Managing Viral Emerging Infectious Diseases via Current and Future Molecular Diagnostics.

Emerging viral infectious diseases have been a constant threat to global public health in recent times. In managing these diseases, molecular diagnostics has played a critical role. Molecular diagnostics involves the use of various technologies to detect the genetic material of various pathogens, including viruses, in clinical samples. One of the most commonly used molecular diagnostics technologies for detecting viruses is polymerase chain reaction (PCR). PCR amplifies specific regions of the viral genetic material in a sample, making it easier to detect and identify viruses. PCR is particularly useful for detecting viruses that are present in low concentrations in clinical samples, such as blood or saliva. Another technology that is becoming increasingly popular for viral diagnostics is next-generation sequencing (NGS). NGS can sequence the entire genome of a virus present in a clinical sample, providing a wealth of information about the virus, including its genetic makeup, virulence factors, and potential to cause an outbreak. NGS can also help identify mutations and discover new pathogens that could affect the efficacy of antiviral drugs and vaccines. In addition to PCR and NGS, there are other molecular diagnostics technologies that are being developed to manage emerging viral infectious diseases. One of these is CRISPR-Cas, a genome editing technology that can be used to detect and cut specific regions of viral genetic material. CRISPR-Cas can be used to develop highly specific and sensitive viral diagnostic tests, as well as to develop new antiviral therapies. In conclusion, molecular diagnostics tools are critical for managing emerging viral infectious diseases. PCR and NGS are currently the most commonly used technologies for viral diagnostics, but new technologies such as CRISPR-Cas are emerging. These technologies can help identify viral outbreaks early, track the spread of viruses, and develop effective antiviral therapies and vaccines.

[Shedding of SARS-CoV-2 Virus in COVID-19 Patients and Neutralizing Antibody Level]. / COVID-19 Hastalarinda SARS-CoV-2 Virüs Saçilimi ve Nötralizan Antikor Düzeyleri.

The coronavirus disease 2019 (COVID-19) turned into a pandemic shortly after emerging in December 2019, in the city of Wuhan, China. In this study, it was aimed to investigate the presence of severe acute respiratory system coronavirus-2 (SARS-CoV-2) RNA in various clinical samples and the scattering profile of the virus and the variation of anti-SARS-CoV-2 IgG and neutralizing antibody levels over time in infected patients during and after the period of COVID-19 disease. The study included COVID-19 patients from the community (CCP) (n= 47) (May-June 2020) and healthcare workers (HCWP) (n= 30) (November-December 2020). To investigate the presence of SARS-CoV-2 in clinical samples, oropharynx (OF), nasopharynx (NF), sputum, stool, blood and urine samples were taken from the CCP group on days 0, 3, 7, 14 and 28. For the detection of anti SARS-CoV-2 IgG and neutralizing antibodies serum samples were taken from the CCP group on days 0, 3, 7, 14, 28, 60, 90 and 120 and on days 14, 28, 60, 90, 120 and 150 from HCWP group. Virus RNA was detected by reverse transcription polymerase chain reaction (RT-PCR), anti SARS-CoV-2 IgG antibody levels by enzyme-linked immunosorbent assay (ELISA), neutralizing antibody levels (NAb) by cell culture neutralization and representative neutralization test (sVNT) methods. With the onset of the vaccination program in our country, 11 of the HCWP group patients had SARS-CoV-2 vaccine after the second month serum samples were taken, the remaining HCWP group patients did not get vaccinated during the study period. SARS-CoV-2 RNA was detected with the highest rates in NF (100%), stool (65.8%), sputum (45.7%), OF (41.3%), blood (5.3%), and urine (2.2%) samples, respectively. It was found that viral shedding continued for 14 days in respiratory tract samples and up to 60 days in stool samples, and no virus was detected in blood samples after the third day. It was observed that the viral load was highest at the time of diagnosis in both upper and lower respiratory tract samples, peaking on the seventh day in stool samples and following an irregular course throughout the disease. Anti-SARS-CoV-2 IgG antibody positivity was found in 41.4% of CCP group patients on the first day of diagnosis, and seroconversion was observed in all patients at the fourth month. During the study period, seropositivity was detected in only 82.1% of the patients in the HCWP group. It was observed that the IgG antibody levels peaked at the 7th day in the CCP group patients and at the third month in the HCWP group patients (S/Co: 9.6 and 2.8, respectively). Anti-SARS-CoV-2 IgG antibody levels detected in the CCP group were found to be significantly higher than the HCWP group (p<0.05). At the end of the first month, NAb was detected in all (100%) patients in the CCP group. It was found that NAb titers peaked (1/256) on the 28th day and showed a decreasing trend from the second month. NAb median titers were observed to peak earlier in the severe HCWP group (14 days in the severe group, 28 days in the mild group, p> 0.05). It was observed that 6 (26.1%) of HCWP group patients had low, 11 (47.8%) moderate, 6 (26.1%) high titers of representative NAb. The distribution of representative NAb levels by vaccine status was examined and no statistically significant difference was found (p= 0.400, p= 0.077 and p= 0.830, respectively). As a result; SARS-CoV-2 RNA was detected in many samples such as sputum, stool, blood and urine, and it was observed that viral shedding in stool samples could continue for months. Anti-SARS-CoV-2 IgG antibody positivity was observed in most of the patients in the fourth month, and it was found that the antibody titers decreased after the third month. It was determined that protective antibody levels continued in the fourth month. These findings are important in vaccination strategies and in the fight against the pandemic. However, considering the emergence of new mutant forms of the virus in today's conditions where the pandemic continues, more detailed and comprehensive studies are needed for viral shedding and antibody titer studies.

