COVID-19 : cells in the lungs, nasal passage and intestines appear to be the main targets for SARS-CoV-2


Researchers at MIT; the Ragon Institute of MGH, MIT, and Harvard; and the Broad Institute of MIT and Harvard; along with colleagues from around the world have identified specific types of cells that appear to be targets of the coronavirus that is causing the Covid-19 pandemic.

Using existing data on the RNA found in different types of cells, the researchers were able to search for cells that express the two proteins that help the SARS-CoV-19 virus enter human cells.

They found subsets of cells in the lung, the nasal passages, and the intestine that express RNA for both of these proteins much more than other cells.

The researchers hope that their findings will help guide scientists who are working on developing new drug treatments or testing existing drugs that could be repurposed for treating Covid-19.

“Our goal is to get information out to the community and to share data as soon as is humanly possible, so that we can help accelerate ongoing efforts in the scientific and medical communities,” says Alex K. Shalek, the Pfizer-Laubach Career Development Associate Professor of Chemistry, a core member of MIT’s Institute for Medical Engineering and Science (IMES), an extramural member of the Koch Institute for Integrative Cancer Research, an associate member of the Ragon Institute, and an institute member at the Broad Institute.

Shalek and Jose Ordovas-Montanes, a former MIT postdoc who now runs his own lab at Boston Children’s Hospital, are the senior authors of the study, which appears today in Cell.

The paper’s lead authors are MIT graduate students Carly Ziegler, Samuel Allon, and Sarah Nyquist; and Ian Mbano, a researcher at the Africa Health Research Institute in Durban, South Africa.

Digging into data

Not long after the SARS-CoV-2 outbreak began, scientists discovered that the viral “spike” protein binds to a receptor on human cells known as angiotensin-converting enzyme 2 (ACE2).

Another human protein, an enzyme called TMPRSS2, helps to activate the coronavirus spike protein, to allow for cell entry.

The combined binding and activation allows the virus to get into host cells.

“As soon as we realized that the role of these proteins had been biochemically confirmed, we started looking to see where those genes were in our existing datasets,” Ordovas-Montanes says.

“We were really in a good position to start to investigate which are the cells that this virus might actually target.”

Shalek’s lab, and many other labs around the world, have performed large-scale studies of tens of thousands of human, nonhuman primate, and mouse cells, in which they use single-cell RNA sequencing technology to determine which genes are turned on in a given cell type.

Since last year, Nyquist has been building a database with partners at the Broad Institute to store a huge collection of these datasets in one place, allowing researchers to study potential roles for particular cells in a variety of infectious diseases.

Much of the data came from labs that belong to the Human Cell Atlas project, whose goal is to catalog the distinctive patterns of gene activity for every cell type in the human body.

The datasets that the MIT team used for this study included hundreds of cell types from the lungs, nasal passages, and intestine.

The researchers chose those organs for the Covid-19 study because previous evidence had indicated that the virus can infect each of them. They then compared their results to cell types from unaffected organs.

“Because we have this incredible repository of information, we were able to begin to look at what would be likely target cells for infection,” Shalek says.

“Even though these datasets weren’t designed specifically to study Covid, it’s hopefully given us a jump start on identifying some of the things that might be relevant there.”

In the nasal passages, the researchers found that goblet secretory cells, which produce mucus, express RNAs for both of the proteins that SARS-CoV-2 uses to infect cells.

In the lungs, they found the RNAs for these proteins mainly in cells called type II pneumocytes.

These cells line the alveoli (air sacs) of the lungs and are responsible for keeping them open.

In the intestine, they found that cells called absorptive enterocytes, which are responsible for the absorption of some nutrients, express the RNAs for these two proteins more than any other intestinal cell type.

“This may not be the full story, but it definitely paints a much more precise picture than where the field stood before,” Ordovas-Montanes says. “Now we can say with some level of confidence that these receptors are expressed on these specific cells in these tissues.”

Fighting infection

In their data, the researchers also saw a surprising phenomenon — expression of the ACE2 gene appeared to be correlated with activation of genes that are known to be turned on by interferon, a protein that the body produces in response to viral infection.

