Instituto Valenciano de Microbiología
(IVAMI)

Masía El Romeral
Ctra. de Bétera a San Antonio Km. 0.3
46117 Bétera (Valencia)
Phone. 96 169 17 02
Fax 96 169 16 37
Email: 
www.ivami.com
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Coronavirus SARS-CoV-2 (COVID-19; 2019nCoV; Wuhan Coronavirus): Molecular diagnosis (Real time RT-PCR).

 

Information 2020-01-22; 2020-01-31; 2020-02-10; 2020-03-06.

SARS-Cov-2 (2019nCoV; Wuhan coronavirus), also called Wuhan seafood market pneumonia virus and Wuhan pneumonia virus, is a virus that belongs to the Coronavirus family (Coronaviridae) with positive single-stranded RNA (+ssRNA).

The pneumonia epidemic due to a new coronavirus from 2019-2020, began in mid-December 2019 in Wuhan City, Hubei Province, in central China, when a group of people with pneumonia of unknown cause appeared, mainly linked to workers from the Huanan Seafood Market, dedicated to the sale of live animals. Subsequently, Chinese scientists isolated a new type of Coronavirus that was called 2019-nCoV, and that has a similarity of at least 70% in its genetic sequence with the SARS-CoV.

The first suspected case was reported on December 31, 2019, after three weeks of the appearance of the first affected with symptoms, on December 8, 2019. The first death from the virus occurred in a 61-year-old male on the 9th of January 2020, a regular customer of the Wuhan market, who was admitted to the hospital for respiratory failure and severe pneumonia. The patient suffered significant underlying diseases, including chronic liver disease (with an abdominal tumour and cirrhosis).

On December 31, 2019, the Wuhan Municipal Health Commission reported a group of 27 cases of pneumonia of unknown etiology, including seven serious cases, which had in common the assistance to a wholesale market of fish and live animals where different animal species are sold. The cases showed common symptoms of various respiratory diseases such as fever, dyspnoea and radiological tests compatible with bilateral pulmonary infiltrates.

The market where the outbreak was thought to have originated was closed on January 1, 2020 and those affected with symptoms were isolated. Some cases reported no exposure to this specific market, but to other food markets in Wuhan. In some cases, there was no direct connection to a food market. On January 9, 2020, WHO confirmed that a new type of Coronavirus had been isolated in a hospitalized person.

Although the virus appears to be transmitted to humans from animals, specific host animals, the route of transmission, the incubation period, the characteristics of the susceptible population and survival rates still need to be identified.

The National Health Commission of China confirmed on January 20, 2020 that this new Coronavirus can be transmitted between people. The World Health Organization warned that an international epidemic could originate, and fears were raised due to the proximity of Chinese New Year celebrations.

When it has spread among people, such as with MERS and SARS Coronaviruses, transmission is believed to occur through respiratory droplets produced when an infected person coughs or sneezes, similar to how other respiratory pathogens spread. It is still unclear how easily 2019-nCoV spreads from person to person.

The transmission potential of 2019-nCoV through substances of human origin (SoHO) is unknown. The possible viremia during the incubation period of the disease, during a possible course of asymptomatic infection or after the resolution of symptoms is also unknown. Therefore, until more information is available on the epidemiology and pathogenesis of this infection, the SoHo safety authorities in the EU/EEE countries recommend following the recommendation used for SARS-CoV and MERS-CoV. This implies a preventive postponement of donation of blood, cell and tissue donors for 21 days after a possible exposure to a confirmed case or after returning from China.

The World Health Organization (WHO) convened a meeting of its Emergency Committee on January 22, in order to determine whether the epidemic constitutes a public health risk of international interest, under the regulations of the International Health Regulations.

On January 22, 2020 the scientific Journal of Medical Virology published a report with the genomic analysis that reflects that snakes in the Wuhan area (Bungarus multicinctus, a highly venomous snake, existing in the Wuhan Food Market) are the reservoir of wildlife animals most likely for the virus, but further research is required to confirm it.

