UNDIAGNOSED PNEUMONIA - CHINA (HUBEI) (07): OFFICIAL CONFIRMATION OF NOVEL CORONAVIRUS
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Date: 9 Jan 2020
Source; CCTV / Xinhua [in Chinese, machine translation]
<http://news.cctv.com/2020/01/09/ARTIMxiGSClHAjC4B1Gy2VcP200109.shtml?spm=C94212.P4YnMod9m2uD.ENPMkWvfnaiV.102>
Preliminary progress in pathogen identification of unexplained viral pneumonia in Wuhan
Original title: Experts say that the new coronavirus is an unknown cause of viral pneumonia in Wuhan
A few days ago, on the issue of the pathogenic identification of unexplained viral pneumonia epidemic in Wuhan, the reporter interviewed Xu Jianguo, the leader of the preliminary assessment of pathogenic test results and a member of the Chinese Academy of Engineering. He said that the expert group believed that the pathogen of this unexplained case of viral pneumonia was initially determined to be a new coronavirus.
Question 1: At present, what progress has been made in the pathogenic identification of unexplained viral pneumonia in Wuhan?
Xu Jianguo [response]: As of 21:00 on [7 Jan 2020], a new coronavirus was detected in the laboratory, and the entire genome sequence of the virus was obtained. A total of 15 positive results of the new coronavirus were detected by nucleic acid detection methods. From 1 positive patient. The virus was isolated from the samples and showed a typical coronavirus appearance under an electron microscope. [Does this refer to 15 samples from 1 single patient? Or initially from 1 patient?]
The expert group believes that the pathogen of this unexplained case of viral pneumonia was initially identified as a new type of coronavirus.
Question 2: How is the pathogen identification carried out?
Xu Jianguo [response]: The tissue laboratory used genomic sequencing, nucleic acid detection, virus isolation and other methods to perform pathogenic tests on patients' alveolar lavage fluid, throat swabs, blood and other samples.
Question 3: What procedures are needed to identify the pathogen?
Xu Jianguo [response]: To confirm the cause of an epidemic disease, usually the following points must be met: (1) Suspicious pathogens must be found in patients, and pathogenic nucleic acids can be detected in clinical samples of patients; (2) From clinical samples of patients The pathogen can be successfully isolated; (3) The isolated pathogen can cause the same disease symptoms after infecting the host animal. The patient's serum antibody titer during the recovery period increased 4-fold, which can help identify the pathogen.
Finding the nucleic acid, genomic and antibody evidence of the pathogen from the patient can be done in a short time. Scientific research, such as pathogen isolation and pathogenicity identification, can take weeks. The development of specific drugs and vaccines against a new pathogen may take years to complete.
Question 4: What is the next step?
Xu Jianguo [response]: The expert group believes that the pathogen of this unexplained case of viral pneumonia is initially determined as a new type of coronavirus. The next step is to conduct expert research and judgement in combination with etiology research, epidemiological investigation and clinical manifestations.
Question 5: What is a coronavirus?
Xu Jianguo [response]: Coronavirus is a type of pathogen that mainly causes respiratory and intestinal diseases. There are many regularly arranged protrusions on the surface of this type of virus particle, and the entire virus particle is like an emperor's crown, hence the name "coronavirus". In addition to humans, coronaviruses can infect many mammals such as pigs, cattle, cats, dogs, marten, camels, bats, mice, hedgehogs, and various birds. So far, there are 6 known human coronaviruses. Four of these coronaviruses are more common in the population and are less pathogenic, generally causing only minor respiratory symptoms similar to the common cold. The other 2 coronaviruses - Severe Acute Respiratory Syndrome Coronavirus and Middle East Respiratory Syndrome Coronavirus, also known as SARS Coronavirus and MERS Coronavirus, can cause severe respiratory diseases. The new coronavirus that caused the epidemic is different from the human coronaviruses that have been discovered, and further understanding of the virus requires further scientific research.
[Editor: Zhang Yuling Responsible editor: Wang Jingdong]
[Byline: Qu Ting]
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Date: 8 Jan 2020
Source: NY Times [Edited]
<https://www.nytimes.com/2020/01/08/health/china-pneumonia-outbreak-virus.html>
China Identifies New Virus Causing Pneumonia-Like Illness
The new coronavirus doesn't appear to be readily spread by humans, but researchers caution that more study is needed.
