressing to a severe symptom stage [35], we proposed the potential infection course of SARS-CoV-2 as follows (Figure 3): upper respiratory infection (mainly by respiratory droplets); lower respiratory infection (mainly presented as pulmonary infection); viremia formation; and transmission to other organs (including the GI tract) and colonization via ACE2. Therefore, different sample types should be chosen for SARS-CoV-2 detection in various infection phases. Fortunately, Sethuraman et al. devised a clinically useful timeline of diagnostic markers for the detection of COVID-19 [36].

Figure 3.

Potential infection course of SARS-CoV-2 and the different specimens for SARS-CoV-2 detection.

First, SARS-CoV-2 infects the upper respiratory system mainly by respiratory droplets (asymptomatic or fever, dry cough, fatigue, myalgia and dyspnoea; high positive RT-PCR results in throat swabs). Subsequently, it infects the lower respiratory tract and massively replicates (mainly presented as pulmonary infection; high positive results of RT-PCR in throat swabs and sputum). Furthermore, virus is released into blood, leading to the formation of viremia (low copy number detected in blood by RT-PCR). Finally, it is transmitted to other organs, including the GI tract, and colonizes via ACE2 (higher positive detection rate in anal swabs).

ACE2: Angiotensin-converting enzyme 2; GI : Gastrointestinal; RT-PCR: Reverse transcriptase-PCR.

In summary, we found that SARS-CoV-2 detection was positive in anal swabs but negative in other sample types of several cured patients. Our findings greatly contribute to a comprehensive understanding of COVID-19. Although the study was limited to a small number of patients, and further longitudinal studies on a larger cohort would help to understand the prognosis of the disease.

The COVID-19 outbreak caused by SARS-CoV-2 has become a global health concern.

SARS-CoV-2 detection is positive in anal swabs but negative in throat swabs and sputum swabs of a few discharged patients.

Anal swabs might be the optimal specimen for SARS-CoV-2 detection to evaluate the hospital discharge of COVID-19 patients.