The virus has spread to Bangkok (Thailand), Tokyo (Japan), Seoul (South Korea), Beijing (China), Shanghai (China), Guangdong (China), Dayuan (Taiwan), Hong Kong (China) Macao (China), USA, Vietnam and Singapore. Also isolated imported cases have bee reported from some European countries (France, Germany, …). There have been at least 17 deaths, mainly in and around Wuhan, and there have been at least 913 known cases (information January 22, 2020). The Medical Research Centre for Global Infectious Disease Analysis at Imperial College in London estimates that up to 4,000 people are infected with Coronovirus in the city of Wuhan.

To limit the epidemic, the Chinese authorities have implemented a series of extraordinary measures of social distancing, such as the cancellation of the Lunar New Year celebrations and the closing of cinemas and theme parks. In addition, public transport systems have been closed, Wuhan Tianhe Airport was closed on January 23 and strict exit controls have been applied from several large cities in Hubei province. On January 24, 2020, all public transportation was suspended in at least 10 cities near Wuhan. On January 26, the authorities ordered a temporary ban on the trade of wild animals throughout China. Although the effectiveness and side effects of these measures are difficult to predict, they are expected to limit the immediate likelihood of further spread of the virus through travelers returning from Hubei Province and China in general.

Case incidence update (2020-03-06):

From December 31, 2019 until March 6, 2020, 98,171 laboratory-confirmed cases of the new coronavirus infection SARS-CoV-2 (COVID-19; 2019-nCoV; Wuhan Coronavirus) have been reported, with more than 9,000 cases imported into other countries around the world , including 5,544 cases reported in the EU / EEA and the United Kingdom and 3,385 deaths (one outside China, in the Philippines). According to the media, one of the deaths was that of a doctor who worked in a hospital in Wuhan and who had treated patients from 2019-nCoV. (ECDC January 31, 2020). Deaths have been reported from China (3,044), Italy (148), Iran (107), South Korea (42), United States (12), France (7), International transport in Japan (6), Japan ( 6), Spain (3), Australia (2), Iraq (2), Philippines (1), San Marino (1), Switzerland (1), Taiwan (1), Thailand (1) and United Kingdom (1) .

On January 20, Chinese health authorities confirmed the transmission from person to person outside Hubei province. Person-to-person transmission is currently evident inside and outside of China (for example, Vietnam, Taiwan, Germany) and cases have been reported among health workers.

On January 24, 2020, the first three cases imported into the European Union from infection by 2019-nCoV were identified in France and an additional case was notified on January 29, 2020. On January 28, a group of four locally acquired cases, with indirect links to Wuhan. On January 29, Finland notified an imported case of infection.

On January 30, 2020, the WHO director declared that the 2019-nCoV outbreak constitutes a PHEIC (Public Health Emergencies of International Concern), that is, a Public Health emergency situation of International interest (see https: // www.who.int/ihr/procedures/pheic/en/), subject to International Health Regulations (IHR: International Health Regulations, 2005) (see https://www.who.int/ihr/publications/9789241596664/en/ ).

In Spain on January 31, 2020, Spanish health authorities reported the first case in La Gomera. It was one of five Germans who had been isolated in a hospital for having been in contact with a person affected by the Coronavirus in Germany.

The origin of the virus is still unclear. The source of infection is unknown and could still be active. There remain many unknowns regarding the virulence / pathogenicity of the new coronavirus, the mode of transmission, the reservoir and the source of infection. Until now, the detailed epidemiological data available are still limited and, therefore, there are significant uncertainties in this risk assessment. The virus was initially isolated from bronchoalveolar lavage fluid samples and viral RNA has subsequently been detected in nasopharyngeal and throat swabs, as well as in serum, blood, rectal swabs, saliva, urine and feces.

In total, the following number of cases have been reported in the following regions and countries:

Africa: Algeria (17), Senegal (4), Egypt (3), Morocco (2), Nigeria (1), South Africa (1) and Tunisia (1).