Researchers in China have identified a new virus that is behind a mysterious pneumonialike illness that has sickened 59 people in Wuhan and caused a panic in the central Chinese region. There's no evidence that the virus, a coronavirus, is readily spread by humans, and it has not been tied to any deaths. But health officials in China and internationally are watching it carefully, as it comes from the same region where the deadly SARS epidemic broke out in the early 2000s.
Experts said the pathogen that caused these unexplained pneumonia cases had been "initially identified" as a new coronavirus, China's state broadcaster, China Central Television, said on Thursday [9 Jan 2020]. They detected this virus among 15 of the people. The new coronavirus "is different from previous human coronaviruses that were previously discovered, and more scientific research is needed for further understanding," CCTV said in its report. Coronaviruses are a large family of viruses that infect animals and people. Some cause only the symptoms known as the common cold -although many other viruses also do that.
The Wuhan government confirmed on [31 Dec 2020] that health authorities were treating dozens of cases of pneumonia of unknown cause. Symptoms of the new illness include high fever, difficulty breathing and lung lesions, the Wuhan health commission has said. No deaths have been reported, but 7 people have become critically ill. On Wednesday [8 Jan 2020], the local health commission said 8 people had been discharged.
The revelations set off a panic in a country where the memory of the SARS outbreak remains fresh. SARS, a dangerous respiratory disease and also a coronavirus, spread from southern China in 2003 and infected more than 3000 people, killing 774.
The new illness appeared just weeks before the Spring Festival, the country's biggest holiday, when hundreds of millions of people travel. The authorities have urged the public to be on alert for pneumonia-like symptoms like fevers, body aches and breathing difficulties.
Until Thursday's [9 Jan 2020] announcement, it was not clear what was causing the illnesses in Wuhan. The World Health Organization said Wednesday [8 Jan 2020] that it had concluded that it was most likely a coronavirus. "More comprehensive information is required to confirm the pathogen," the W.H.O. said in a statement.
Early reports on ProMED, a disease-alert service, said there was no evidence of human-to-human transmission.
Last weekend, laboratory tests in China ruled out SARS; the deadly Middle East Respiratory Syndrome, or MERS; the flu; bird flu; adenoviruses; and other common pathogens that cause pneumonia.
The initial cases of pneumonia were linked to workers at a market in Wuhan that sold live fish, animals and birds. Workers disinfected and shut down the market in Wuhan after the city health department said it traced many of the cases to it.
Health authorities in Asia have stepped up screenings and isolated patients with flulike symptoms who have traveled to Wuhan. In Hong Kong, 8 people with fever and respiratory symptoms who had traveled recently to Wuhan were hospitalized as of Wednesday [8 Jan 2020]. In South Korea, the authorities said on Wednesday [8 Jan 2020] that they had put a Chinese woman under isolated treatment after she was found to have pneumonia after trips to China, including Wuhan. In Singapore, the authorities placed a Chinese girl with pneumonia in isolation because she had traveled to Wuhan, then said on Sunday [5 Jan 2020] that doctors had found that the child had a common childhood viral illness. Officials in Hong Kong have installed additional thermal imaging systems at its airport to monitor passengers coming from Wuhan, scanning for people with fevers.
SARS is believed to have jumped to humans from live-animal markets. It was eventually traced to civet cats, raccoon dogs and some other species that were raised and slaughtered for the exotic food trade. The virus normally circulates in bats, and the animals may have gotten it from them, possibly from eating food contaminated by bat droppings.
Most outbreaks of MERS, which appeared in 2012, have been traced to people who raise or sell camels, which are kept in the Middle East for meat, milk, racing, hauling cargo and as pets. Like SARS, it can jump from person to person, particularly in hospitals. Some patients infected many others after they were put on machines to help them breathe - the mechanisms helped spew viral particles into the air as they exhaled.
Virologists want to know which patients tend to get the virus, what symptoms they show, what animals - if any - the virus has been found in and what behavior helped the virus jump from animals to humans.
And they want to quickly figure out what countermeasures, such as antiviral drugs or breathing machines, help treat the illness.
[Bylines: Sui-Lee Wee and Donald G. McNeil Jr.]
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[The above interview is further confirmation that the Wuhan Institute of Virology expert group identified a novel coronavirus [CoV]. The fact that this novel coronavirus was identified in 15 people is highly suggestive that at least 15 of the 59 suspected cases may have been infected by the same CoV.