To explore this further, the researchers performed new experiments in which they treated cells that line the airway with interferon, and they discovered that the treatment did indeed turn on the ACE2 gene.

Interferon helps to fight off infection by interfering with viral replication and helping to activate immune cells. It also turns on a distinctive set of genes that help cells fight off infection.

Previous studies have suggested that ACE2 plays a role in helping lung cells to tolerate damage, but this is the first time that ACE2 has been connected with the interferon response.

The finding suggests that coronaviruses may have evolved to take advantage of host cells’ natural defenses, hijacking some proteins for their own use.

“This isn’t the only example of that,” Ordovas-Montanes says.

“There are other examples of coronaviruses and other viruses that actually target interferon-stimulated genes as ways of getting into cells. In a way, it’s the most reliable response of the host.”

Because interferon has so many beneficial effects against viral infection, it is sometimes used to treat infections such as hepatitis B and hepatitis C.

The findings of the MIT team suggest that interferon’s potential role in fighting Covid-19 may be complex.

On one hand, it can stimulate genes that fight off infection or help cells survive damage, but on the other hand, it may provide extra targets that help the virus infect more cells.

This shows coronavirus
This scanning electron microscope image shows SARS-CoV-2 (orange)—also known as 2019-nCoV, the virus that causes COVID-19—isolated from a patient in the U.S., emerging from the surface of cells (green) cultured in the lab. Image is credited to NIAID-RML.

“It’s hard to make any broad conclusions about the role of interferon against this virus. The only way we’ll begin to understand that is through carefully controlled clinical trials,” Shalek says.

“What we are trying to do is put information out there, because there are so many rapid clinical responses that people are making. We’re trying to make them aware of things that might be relevant.”

Shalek now hopes to work with collaborators to profile tissue models that incorporate the cells identified in this study. Such models could be used to test existing antiviral drugs and predict how they might affect SARS-CoV-2 infection.

The MIT team and their collaborators have made all the data they used in this study available to other labs who want to use it. Much of the data used in this study was generated in collaboration with researchers around the world, who were very willing to share it, Shalek says.

“There’s been an incredible outpouring of information from the scientific community with a number of different parties interested in contributing to the battle against Covid in any way possible,” he says.

“It’s been incredible to see a large number of labs from around the world come together to try and collaboratively tackle this.”

Funding: The research was funded by the Searle Scholars Program, the Beckman Young Investigator Program, the Pew-Stewart Scholars Program for Cancer Research, a Sloan Fellowship in Chemistry, the National Institutes of Health, the Aeras Foundation, the Bill and Melinda Gates Foundation, the Richard and Susan Smith Family Foundation, the National Institute of General Medical Sciences, the UMass Center for Clinical and Translational Science Project Pilot Program, and the Office of the Assistant Secretary of Defense for Health Affairs.

The infection begins

When an infected person expels virus-laden droplets and someone else inhales them, the novel coronavirus, called SARS-CoV-2, enters the nose and throat.

It finds a welcome home in the lining of the nose, according to a preprint from scientists at the Wellcome Sanger Institute and elsewhere.

They found that cells there are rich in a cell-surface receptor called angiotensin-converting enzyme 2 (ACE2). Throughout the body, the presence of ACE2, which normally helps regulate blood pressure, marks tissues vulnerable to infection, because the virus requires that receptor to enter a cell.

Once inside, the virus hijacks the cell’s machinery, making myriad copies of itself and invading new cells.

As the virus multiplies, an infected person may shed copious amounts of it, especially during the first week or so. Symptoms may be absent at this point. Or the virus’ new victim may develop a fever, dry cough, sore throat, loss of smell and taste, or head and body aches.

If the immune system doesn’t beat back SARS-CoV-2 during this initial phase, the virus then marches down the windpipe to attack the lungs, where it can turn deadly.

The thinner, distant branches of the lung’s respiratory tree end in tiny air sacs called alveoli, each lined by a single layer of cells that are also rich in ACE2 receptors.