 

Asia: China (80,667), South Korea (6 284), Iran (3513), Japan (349), Singapore (117), Kuwait (58), Bahrain (52), Malaysia (50), Thailand (47), Taiwan (44), Iraq (38), India (29), United Arab Emirates (29), Israel (17), Lebanon (16), Oman (16), Vietnam (16), Qatar (8), Palestine* (7), Pakistan (5), Saudi Arabia (5), Philippines (3), Indonesia (2), Afghanistan (1), Bhutan (1), Cambodia (1), Jordan (1), Nepal (1) and Sri Lanka (1).

America: United States (233), Canada (45), Ecuador (13), Brazil (8), Mexico (5), Chile (4), Argentina (2) and Dominican Republic (1).

Europe: Italy (3858), France (423), Germany (400), Spain (261), United Kingdom (115), Switzerland (87), Norway (86), Netherlands (82), Sweden (61), Belgium (50), Austria (41), Iceland (35), Greece (32), San Marino (22), Denmark (20), Ireland (13), Czech Republic (12), Finland (12), Croatia (10) , Georgia (9), Portugal (9), Azerbaijan (6), Belarus (6), Romania (6), Slovenia (6), Estonia (5), Russia (4), Bosnia and Herzegovina (2), Hungary ( 2), Andorra (1), Armenia (1), Latvia (1), Liechtenstein (1), Lithuania (1), Luxembourg (1), Monaco (1), North Macedonia (1), Poland (1) and Ukraine (1).

Oceania: Australia (59) and New Zealand (4).

Characteristics of the virus and its pathology

This new Coronavirus SARS-CoV-2 (2019-nCoV; Wuhan Coronavirus; COVID-19) belongs to the Phylum Riboviria, Order Nidovirales, Family Coronaviridae, Genus Betacoronavirus, Subgenus Sarbecovirus. Its current synonyms are: COVID-19, Wuhan Coronavirus, Wuhan flu, Wuhan pneumonia, Yewi (wild animal) pneumonia, or Wuhan seafood market pneumonia virus.

Coronaviruses are a large family of viruses that are common in many different species of animals, including camels, cows, cats and bats. Rarely, animal coronaviruses can infect people and then spread among people, as is the case with the coronavirus that causes MERS and SARS.

This outbreak recalls the outbreak of Coronavirus previously occurred in China in 2003, which causes severe acute respiratory syndrome (SARS), caused by the new Coronavirus SARS-CoV. SARS-CoV spread rapidly to other countries from South China in 2003 and infected more than 3,000 people, causing the death of 774 people in 2004, although it subsequently disappeared.

However, the Middle East Respiratory Syndrome Coronavirus (MERS) (MERS-CoV), a lethal zoonotic pathogen that was first identified in humans in the Kingdom of Saudi Arabia (KSA) in 2012, continues to emerge and reappear with cases Sporadic intermittent, community groups and nosocomial outbreaks.

The basic reproductive number (R0), to estimate the speed with which a disease can spread in a population, has been calculated at 2.2 (95% CI 1.4 to 3.9). This implies a transmissibility similar to SARS (pre-intervention R0 = 2 to 3) and higher than MERS (R0 = 0.7). It is estimated that the average incubation period is 5.2 days (95% CI, 4.1 to 7.0), with the 95th percentile of the distribution at 12.5 days, allowing 14 days to be used as an operational definition for the follow-up and monitoring of contacts.