A question that comes to mind is whether Hong Kong could identify the novel coronavirus in those suspected cases with history of travel to Wuhan who presented with febrile respiratory illnesses but did not have etiologic agents identified (see Undiagnosed pneumonia
- China (06): (HU) Hong Kong surveillance, USA CDC alert http://promedmail.org/post/20200108.6876648 and Undiagnosed pneumonia
- China (04): (HU) Hong Kong surveillance
http://promedmail.org/post/20200106.6874277 for details.). An updated line listing of suspected cases followed by Hong Kong can be found at: <https://www.chp.gov.hk/files/pdf/enhanced_sur_pneumonia_wuhan_eng.pdf>.
We await further information from knowledgeable sources on the detailed sequence(s) of the novel coronavirus and where on the phylogenetic tree this novel coronavirus sits, i.e., which other known coronaviruses are close relatives. There are many questions that remain, including whether this virus has been identified in any of the wildlife from this market. And more clinical and epidemiologic
details on the suspected and presumably confirmed cases. And are other "undiagnosed pneumonia" cases in Wuhan being tested for this novel coronavirus?
Making the sequence available as quickly as possible would allow diagnostic testing to be performed elsewhere and allow us to know whether this virus has appeared elsewhere in humans or other species.
A map of China showing locations of major cities in China can be found at <https://www.chinadiscovery.com/china-maps/city-maps.html>.
The HealthMap/ProMED map of China: <http://healthmap.org/promed/p/155>
- Mod.MPP]
NOVEL CORONAVIRUS (09): CHINA, FIRST DIAGNOSTIC TEST
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In this update:
[1] Subscriber query re: laboratory testing
[2] Laboratory testing available - media report
[3] WHO Interim Guidance on Laboratory testing for 2019 novel
coronavirus (2019-nCoV) in suspected human cases
[4] Diagnostic detection of Wuhan coronavirus 2019 by real-time
RT-PCR
[5] Japan: Detection of WN-Human1 sequence from clinical specimen.
[1] Subscriber query re: laboratory testing
Date: 17 Jan 2020 8:34 PM
From: J Richard Gould MD <Richard.Gould@york.ca> [edited]
Would it be possible to provide more information on the tests being performed to confirm cases? Whatever techniques are being used seem to have been developed very quickly. That can be extremely valuable and helpful. However, what information is available about the sensitivity and specificity of these tests, especially the latter?
J Richard Gould MD MHSc FRCPC
Associate Medical Officer of Health York Region Public Health
<Richard.Gould@york.ca>
[Good request. See below for information on the laboratory testing.
- Mod.MPP]
[2] Laboratory testing available - media report
Date: 19 Jan 2020
Source: Live Mint [edited]
<https://www.livemint.com/>
The Chinese virus, which 1st emerged in Wuhan, and can cause severe pneumonia, can now be detected in the laboratory. The test will help scientists to understand whether the new virus is capable of spreading from human to human.
Researchers have developed the 1st diagnostic test to detect the novel Chinese coronavirus, which is likely to spread globally.
The assay protocol has now been published by the World Health Organization (WHO) as a guideline for diagnostic detection. The new method also enables suspected cases to be tested quickly.
The virus, which 1st emerged in Wuhan, China and can cause severe pneumonia, can now be detected in the laboratory.
"Now that this diagnostic test is widely available, I expect that it won't be long before we are able to reliably diagnose suspected cases," said study researcher Christian Drosten, Director of the Institute of Virology on Campus Charite Mitte in Germany.
"This will also help scientists understand whether the virus is capable of spreading from human to human; this is an important step in our fight against this new virus," Drosten added.
Developed by researchers from the German Centre for Infection Research, the world's 1st diagnostic test for the coronavirus has now been made publicly available.
Following its online publication by the WHO, the test protocol will now serve as a guideline for laboratories. An international consortium is currently conducting a joint evaluation study.
The Union Ministry of Health and Family Welfare on Friday [17 Jan 2020] issued an advisory for travellers visiting China in the wake of the novel coronavirus outbreak in the neighbouring country.
As of [11 Jan 2020], 41 novel coronavirus confirmed infection cases have been reported from China, of which one has died. One travel related case each has been reported in Thailand and Japan.
The clinical signs and symptoms are mainly fever with a few patients having difficulty in breathing. The mode of transmission is unclear as of now. However, so far, there is little evidence of significant human-to-human transmission.
