Corona Virus

Estimates

Based on cases reported and assuming a 10-day delay between infection and detection, researchers at Northeastern University and Imperial College London estimated that the number of actual infections may be 10 times higher than those confirmed at the time of reporting. Imperial College estimated 4,000 cases with 440 confirmed by 21 January 2020, Northeastern University estimated 21,300 infections by 26 January, increasing to 26,200 infections by 27 January (with a confidence of 95% within the interval 19,200–34,800). On 31 January 2020, an article published in the Lancet estimated that 75,815 individuals have been infected in Wuhan as of 25 January 2020. There are concerns about whether adequate medical personnel and equipment are available in regions affected by the outbreak for hospitals to correctly identify coronavirus cases instead of misdiagnosing suspected cases as "severe pneumonia". Many of those experiencing symptoms were told to self-quarantine at home instead of going to a hospital to avoid close contact with other patients with different levels of symptoms.[80] After 2 repatriation flights were conducted from Wuhan to Japan in late January, 5 out of approximately 400 persons repatriated were diagnosed with the virus, of whom 1 was symptomatic and 4 were not.

Signs and Symptoms

Those afflicted may be asymptomatic, although those manifesting symptoms may have fever, cough, shortness of breath, and diarrhea,[84] and may vary from slight to very severe. The number of severe cases as of 3 February 2019 is 2,298 out of 17,393, with 488 having recovered. Cases of severe infection can result in pneumonia, kidney failure, and death. Upper respiratory symptoms such as sneezing, a runny nose or sore throat are less frequent. The time from exposure to onset of symptoms is estimated at 2 to 10 days by the World Health Organization and 2 to 14 days by the US Centers for Disease Control and Prevention (CDC). Among the first 41 confirmed cases admitted to hospitals in Wuhan, 13 (32%) individuals had another chronic condition, like diabetes or hypertension. Overall, 13 (32%) individuals required intensive care, and 6 (15%) individuals died. Many of those who died had other conditions such as advanced age, hypertension, diabetes, or cardiovascular disease that impaired their immune systems.

Cause

Spread
Coronaviruses are primarily spread through air droplets expelled when an infected individual coughs or sneezes within a range of about 3 feet (0.91 m) to 6 feet (1.8 m). Viral RNA was also detected in stool specimens collected from the first confirmed case though it was unclear if infectious virus was present to suggest fecal-oral transmission. It can also spread via handles and railings like other corolavira. Of the initial 41 cases, two-thirds had a history of exposure to the Huanan Seafood Wholesale Market.
A super-spreader was reported to have infected 14 different members of medical staff. On 25 January 2020, Gao Fu, the head of Chinese Center for Disease Control and Prevention, in an announcement made to the Xinhua News Agency, denied that the said person should be considered a "super spreader" simply because he was moved to multiple wards. Earlier the same day, however, China Newsweek (operated by another official news agency, China News Service), citing an expert from Peking University, claimed that the aforementioned patient could be considered a super-spreader already and criticised the hospitals involved for not having properly protected the staff who came into contact. China Newsweek also criticised the government's censorship, saying healthcare providers, except those in the fever clinic, have only a mask for protection.
Basic reproduction number
The spread of the virus between people has been variable, with some affected people not transmitting the virus to others while others have been able to spread the infection to several people. There have been various estimates for the basic reproduction number, ranging from 2.13 to 3.11. The number describes how many people a newly infected person is likely to pass the virus onto. The new coronavirus has been reportedly able to transmit down a chain of up to four people so far. This is similar to severe acute respiratory syndrome-related coronavirus (SARSCoV).
Virology
The natural wildlife reservoir of the 2019‐nCoV and intermediate host that transmitted the 2019-nCoV to humans has not been confirmed.[101] However, it is likely that the primary reservoir for the virus is bats. Of 585 animal specimens taken from the market, 33 showed evidence[clarification needed] of 2019-nCoV. An updated preprint paper published 23 January 2020 on bioRxiv from members of the Wuhan Institute of Virology, Wuhan Jinyintan Hospital, University of Chinese Academy of Sciences and the Hubei Provincial Center for Disease Control and Prevention suggest that the 2019 novel coronavirus has possible bat origins, as their analysis shows that nCoV-2019 is 96% identical at the whole genome level to a bat coronavirus identified in 2013. A report published one day earlier from Peking University, Guangxi Traditional Chinese Medical University, Ningbo University and Wuhan Biology Engineering College compares the codon usage bias of 2019-nCoV with "humans, bats, chickens, hedgehogs, pangolins, and two species of snakes",[104] and they concluded that "snake is the most probable wildlife animal reservoir for the 2019‐nCoV" which then transmitted to humans. This claim has been widely disputed: some argued that the reservoir must be bats and the intermediate host, bird or mammal, not snakes (as snakes, unlike humans, are poikilotherms), while others used data on recombination and SARS/MERS codon usage bias refute the reasoning. The recombination event mentioned probably happened in bats instead. Phylogenetic studies of 2019-nCoV examine the evolutionary history of the virus and its relationships with other organisms. The seventh member of the family of coronaviruses that can infect humans, 2019-nCoV has been reported to have a genome sequence 75% to 80% identical to the SARS-CoV and to have more similarities to several bat coronaviruses.[54][55] At least five genomes of the novel coronavirus have been isolated and reported. These show that the virus is genetically distinct from other known coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV). Like SARS-CoV, it is a member of Beta-CoV lineage B.
A peer-reviewed paper by Domenico Benvenuto et al. describes a phylogenetic tree built from 15 available whole genome sequence of 2019-nCoV and 12 whole genome sequences of 2019-nCoV and 12 highly similar whole genome sequences available in gene bank. Genomic analysis shows that the Nucleocapsid and the Spike Glycoprotein have some sites under positive selective pressure[how?]. Homology modelling indicated certain molecular and structural differences among the viruses. The phylogenetic tree showed that 2019-nCoV significantly clustered with a Bat SARS-like Coronavirus sequence, whereas structural analysis revealed mutations in Spike Glycoprotein and nucleocapsid protein. The authors concluded 2019-nCoV is a coronavirus distinct from SARS virus that probably was transmitted from bats or another host that provided the ability to infect humans.
Coronaviruses (CoVs) belong to the subfamily Orthocoronavirinae in the family Coronaviridae and the order Nidovirales. CoVs have an enveloped, crown-like viral particle from which they were named after. The CoV genome is a positive-sense, single-strand RNA (+ssRNA), 27–32 kb in size, which is the second largest of all RNA virus genomes. Typically, two-thirds of the genomic RNA encodes for two large overlapping polyproteins, ORF1a and ORF1b, that are processed into the viral polymerase (RdRp) and other nonstructural proteins involved in RNA synthesis or host response modulation. The other third of the genome encodes for four structural proteins (spike (S), envelope (E), membrane (M), and nucleocapsid (N)) and other accessory proteins. While the ORF1a/ORF1b and the four structural proteins are relatively consistent, the length of the CoV genome is largely dependent on the number and size of accessory proteins.

Diagnosis

On 15 January 2020, the WHO published a protocol for testing for 2019-nCoV. Since then, several other testing protocols have been proposed, and published by the WHO.
Testing uses real time reverse transcription-polymerase chain reaction (rRT-PCR). The test can be done on respiratory or blood samples. Results are generally available within a few hours to days.



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