Diagnosis and monitoring of mutations in SARS-CoV-2, other viruses and opportunistic microorganisms that cause respiratory diseases in humans

The new coronavirus (SARS-CoV-2) has been identified as the cause of an outbreak of respiratory disease in Wuhan, Hubei province, China, as of December 2019 and has spread rapidly to an increasing number of countries. The World Health Organization (WHO) has declared SARS-CoV-2 infection as a pandemic. Efforts to contain the virus are underway; however, given the many uncertainties regarding the transmissibility and virulence of the virus, the effectiveness of these efforts is still unknown. Many molecular biology methods are being used for the diagnosis and surveillance of SARS-CoV-2. The detection methodology most used today is the polymerase chain reaction with reverse transcription (RT-PCR). Despite the great sensitivity, it is known that there are cases of false negatives, probably due to the loss or degradation of the viral RNA in the sampling process, or even mutation of the virus genome in the position of the primers and probes used. In addition, the demand for reagents for RT-PCR has increased considerably in the last few months, and there are not enough reagents being produced to meet global demand. The fraction of undocumented but infectious cases is a critical epidemiological feature that modulates the pandemic potential of an emerging respiratory virus. In addition, the test is specific for SARS-CoV-2, and does not test for other possible viruses that cause respiratory diseases, such as influenza. Therefore, the development of alternative methods, with high sensitivity, is essential to accompany the pandemic and the diversity of viruses and circulating strains.Next generation sequencing (NGS) provides a new and effective way to track samples and detect viruses without prior knowledge of the infectious agent. NGS strategies can provide additional confirmation, in addition to diagnosing other viruses, with strain specific discrimination in a single test. The monitoring of recurrent mutations in these viruses, including mutations in proteins responsible for the mechanism of entry into the host cell, has an impact on the understanding of pathogenicity and the composition of vaccines. The Centers for Disease Control and Prevention (CDC) in the United States annually uses information on genetic changes in influenza viruses to determine whether vaccines and antiviral drugs will work against current influenza viruses. The same monitoring should be used for the SARS-CoV-2 virus. In addition, with NGS it is possible to identify the airway microbiota and have a better prognosis for the evolution of the disease. Thus, understanding the associated microbiota can help to predict the outcome and reduce complications. Therefore, it is proposed here to use molecular biology strategies, such as new generation sequencing to diagnose viruses and bacteria that cause respiratory diseases and to monitor the mutational diversity of circulating strains. The evolution and rate of infection observed to date show an urgent need to develop public health activities to better understand the epidemiology of the new virus and characterize its potential impact on public health.