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[3] WHO Interim Guidance on Laboratory testing for 2019 novel coronavirus (2019-nCoV) in suspected human cases
Date: 17 Jan 2020
Source: WHO/2019-nCoV/laboratory/2020.3 [edited]
<https://www.who.int/docs/default-source/coronaviruse/20200117-interim-laboratory-guidance-version-final.pdf?sfvrsn=cd45dc4b_2&download=true>
This document is entitled: Laboratory testing for 2019 novel coronavirus (2019-nCoV) in suspected human cases; Interim guidance [17 Jan 2020].
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[See below for specifics on real-time RT-PCR testing. - Mods.MPP/UBA]
[4] Diagnostic detection of Wuhan coronavirus 2019 by real-time RT-PCR
Date: 13 Jan 2020
Source: WHO [abridged, edited]
<https://www.who.int/docs/default-source/coronaviruse/wuhan-virus-assay-v1991527e5122341d99287a1b17c111902.pdf?sfvrsn=d381fc88_2>
Abbreviations and taxonomy related to the Wuhan virus are not used in any systematic way, i.e., there are multiple different designations and abbreviations for the "Wuhan virus" in this document. We use the term "SARS-related coronavirus" to include the SARS virus as well as the clade of betacoronaviruses known to be associated with (mainly) rhinolophid bats across the Palearctic.
The latest taxonomy classifies these viruses in a subgenus termed Sarbecovirus.
"HCoV229E (VR740) and MERS-CoV (EMC) could be used as positive control for pan coronavirus primer set, but there was no positive control for WN-human1 specific primers. Water only was used as negative control."
Background
We used known SARS-and SARS-related coronaviruses (bat viruses from our own studies as well as literature sources) to generate a non-redundant alignment (excerpts shown in Annex). We designed candidate diagnostic RT-PCR assays before release of the 1st sequence of the Wuhan virus. Upon sequence release, 3 assays were selected based on their matching to the Wuhan virus as per inspection of the sequence alignment. All assays can use SARS-CoV genomic RNA as positive control.
Synthetic control RNA for Wuhan virus will be provided shortly.
1st line screening assay: E gene assay
Confirmatory assay: RdRp gene assay
Additional confirmatory assay: N gene assay
Materials and assay formulation
Clinical samples and CoV cell culture supernatants Respiratory samples were obtained during 2019 from patients hospitalized at Charite medical center and tested by the NxTAG Respiratory Pathogen Panel (Luminex) or in cases of MERS-CoV by the MERS-CoV upE assay as published before (1). Cell culture super-natants from typed coronaviruses were available at our research and clinical laboratories. The typed avian influenza virus RNA (H5N1) was obtained from the German Society for Promotion of Quality Assurance in Medical Laboratories (INSTAND) proficiency testing panels. RNA was extracted from clinical samples by using the MagNA Pure 96 system (Roche) and from cell culture super-natants by the viral RNA mini kit (Qiagen).
Assay design: For oligonucleotide design and in-silico evaluation, we downloaded all complete and partial (if over 400 nucleotides) SARS-related virus sequences available at GenBank by 1 Jan 2020. The list (n=729 entries) was manually checked and artificial sequences (lab-derived, Berlin, 13.01.2020 synthetic etc.) as well as sequence duplicates removed, resulting in a final list of 375 sequences. These sequences were aligned and the alignment used for assay design. The alignment was later complemented by sequences released from the Wuhan cluster. All presently released sequences match the amplicons.
Real-time reverse-transcription polymerase chain reaction
All assays used the same conditions. Primer and probe sequences, as well as optimized concentrations are shown in Table 1. A 25-ul reaction was set up containing 5 ul of RNA, 12.5 ul of 2 X reaction buffer provided with the Superscript III one step RT-PCR system with Platinum Taq Polymerase (Invitrogen; containing 0.4 mM of each deoxyribonucleotide triphosphates (dNTP) and 3.2 mM magnesium sulfate), 1 ul of reverse transcriptase/Taq mixture from the kit, 0.4 ul of a 50 mM magnesium sulfate solution (Invitrogen -not provided with the kit), and 1 ug of non-acetylated bovine serum albumin (Roche). All oligonucleotides were synthesized and provided by Tib-Molbiol, Berlin. Thermal cycling was performed at 55 C for 10 min for reverse transcription, followed by 95 C for 3 min and then 45 cycles of 95 C for 15 s, 58 C for 30 s.....