The SARS-CoV-2 (COVID-19; 2019nCoV; Wuhan Coronavirus) sequences show similarities with the betacoronavirus found in bats; however, the virus is genetically distinct from other coronaviruses such as the Coronavirus related to the respiratory syndrome (SARS) and the Coronavirus related to the respiratory syndrome of the Middle East (MERS). Like SARS-CoV, it is a member of the Beta-CoV B lineage (i.e., subgenus Sarbecovirus). At the Chinese Center for Disease Control and Prevention, Institute of Pathogen Biology of China, and Wuhan Jinyintan Hospital, 18 strains of the new Coronavirus have been isolated having reported the genomes of the new Coronavirus, including BetaCoV/Wuhan/IVDC-HB-01/2019; BetaCoV/Wuhan/IVDC-HB-04/2020; BetaCoV/Wuhan/IVDC-HB-05/2019; BetaCoV/Wuhan/WIV04/2019 and BetaCoV/ Wuhan/IPBCAMS-WH-01/2019. Its RNA sequence is approximately 30,000 nucleotides in length. The new genome has led to several experiments in modeling protein nCoV spike (S) receptor binding (RBD). Two Chinese groups, as of January 23, 2020, believe that the S protein has sufficient affinity with the SARS receptor (angiotensin 2 converting enzyme, ACE2) to use it as a cellular input mechanism.

Symptoms of the infection include fever (> 90% of cases), malaise, dry cough (80%), shortness of breath (20%) and respiratory distress (15%). Vital signs are stable in most cases, while leukopenia and lymphopenia are frequent. The clinical criteria of the CDC (USA) for a patient under investigation for 2019-nCoV infection have been developed on the basis of what is known about MERS-CoV and SARS-CoV and are subject to change as available of additional information. At this time the symptoms of SARS-CoV-2 may appear in just 2 days or up to 14 after exposure, based on what has been seen previously as the MERS virus incubation period.

Estimates of severity and lethality rate should be interpreted with caution at this stage. Reported fatality rates vary from 4% in the WHO Emergency Committee Statement, to 14% when only recovered cases and deaths are included in the denominator, and 15% in the publication of a small series of hospitalized patient cases. A more recent study of 99 hospitalized cases between January 1 and January 20 reported that as of January 25, 31% had been discharged, 11% had died and 58% were still admitted with unknown final results in this moment. Mortality increases with age, with the highest mortality among people over 80 years (CFR 21.9%).

Any person who meets the epidemiological and clinical criteria should be tested for 2019-nCoV:

Epidemiological criteria: people with a history of traveling to the city of Wuhan, China, in the 14 days before the onset of the disease; or any person who is in close contact with a laboratory-confirmed case of 2019-nCoV within 14 days prior to the onset of the disease.

Clinical criteria: people with clinical symptoms compatible with severe acute respiratory infection who seek medical attention or who enter the hospital with clinical or radiological evidence of pneumonia; or anyone with a fever or a recent history of fever (≥ 38°C) and acute respiratory infection (sudden onset of respiratory infection with one or more of the following symptoms: shortness of breath, cough or sore throat).

There is no specific recommended antiviral treatment or vaccine against the 2019-nCoV virus currently available.

Although there is no specific treatment for human Coronaviruses in general, the Center for Disease Control and Prevention (CDC, USA) advises the same generic care as for an infected person can relieve symptoms by taking regular flu medications regularly, drinking liquids and resting.

To prevent infection, WHO recommends "regular hand washing, covering your mouth and nose when coughing and sneezing, and avoiding close contact with people who show symptoms of respiratory diseases, such as coughing or sneezing." The best way to prevent infection is to avoid exposure to this virus.

Tests performed in IVAMI:

Sample recommended:

Respiratory (nasopharyngeal and oropharyngeal swab in outpatients and sputum (if it occurs) and/or endotracheal aspirate in patients with more severe respiratory disease).

Nasopharyngeal and oropharyngeal swab: Dacron or polyester swabs, ≤ 5 days: 4°C, > 5 days: -70°C.

Bronchoalveolar lavage: sterile container: ≤ 48 hours: 4°C, > 48 hours: –70°C.

Endotracheal, nasopharyngeal, aspirated or nasal lavage aspirate: sterile container: ≤ 48 hours: 4°C; > 48 hours: freeze at –70°C.

Biopsy or necropsy lung tissue: sterile container with saline solution: ≤ 24 hours: 4°C; > 24 hours: freeze at –70°C.

Storage and shipment of the sample:

Samples must be storage and sent in a biosafety container for infectious samples.

Delivery of results:

Cost of the test: