Short Communication on Coronavirus 2019-CoV
Why Real Time PCR gives false negative results for clinically confirmed corona patients?
Zahir Abbas Hilmi
*Department of Biocheistry and Molecular Biology, Faculty of Science, Gezira University
* Medicine Program, Napata College
In November, 2002, an epidemic caused by a novel Betacoronavirus – SARS –CoV emerged in Guangdong, southern China. SARS or severe acute respiratory syndrome, resulted in more than 8000 human infections and 774 deaths in 37 countries during 2002–03.
In 2012, the Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV), which was first detected in Saudi Arabia. MERS infected 2494 patients and kills 858 since September, 2012, including 38 deaths following a single introduction into South Korea.
In 2019 December, a new human-infecting betacoronavirus 2019-nCoV pandemic started in Wuhan in China. 2019-nCoV is sufficiently divergent from SARS-CoV . The phylogenetic analysis suggests that bats might be the original host of this virus (Lu et. al., 2020). The bats were likely to be the reservoir for 2019-nCoV as it is most closely related to other betacoronaviruses of bat origin.
The new pandemic 2019- CoVID started in December 2019 and up to 24 March 2020, within 67 days the number of infected patients in 196 countries was 410,213 , with 18,266 deaths, 107,182 recovered. The new pandemic now is out of control and the numbers of victims increased in a logarithmic way.
The coronavirus epidemic in the world started in Wuhan in China, caused by a new novel type of the Family Coronaviride the 2019 nCoV. According to Baltimore’s nucleic acid based taxonomy of viruses, members of Coronaviridae belonged to Group IV positive single stranded RNA viruses (+ssRNA). Coronavirus is the largest RNA viruses their genome ranged from 26000bp to 32000bp . The Coronaviridae genome is replicated by RNA dependant RNA polymerase , that induce more mutations 1 in every 1000 base pairs.
The complete genome sequences of the novel virus 2019-nCoV was 29,844 bp and was compared to genome other coronaviruses ( Lu et. al., 2020). The genome sequence of 2019-nCoV is most closely related (87.237 %) to two bats coronovirus that collected 2018 in Zhoushan, eastern China ; Bats- SL-CoVZC45 (29732bp) and bat-SL-CoVZXC21 . 2019-nCoV is less genetically similar to SARS- CoV (79%); with a genome of 29751bp. 2019-CoV The genome of MERS-CoV (30,119 bp) was found to be the least related 50% to 2019- CoV.
Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, Accordingly, the realtime PCR kits or other immunodiagnostic kits might not be able to detect the new virus with high percentages of false negatives due to sequence variation.
Diagnosis of 2019 nC0VID is very important to find out the first few cases and to isolate them, to prevent unchecked community spread. Confirmation of clinical diagnosis and follow up of viral load in patients before and after treatment, to ensure complete cure.
Many scientific reports showed that early Chinese may have had false negative rate as high as 50%. In USA many test kits released by the CDC on Feb.2020 were defective. Accordingly, the magnitude of this epidemic is still unknown. Also lower numbers of people were tested.