Normally, oxygen crosses the alveoli into the capillaries, tiny blood vessels that lie beside the air sacs; the oxygen is then carried to the rest of the body. But as the immune system wars with the invader, the battle itself disrupts this healthy oxygen transfer.

Front-line white blood cells release inflammatory molecules called chemokines, which in turn summon more immune cells that target and kill virus-infected cells, leaving a stew of fluid and dead cells-pus-behind.

This is the underlying pathology of pneumonia, with its corresponding symptoms: coughing; fever; and rapid, shallow respiration (see graphic). Some COVID-19 patients recover, sometimes with no more support than oxygen breathed in through nasal prongs.

But others deteriorate, often quite suddenly, developing a condition called acute respiratory distress syndrome (ARDS). Oxygen levels in their blood plummet and they struggle ever harder to breathe. On x-rays and computed tomography scans, their lungs are riddled with white opacities where black space-air-should be. Commonly, these patients end up on ventilators. Many die. Autopsies show their alveoli became stuffed with fluid, white blood cells, mucus, and the detritus of destroyed lung cells.

Etiology and pathogenesis of COVID-19

SARS-CoV-2 is the seventh member of the family of CoVs that infect humans. Four human CoVs (HCoV-229E, HCoV-NL63, HCoV-OC43 and HCoV-HKU1) are able to cause a wide range of upper respiratory tract infections (common cold), whereas SARS-CoV and MERS-CoV are responsible for atypical pneumonia.

The causes of different infection sites are likely related to the presence of dipeptidyl peptidase 4 (DPP4) and angiotensin-converting enzyme 2 (ACE2) in the lower respiratory tract, which are the major human receptors for the surface spike (S) glycoprotein of MERS-CoV and SARS-CoV, respectively [22], [23], [24]. The genetic sequence of SARS-CoV-2 is ≥70% similar to that SARS-CoV, and SARS-CoV-2 is capable of using the same cell entry receptor (ACE2) as SARS-CoV to infect humans [25,26].

However, there are more differences in the key S proteins that the viruses use to interact with host cells. SARS-CoV-2 spike binds to human ACE2 with approximately 10–20-fold higher affinity than the SARS-CoV spike [19], making it easier to spread from human to human.

Upon entry into alveolar epithelial cells, SARS-CoV-2 replicates rapidly and triggers a strong immune response, resulting in cytokine storm syndromes and pulmonary tissue damage. Cytokine storm syndromes, also known as hypercytokinaemia, are a group of disorders characterised by the uncontrolled production of pro-inflammatory cytokines and are important causes of acute respiratory distress syndrome (ARDS) and multiple organ failure [27], [28], [29].

Analysis of the first 99 confirmed cases of SARS-CoV-2 infection revealed that cytokine storm syndromes occurred in patients with severe COVID-19; 17 patients (17%) had ARDS, among whom 11 (11%) deteriorated within a short period of time and died of multiple organ failure [30].

In addition, the numbers of total T-cells, CD4+ T-cells and CD8+ T-cells are decreased in patients with SARS-CoV-2 infection, and the surviving T-cells are functionally exhausted [31], suggesting a decreased immune function in SARS-CoV-2-infected patients. ARDS, decreased immune function and secondary infection further worsens respiratory failure.

Transmission route of SARS-CoV-2

The novel CoV can be transmitted between humans via respiratory droplets. Notably, the respiratory tract is probably not the only route of transmission. Close contact is also a source of transmission of SARS-CoV-2. For example, SARS-CoV-2 can be transmitted through direct or indirect contact with mucous membranes in the eyes, mouth or nose [37], [38], [39].

There is also a possibility of aerosol transmission in a relatively closed environment with continuous exposure to high concentrations of aerosol. Moreover, it has been reported that COVID-19 patients have some gastrointestinal symptoms, including diarrhoea, nausea and vomiting [40,41].

