According to WHO, viruses are continuing to emerge and has been posing challenges to public health. The emerging viruses that of 2002: Severe Acute Respiratory Syndrome coronavirus (SARS-CoV)), 2009: H1N1 influenza, 2012: Middle East Respiratory Syndrome coronavirus (MERS-CoV) and recently 2019: Novel coronavirus (COVID-19) are such viruses which has caused human existence nearly to its dead end. Viruses are acellular infectious entities capable of surviving only in a specific host utilizing the protein synthetic machinery. Hence, they are called as obligatory parasites having no existence outside living host.
WHO says that 70-80% of emerging and re-emerging infectious disease are known to be of zoonotic origin. It means they have been transmitted between animals and humans. The factors like population growth, climate change, increasing urbanization and international travel and migration all increase the risk of emergence and spread of respiratory pathogens. COVID-19 is one of them. COVID-19 belongs to family of coronaviruses that exhibits illness ranging from the common cold to more severe diseases (as for instances, MERS and SARS). SARS-CoV was transmitted from civet cats to human in China in 2002 and MERS-CoV from dromedary camels to humans in Saudi Arabia in 2012. However, several coronaviruses are circulating in animals that have not yet infected humans. A spillover event is when a virus that is circulating in an animal species is found to have been transmitted to human(s).
An infection can be laboratory-confirmed by detection of viral nuclei acid or possibly using serology to demonstrate antibodies. In case of COVID-19, viral nuclei acid detection by Polymerase Chain Reaction (PCR) offers promising method to diagnose with higher sensitivity and specificity. The specimen for the PCR involves the specimen collected from lower respiratory and upper respiratory tract. However, nasophryngeal and orophryangeal swabs taken from upper respiratory tract can be utilized to the patients with (within 14 days) or without any symptoms.
All health-care workers who collect specimens from patients suspected or confirmed to be infected with the COVID-19 virus must wear personal protective equipment (PPE). All those involved in collection and transporting specimen should be trained in safe handling practices and decontamination procedure. The specimen should be stored and shipped to laboratory maintaining 4 degree centigrade in less than 72 hours. However, when delay of more than 72 hours is anticipated, the specimen should be stored at minus 80 degree centigrade and shipped on dry ice or liquid nitrogen to the laboratory.
Sometimes, negative results might be obtained from an infected individuals due to poor quality of the specimen, late or very early collection, improper handling and shipping , techinical reasons inherent in the test (e.g. virus mutation or PCR inhibition), etc. According to WHO, laboratories that have not validated their capacity to detect coronavirus should send the first 5 positive and the first 10 negative samples to one of the international reference laboratories. Retesting for the highly suspicious cases need to be done by collecting new specimen including some from the lower respiratory tract (if possible).
A high throughput technology called real-time Reverse-Trascriptase-Polymerase Chain Reaction (RT-PCR) detects the COVID-19 infection utilizing primers and probes. The specific primers detect the marker genes viz. RdRP gene (encodes RNA dependent RNA polymerase enzyme), E gene (encodes envelope protein) and N gene (encodes nucleocapsid protein). The RdRP gene primers should be specific to detect 2019-nCoV without detecting SARS-CoV and bat-SARS-related CoV (Corman et al 2020). Detection of SARS-CoV-2 (COVID-19) infection is done by sequential steps. Firstly, RNA isolation of specimen from upper and lower respiratory tract is done followed by its purification. Reverse transcription of the purified single-stranded RNA to double stranded chromosomal DNA (cDNA) is done. The cDNA is further amplified with Real-Time PCR instrument which uses the aforementioned primers. The probes present in the master mix will fluorescence giving electronic signals for amplication of viral genes. Thus, detection of COVID-19 is done.
Sometimes, negative results might be obtained from an infected individuals due to poor quality of the specimen, late or very early collection, improper handling and shipping , techinical reasons inherent in the test (e.g. virus mutation or PCR inhibition), etc. According to WHO, laboratories that have not validated their capacity to detect coronavirus should send the first 5 positive and the first 10 negative samples to one of the international reference laboratories. Retesting for the highly suspicious cases need to be done by collecting new specimen including some from the lower respiratory tract (if possible).
A high throughput technology called real-time Reverse-Trascriptase-Polymerase Chain Reaction (RT-PCR) detects the COVID-19 infection utilizing primers and probes. The specific primers detect the marker genes viz. RdRP gene (encodes RNA dependent RNA polymerase enzyme), E gene (encodes envelope protein) and N gene (encodes nucleocapsid protein). The RdRP gene primers should be specific to detect 2019-nCoV without detecting SARS-CoV and bat-SARS-related CoV (Corman et al 2020). Detection of SARS-CoV-2 (COVID-19) infection is done by sequential steps. Firstly, RNA isolation of specimen from upper and lower respiratory tract is done followed by its purification. Reverse transcription of the purified single-stranded RNA to double stranded chromosomal DNA (cDNA) is done. The cDNA is further amplified with Real-Time PCR instrument which uses the aforementioned primers. The probes present in the master mix will fluorescence giving electronic signals for amplication of viral genes. Thus, detection of COVID-19 is done.
Further reading:
> Coronaviruses http://www.who.int/emergencies/diseases/novel-coronavirus-2019
> Guidance and tools: Laboratory guidance for COVID-19
http://www.who.int/health-topics/coronavirus/laboratory-diagnostics-for-novel-coronavirus
> Corman, V. M., Landt, O., Kaiser, M., Molenkamp, R., Meijer, A., Chu, D., Bleicker, T., Brünink, S., Schneider, J., Schmidt, M. L., Mulders, D., Haagmans, B. L., van der Veer, B., van den Brink, S., Wijsman, L., Goderski, G., Romette, J. L., Ellis, J., Zambon, M., Peiris, M., … Drosten, C. (2020). Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25(3), 2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045
> Guidance and tools: Laboratory guidance for COVID-19
http://www.who.int/health-topics/coronavirus/laboratory-diagnostics-for-novel-coronavirus
> Corman, V. M., Landt, O., Kaiser, M., Molenkamp, R., Meijer, A., Chu, D., Bleicker, T., Brünink, S., Schneider, J., Schmidt, M. L., Mulders, D., Haagmans, B. L., van der Veer, B., van den Brink, S., Wijsman, L., Goderski, G., Romette, J. L., Ellis, J., Zambon, M., Peiris, M., … Drosten, C. (2020). Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, 25(3), 2000045. https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045
No comments:
Post a Comment