Can prognostic nutritional index and systemic immune-inflammatory index predict disease severity in COVID-19?

BACKGROUND: Prognostic nutritional index (PNI) and systemic immune-inflammatory index (SII) are inflammation-based novel markers that predict the prognosis in various patient populations. We have investigated the relationship between the disease severity in COVID-19, and the PNI and SII scores in the present study. MATERIALS AND METHODS: This cross-sectional retrospective study included 118 hospitalised patients with a confirmed diagnosis of COVID-19. The patients were divided into two groups as those who were hospitalised at the intensive care unit (ICU) and those who had been internalised at the clinic (non-ICU). RESULTS: Of the 118 patients, 50.8% were male. The mean age was 57.7 ± 17.5 years in non-ICU patients and 70.3 ± 11.7 years in ICU patients and the difference was statistically significant (P < .001). The lymphocyte count and the albumin levels were significantly lower in ICU patients (P < .001, P < .001, respectively). The PNI score was significantly lower in ICU patients compared with non-ICU patients (P < .001). The SII score was found to be significantly higher in ICU patients compared with non-ICU patients (P < .001). The value of PNI and SII scores in prediction of the disease severity in COVID-19 was evaluated with the ROC analysis (PNI: AUC = 0.796, 95%CI: 0.715-0.877, P < .001; SII: AUC =0.689, 95% CI: 0.559-0.819, P=.004). When the cut-off value was taken as ≤36.7 for the PNI score, it was found to have 73.4% sensitivity and 70.8% specificity for predicting of the disease severity and ICU admission probability was 4.4 times higher. When the cut-off value was taken as ≥813.6 for SII score, it was found to have 70.8% sensitivity and 66.0% specificity for predicting of the disease severity and ICU admission probability was six times higher. CONCLUSION: The PNI and the SII scores are independent predictors of the prognosis and the disease severity in COVID-19 patients who require hospitalisation at the ICU.

Evaluation of the presence of SARS-COV-2 in the vaginal fluid of reproductive-aged women.

OBJECTIVES: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is mainly transmitted through respiration and direct contact. The status of the infection in the female genital system is still unknown. The study aimed to evaluate whether SARS-CoV-2 is present in the vaginal fluid of women with COVID-19 infection in reproductive period. MATERIAL AND METHODS: Women who were between the ages of 18-50 years and clinically confirmed to have COVID-19 infection at our hospital between 20 April-31 May 2020 were included in the study. Women who were in their menstrual cycle during the study and who had a known cervical intraepithelial lesion and/or cancer, sexually transmitted disease and history and/or symptoms of vaginitis were excluded from the study. In patients in whom no pathology was detected during the examination, a sample was taken from the vaginal fluid for PCR by using Dacron tip swab. Analysis was performed with Genesig Real-Time PCR COVID-19 kit (Primer Design, England). RESULTS: Eighteen women who were in reproductive period and diagnosed with severe COVID-19 pneumonia were included in the study. The mean age of the patients was 38.16 ± 8.54. None of the patients were in their menopause period. The clinical symptoms of these women were similar to those of confirmed severe COVID-19 cases. SARS-CoV-2 was found to be negative in the samples taken from the vaginal fluid in all patients. CONCLUSIONS: SARS-CoV-2 virus was not detected in the vaginal fluid of the patients who tested positive for COVID-19 in reproductive period.

Emerging technologies for the diagnosis of viral infections and SARS-CoV-2

Coronavirus disease 2019 (COVID-19) is a newly emerging infection caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). Based on the rapid increase in the rate of human infection, the World Health Organization (WHO) has classified the COVID-19 outbreak as a pandemic. Considering that there is no specific drug or vaccine yet for COVID-19, effective rapid diagnosis of viruses has become very important in terms of early detection and control of the outbreak. The routine difficulties of isolating the virus necessitated the diagnosis to be made with more serological tests for many years. However, in recent years, molecular tests that provide fast and high-quality viral diagnosis information have started to take their place in laboratories. Syndrome-based PCR tests after PCR and multiplex PCR tests are also approaches that question the direct factor and accelerate the diagnosis and treatment. LAMP PCR technology has also developed rapidly, and the diagnosis time has been shortened in the field or at the bedside with very small portable devices. As a new technology, CRISPR diagnostic methods and portable DNA sequencing devices will be very useful in the diagnosis of viral infections in the clinic for rapid results per patient. With immunoprecipitation systems using luciferase-labeled antigens, virus identification, quantitation, antiviral efficacy can be monitored. COVID-19 outbreak management increased the need for very fast and reliable tests and triggered the laboratory biotechnology industry. The entire world is experiencing a dynamic pandemic process in which the benefits of new, highly sensitive, accessible and portable identification methods will be tested. The presence of a large number of applications in the approval process for these methods provides strong evidence that SARS-CoV-2 diagnostic algorithms will have richer and productive solutions in the near future. Experiences will be guiding in better understanding of other viral infections, establishing bedside diagnostic solutions, providing more effective treatments.