A recent study showed that the enteric symptoms of COVID-19 pneumonia are associated with invaded ACE2-expressing enterocytes [42], suggesting that the digestive tract is a potential route of SARS-CoV-2 infection besides the respiratory tract. However, additional studies are required to test this possibility. In addition, whether transmission of SARS-CoV-2 can occur via breast milk or vertically from mother to infant has not been determined.

Gastrointestinal symptoms of Covid‐19 patients

While Covid‐19 patients typically present with a respiratory illness, some patients reported gastrointestinal symptoms including diarrhea, vomiting, and abdominal pain during course of the disease.

In the first case of Covid‐19 in a 35‐year‐old man in the United States,4 the patient presented with a 2‐day history of nausea and vomiting upon hospital admission, followed by diarrhea and abdominal discomfort on the second day of hospitalization.

The SARS‐CoV‐2 RNA was detected in stool of the patient by reverse transcriptase polymerase chain reaction on illness day 7.4 Similarly, in the familial cluster of Covid‐19 cases during the early epidemic,9 diarrhea was described in two young adults (aged 36 and 37 years) out of the six patients, with reported bowel openings of up to eight times a day.

Subsequent cohorts have consistently reported gastrointestinal symptoms among Covid‐19 patients.

In a large study that collected data from 1,099 patients from 552 hospitals in China, it reported nausea or vomiting in 55 (5.0%) and diarrhea in 42 (3.8%) patients.10 Several other cohorts have reported frequencies of diarrhea ranging 2.0–10.1% and nausea and/or vomiting ranging 1.0–10.1% (Table 1).111820 

In the cohort of 140 Covid‐19 patients in Wuhan, gastrointestinal symptoms were described in up to 39.6% of the patients,19 including nausea in 24 (17.3%), diarrhea in 18 (12.9%), and vomiting in 7 (5.0%) patients.

Similarly, the rate of diarrhea was up to 35.6% in a cohort of 73 patients.7 These rates were higher than some other cohorts and highlighted the variability of clinical presentations. On the other hand, abdominal pain or discomfort was sparingly described4 and was reported in 2.2–5.8% in patient cohorts1619(Table 1).

Table 1. Presentation of gastrointestinal symptoms in coronavirus infection: a comparison of Covid‐19, SARS, and MERS in major clinical cohorts

SubjectDiarrheaNauseaVomitingAbdominal pain
Chen N et al11992 (2.0%)1 (1%)1 (1%)NA
Guan W et al10109942 (3.8%)55 (5.0%)55 (5.0%)NA
Huang C et al12381 (2.6%)NANANA
Liu K et al1313711 (8%)NANANA
Lu X et al1417115 (8.8%)NA11 (6.4%)NA
Shi H et al15813 (3.7%)NA4 (4.9%)NA
Wang D et al1613814 (10.1%)14 (10.1%)5 (3.6%)3 (2.2%)
Xiao F et al77326 (35.6%)NANANA
Xu XW et al17623 (4.8%)NANANA
Yang X et al1852NANA2 (3.8%)NA
Zhang JJ et al1913918 (12.9%)24 (17.3%)7 (5.0%)8 (5.8%)
Zhou F et al201419 (4.7%)7 (3.7%)7 (3.7%)NA
Booth CM et al2114434 (23.6%)28 (19.4)28 (19.4)5 (5.0%)
Cheng VC et al2214269 (48.6%)NANANA
Choi KW et al2326741 (15.4%)NA19 (7.1%)NA
Jang TN et al24294 (13.8%)5 (17.2%)5 (17.2%)NA
Kwan AC et al2524049 (20.4%)NANANA
Lee N et al2613827 (19.6%)27 (19.6%)27 (19.6%)NA
Leung CW et al27449 (20.5%)13 (29.5%)13 (29.5%)4 (9.1%)
Leung WK et al2813853 (38.4%)NANANA
Liu CL et al295335 (66.0%)6 (11.3%)5 (9.4%)5 (9.4%)
Peiris JS et al307555 (73.3%)NANANA
Al Ghamdi M et al315113 (25.5%)NA12 (23.5%)NA
Almekhlafi GA et al32316 (19.4%)NA4 (12.9%)9 (29.0%)
Arabi YM et al3333038 (11.5%)58 (17.6%)58 (17.6%)47 (14.2%)
Assiri A et al344712 (25.5%)10 (21.2%)10 (21.2%)8 (17.0%)
Assiri A et al35235 (21.7%)NA4 (17.4%)NA
Choi WS et al3618636 (19.4%)26 (14.0%)26 (14.0%)15 (8.1%)
Kim KM et al37367 (19.4%)5 (13.9%)5 (13.9%)NA
Nam HS et al38258 (32.0%)8 (32.0%)8 (32.0%)8 (32.0%)
Saad M et al397021 (30%)NA21 (30%)17 (24.3%)
Sherbini N et al40298 (27.6%)8 (27.6%)8 (27.6%)NA
  • Case reports, series, or cohorts with less than 20 subjects are not included.
  • Covid‐19, novel coronavirus disease; MERS, Middle East Respiratory Syndrome Coronavirus; SARS, severe acute respiratory syndrome coronavirus.