Specificity testing
1. Chemical stability
To exclude non-specific reactivity of oligonucleotides among each other, all assays were tested 40 times in parallel with water and no other nucleic acid except the provided oligonucleotides. In none of these reactions was any positive signal detected.
2. Cross-reactivity with other coronaviruses: Cell culture super-natants containing human coronaviruses (HCoV)-229E, -NL63, -OC43, and -HKU1 as well as MERS-CoV were tested in all 3 assays (Table 2). For the non-cultivable HCoV-HKU1, super-natant from human airway culture was used. Virus RNA concentration in all samples was determined by specific real-time RT-PCRs and in-vitro transcribed RNA standards designed for absolute viral load quantification.
3. Tests of human clinical samples previously tested to contain respiratory viruses. All tests returned negative results.
Document Authors
-Victor Corman, Tobias Bleicker, Sebastian Brunink,
Christian Drosten Charite Virology, Berlin, Germany
Olfert Landt, Tib-Molbiol, Berlin, Germany
Marion Koopmans Erasmus MC, Rotterdam, The Netherlands
Maria Zambon Public Health England, London
Additional advice by Malik Peiris, University of Hong Kong
Contact:
<christian.drosten@charite.dehttps://virologie-ccm.charite.de/en/>
Positive control material is available from Charite, Berlin, viaEVAg
(<https://www.european-virus-archive.com/>).
We acknowledge the originators of sequences in GISAID
(<http://www.gisaid.org>):
National Institute for Viral Disease Control and Prevention, China,
Institute of Pathogen Biology, Chinese Academy of Medical Sciences,
Peking Union Medical College, China, and Wuhan Jinyintan Hospital
Wuhan Institute of Virology, Chinese Academy of Sciences, China).
We acknowledge Professor Yong-Zhen Zhang, Shanghai Public Health
Clinical Center & School of Public Health, Fudan University, Shanghai,
China for release of another sequence (MN908947).
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[The complete protocol can be accessed at the URL above. In laboratories that have validated broad coronavirus RT-PCR assays, it is advised to check the primers against the published 2019-nCoV sequence and check whether primers are overlapping and have the capacity to detect the 2019-nCoV. On a positive result, sequencing should be performed to determine the precise virus detected (e.g. on an amplicon of a non-conserved region), or refer for confirmation to a national, regional or global reference laboratory.
- Mod.UBA]
[5] Japan: Detection of WN-Human1 sequence from clinical specimen.
Date: 17 Jan 2020
Source: NIID webpage [edited]
<https://www.niid.go.jp/niid/images/epi/corona/Method_NIID_20200114_Na.pdf>
Detection of WN-Human1 sequence from clinical specimen. Naganori Nao,
Kazuya Shirato, Shutoku Matsuyama, and Makoto Takeda.
Laboratory of Acute Viral Respiratory Infections and Cytokines,
Department of Virology III, National Institute of Infectious Diseases, 4-7-1 Gakuen,
Musashimurayama, 208-0011 Tokyo, Japan.
Communicated by:
ProMED-mail Rapporteur Kunihiko Iizuka
[Rapid collection and testing of appropriate specimens from suspected cases is a priority. However, extensive testing is still needed to confirm the 2019-nCoV, and the role of mixed infection has not been verified; multiple tests may need to be performed, and sampling sufficient clinical material is recommended.
Furthermore, in view of the latest WHO guidance, all labs must assure that appropriate Standard Operating Procedures (SOPs) are available and that the appropriate staff are trained and available for appropriate collection, specimen storage, packaging and transport. There is still limited information on the risk posed by the reported coronavirus found in Wuhan, but it would appear that samples prepared for molecular testing could be handled as would samples of suspected human influenza. However, attempts to culture the virus may require heightened biosafety control measures (see
<https://www.who.int/docs/default-source/coronaviruse/20200117-interim-laboratory-guidance-version-final.pdf?sfvrsn=cd45dc4b_2&download=true>).
- Mod.UBA]
[There is also the need to develop serologic tests. To get a better understanding of whether there has been significant person-to-person transmission, serologic testing of close contacts, especially those who tested negative for the virus by RT-PCR, would be helpful. But a caution reminder is that studies in Saudi Arabia on the MERS-CoV have demonstrated loss of antibodies within 3-6 months following infection, especially in those individuals with a mild clinical presentation when infected with the MERS-CoV.
- Mod.MPP