Similar to adults, gastrointestinal symptoms were observed in a cohort of 171 pediatric patients with Covid‐19.14 Diarrheal and vomiting were observed in 15 (8.8%) and 11 (6.4%) of these children, respectively.

In another study that investigated viral shredding in pediatric Covid‐19 patients, diarrhea was observed in 3 out of the 10 infected children.3 Although different clinical features, such as a milder disease course14 and less respiratory symptoms3 have been proposed in Covid‐19 children, the gastrointestinal symptoms appear to be similar, although more clinical data are needed to arrive at such a conclusion.

It is evident that patients can present with gastrointestinal symptoms early in the disease course. For example, the first Covid‐19 patient in the USA had nausea and vomiting 2 days before going to hospital, and developed diarrhea on the second day of admission,4 whereas the two young adults in the early familial Covid‐19 cluster had diarrhea upon presentation to the hospital.9 Diarrhea can be one initial symptom and may even occur earlier than pyrexia or respiratory symptoms in some cases.1316

Diarrhea was a common symptom of SARS during its outbreak back in 2003. Among the SARS patients in Hong Kong, approximately 20% had with diarrhea on disease presentation.2628 

The mean duration of diarrhea was 3.7 days, and most was self‐limiting.28 There were higher rates of diarrhea during the course of illness,222829 up to 73% of SARS patients in one study30 (Table 1).

Gastrointestinal symptoms were also frequent in Middle East respiratory syndrome coronavirus (MERS),41 with cohorts reporting diarrhea, nausea, vomiting, and abdominal pain in 11.5–32% of the patients (Table 1). Comparing with these figures, the gastrointestinal symptoms in Covid‐19 appeared to be less common (Table 1). This may signify the differences in viral tropism as compared with SARS‐CoV and MERS‐CoV.

Liver injury in Covid‐19 patients

Apart from gastrointestinal symptoms, patients with Covid‐19 can have liver injury with raised enzymes found in blood tests. Current data indicated that 14.8–53.1% of Covid‐19 patients had abnormal levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) during the course of disease, with mostly mild elevation in serum bilirubin.1012151842 

In a commentary that described a cohort of 56 Covid‐19 patients, gamma‐glutamyl transferase (GGT) was elevated in 54% of the patients.43 Most of the liver injuries are mild and transient, although severe liver damage can occur.

The proportion of liver injury was also higher in patients with severe Covid‐19 disease.1012 In the cohort that described 99 patients in Wuhan, 43 patients had raised ALT or AST; one patient with critical Covid‐19 had severe hepatitis with serum ALT increased up to 7590 U/L.11

While the mechanism of liver injury is not fully understood, the injury can be because of direct viral infection of hepatocytes, immune‐related injury, or drug hepatotoxicity.44 There is also suggestion that the virus may bind to cholangiocytes through the ACE2 receptor to dysregulate the liver function.43 

Notably, histological examination of the liver biopsy from a deceased Covid‐19 patient showed microvesicular steatosis and mild lobular activity.45 These histological changes could be caused by SARS‐CoV‐2 infection or drug‐induced liver injury. Nevertheless, no viral inclusion was observed in the liver.

It remains to be studied whether SARS‐CoV‐2 may target the liver in a similar manner to SARS‐CoV,4648 and whether other mechanisms play an important role in the liver injury.

Mechanisms of gastrointestinal tract involvement

Evidence from previous SARS studies indicated that coronavirus has a tropism to the gastrointestinal tract. The SARS‐CoV RNA could be readily detected in stool specimens of SARS patients,49 and electron microscopy on biopsy and autopsy specimens showed active viral replications in both small and large intestines.28 

Similarly, enteric infection could occur with MERS‐CoV, as human intestinal epithelial cells were highly susceptible to the virus and could sustain robust viral replication.50 This gastrointestinal tropism may explain the frequent occurrence of diarrhea in coronavirus infection.

This fecal source can lead to fomite transmission, especially when infective aerosols are generated from the toilet plume.51

Although at a lower frequency compared with SARS, some Covid‐19 patients do develop diarrhea during their disease course. This suggests the possible tropism of SARS‐CoV‐2 to the gastrointestinal tract.

Genome sequences showed that SARS‐CoV‐2 shared 79.6% sequence identity to SARS‐CoV, both encoding and expressing the spike (S) glycoproteins that could bind to the entry receptor ACE2 to enter human cells.5254 

The receptor binding domain on SARS‐CoV‐2 could bind to human ACE2 with high affinity, correlating with the efficient spread of the virus among humans.5556 While ACE2 is highly expressed in type II alveolar cells (AT2) in the lungs, the receptor is also abundantly expressed in the gastrointestinal tract, especially in the small and large intestines.78 

Staining of viral nucleocapsid protein was visualized in cytoplasm of gastric, duodenal, and rectal epithelium.42 These data have provided valuable insights into the receptor‐mediated entry into the host cells and provided basis for its possible transmission route through the fecal contents.

Susceptible population

All populations are generally susceptible to SARS-CoV-2. The elderly and people with underlying diseases or low immune function are more likely to become severe cases [30,43]. In addition, pregnant women and newborns infected with SARS-CoV-2 are also prone to develop severe pneumonia [44,45]. Thus, these vulnerable patients should be considered as a focus in the prevention and management of SARS-CoV-2 infection.

Incubation period

The mean incubation period of SARS-CoV-2 is estimated to be 3–7 days (range, 2–14 days) [46,47], indicating a long transmission period of SARS-CoV-2. It is estimated that SARS-CoV-2 latency is consistent with those of other known human CoVs, including non-SARS human CoVs (mean 3 days, range 2–5 days) [48], SARS-CoV (mean 5 days, range 2–14 days) [49] and MERS-CoV (mean 5.7 days, range 2–14 days) [50].

Moreover, it has been reported that asymptomatic COVID-19 patients during their incubation periods can effectively transmit SARS-CoV-2 [51,52], which is different from SARS-CoV because most SARS-CoV cases are infected by ‘superspreaders’ and SARS-CoV cases cannot infect susceptible persons during the incubation period [53]. Taken together, these data fully support the current period of active monitoring recommended by the WHO of 14 days.

Basic reproduction number (R0) of SARS-CoV-2

The basic reproduction number is a very important threshold related to the transmissibility of the virus, which is usually expressed as R nought (R0). The R0 can be implicitly defined as the average number of secondary infections produced by an infectious person. It is generally believed that if R0 is >1, the number of infected cases will increase exponentially and cause an epidemic or even a pandemic. Liu et al. reviewed the R0 of SARS-CoV-2 and found that the estimates ranged from 1.4–6.49, with a mean of 3.28 [54], which is higher than that of SARS-CoV (R0 of 2~5).

Clinical presentation

At the onset of the disease, the main manifestations of COVID-19 are fatigue, fever, dry cough, myalgia and dyspnoea, with less common symptoms being nasal congestion, headache, runny nose, sore throat, vomiting and diarrhoea. Severe patients often have dyspnoea and/or hypoxemia 1 week after onset, after which septic shock, ARDS, difficult-to-correct metabolic acidosis, and coagulation dysfunction develop rapidly.

Of note, severe and critical patients can also only present with a low fever, or even no obvious fever, and mild patients show only low fever, mild fatigue and no pneumonia [40,43]. These asymptomatic or mild cases can also spread SARS-CoV-2 between humans.

Pathological characteristics

Recently, Xu et al. reported the pathological features of the first patient known to have died from SARS-CoV-2 infection [55]. Biopsy samples were obtained from lung tissue of the patient and it was found that the pathological features of COVID-19 are related to ARDS.

For example, evident desquamation of pneumocytes and hyaline membrane formation were seen in the lung tissue, indicating ARDS. Moreover, interstitial mononuclear inflammatory infiltration was observed in lung tissue.

Multinucleated giant cells with atypical enlarged pneumocytes characterised by large nuclei, prominent nucleoli and amphophilic granular cytoplasm were observed in the intra-alveolar spaces, suggesting viral cytopathic-like changes [55]. These pathological characteristics of COVID-19 are highly similar to those seen in SARS-CoV and MERS-CoV infection [56,57].

Taken together, understanding the pathological characteristics of this severe case of COVID-19 could help to provide new insights into the pathogenesis of SARS-CoV-2-infected pneumonia, which may help physicians to formulate a timely strategy for the treatment of similar severe patients and to decrease mortality.

Computed tomography (CT) imaging characteristics

CT is often found to be positive when patients with SARS-CoV-2 develop a persistent cough, fever and unexplained fatigue. Typical CT presentations of COVID-19 patients include bilateral pulmonary parenchymal ground-glass opacity, pulmonary consolidation and nodules, bilateral diffuse distribution, sometimes with a rounded morphology, and a peripheral lung distribution [58,59]. In the early course of disease, chest images show multiple small patchy shadows and interstitial changes, which are evident in the lung periphery. Severe cases can spread to the bronchi with progress of the disease, gradually spread to the whole lung, and with infrequent interlobar pleural thickening and pleural effusion.

Detection of SARS-CoV-2

Rapid and accurate detection of SARS-CoV-2 is essential to control the outbreak of COVID-19. Nucleic acid detection is a major method of laboratory diagnosis. Reverse transcription quantitative PCR (RT-qPCR) is a molecular biological diagnosis technology based on nucleic acid sequences. The complete SARS-CoV-2 genome sequences are available in GenBank.

Thus, the nucleic acid of SARS-CoV-2 can be detected by RT-qPCR or by viral gene sequencing of nasopharyngeal and oropharyngeal swabs, stool, sputum or blood samples [60,61].

However, collection of these specimen types by healthcare workers requires close contact with patients, which poses a risk of spreading the virus to healthcare workers. Moreover, collection of nasopharyngeal or oropharyngeal specimens may cause bleeding, especially in patients with thrombocytopenia [32].

Importantly, To et al. found that SARS-CoV-2 could be effectively detected in the saliva specimens of infected patients [62], suggesting that saliva is a promising non-invasive specimen type for diagnosis, monitoring and infection control of COVID-19 patients.

Besides RT-qPCR, Zhang et al. described a protocol using the CRISPR-based SHERLOCK (Specific High-sensitivity Enzymatic Reporter UnLOCKing) technique for the detection of SARS-CoV-2 [63]. Using synthetic SARS-CoV-2 virus RNA fragments, the authors found that this technique is able to consistently detect target sequences of SARS-CoV-2 in a range between 20 and 200 aM (10–100 copies per microlitre of input).

This test can be read out using a dipstick in <1 h, without requiring elaborate instrumentation [63]. Compared with RT-qPCR, the SHERLOCK technique is more accurate and the detection time is reduced by one-half. Thus, use of the SHERLOCK technique for the detection of SARS-CoV-2 in clinical patient samples is expected.



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