SARS-CoV-2 is a novel coronavirus that causes a potentially fatal respiratory disease known as coronavirus disease (COVID-19) and is responsible for the ongoing pandemic with increasing mortality. Understanding the host-virus interaction involved in SARS-CoV-2 pathophysiology will enhance our understanding of the mechanistic basis of COVID-19 infection. The characterization of post-transcriptional gene regulatory networks, particularly pre-mRNA splicing, and the identification and characterization of host proteins interacting with the 5' and 3'UTRs of SARS-CoV-2 will improve our understanding of post-transcriptional gene regulation during SARS-CoV-2 pathogenesis. Here, we demonstrate that either SARS-CoV-2 infection or exogenous overexpression of the 5' and 3'UTRs of the viral genomic RNAs, results in reduced mRNA levels possibly due to modulation of host cell pre-mRNA splicing. Further, we have investigated the potential RNA-binding proteins interacting with the 5' and 3'UTRs, using in-silico approaches. Our results suggest that 5' and 3'UTRs indeed interact with many RNA-binding proteins. Our results provide a primer for further investigations into the UTR-mediated regulation of splicing and related molecular mechanisms in host cells.
{"title":"The SARS-CoV-2 UTR's Intrudes Host RBP's and Modulates Cellular Splicing.","authors":"Anjali Singh, Kush Kumar Pandey, Shubham Kumar Agrawal, Rupesh K Srivastava, Sankar Bhattacharyya, Bhupendra Verma","doi":"10.1155/2023/2995443","DOIUrl":"https://doi.org/10.1155/2023/2995443","url":null,"abstract":"<p><p>SARS-CoV-2 is a novel coronavirus that causes a potentially fatal respiratory disease known as coronavirus disease (COVID-19) and is responsible for the ongoing pandemic with increasing mortality. Understanding the host-virus interaction involved in SARS-CoV-2 pathophysiology will enhance our understanding of the mechanistic basis of COVID-19 infection. The characterization of post-transcriptional gene regulatory networks, particularly pre-mRNA splicing, and the identification and characterization of host proteins interacting with the 5' and 3'UTRs of SARS-CoV-2 will improve our understanding of post-transcriptional gene regulation during SARS-CoV-2 pathogenesis. Here, we demonstrate that either SARS-CoV-2 infection or exogenous overexpression of the 5' and 3'UTRs of the viral genomic RNAs, results in reduced mRNA levels possibly due to modulation of host cell pre-mRNA splicing. Further, we have investigated the potential RNA-binding proteins interacting with the 5' and 3'UTRs, using <i>in-silico</i> approaches. Our results suggest that 5' and 3'UTRs indeed interact with many RNA-binding proteins. Our results provide a primer for further investigations into the UTR-mediated regulation of splicing and related molecular mechanisms in host cells.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"2995443"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10098413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9318480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Due to the coronavirus disease 2019 (COVID-19), researchers all over the world have tried to find an appropriate therapeutic approach for the disease. The angiotensin-converting enzyme 2 (ACE2) has been shown as a necessary receptor to cell fusion, which is involved in infection due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is commonly crucial for all organs and systems. When ACE2 is downregulated via the SARS-CoV-2 spike protein, it results in the angiotensin II (Ang II)/angiotensin type 1 receptor axis overactivation. Ang II has harmful effects, which can be evidenced by dysfunctions in many organs experienced by COVID-19 patients. ACE2 is the SARS-CoV-2 receptor and has an extensive distribution; thus, some COVID-19 cases experience several symptoms and complications. We suggest strategy for the potential protective effect of ACE2 to the viral infection. The current review will provide data to develop new approaches for preventing and controlling the COVID-19 outbreak.
{"title":"The Protective Potential Role of ACE2 against COVID-19.","authors":"Fereshteh Golab, Gelareh Vahabzadeh, Leila SadeghRoudbari, Arefeh Shirazi, Robabeh Shabani, Sara Tanbakooei, Lida Kooshesh","doi":"10.1155/2023/8451931","DOIUrl":"https://doi.org/10.1155/2023/8451931","url":null,"abstract":"<p><p>Due to the coronavirus disease 2019 (COVID-19), researchers all over the world have tried to find an appropriate therapeutic approach for the disease. The angiotensin-converting enzyme 2 (ACE2) has been shown as a necessary receptor to cell fusion, which is involved in infection due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is commonly crucial for all organs and systems. When ACE2 is downregulated via the SARS-CoV-2 spike protein, it results in the angiotensin II (Ang II)/angiotensin type 1 receptor axis overactivation. Ang II has harmful effects, which can be evidenced by dysfunctions in many organs experienced by COVID-19 patients. ACE2 is the SARS-CoV-2 receptor and has an extensive distribution; thus, some COVID-19 cases experience several symptoms and complications. We suggest strategy for the potential protective effect of ACE2 to the viral infection. The current review will provide data to develop new approaches for preventing and controlling the COVID-19 outbreak.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"8451931"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10238138/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9582656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The monkeypox virus was still spreading in May 2022, with the first case identified in a person with travel ties to Nigeria. Using molecular docking-based techniques, we evaluated the efficiency of different bioactive chemicals obtained from plants against the monkeypox virus. A total of 56 plant compounds were evaluated for antimonekypox capabilities, with the top four candidates having a higher binding affinity than the control. We targeted the monkeypox profilin-like protein, which plays a key role in viral replication and assembly. Among the metabolites, curcumin showed the strongest binding affinity with a value of -37.43 kcal/mol, followed by gedunin (-34.89 kcal/mol), piperine (-34.58 kcal/mol), and coumadin (-34.14 kcal/mol). Based on ADME and toxicity assessments, the top four substances had no negative impacts. Furthermore, four compounds demonstrated resistance to deformability, which was corroborated by normal mode analysis. According to the bioactivity prediction study, the top compound target class was an enzyme, membrane receptor, and oxidoreductase. Furthermore, the study discovered that wortmannin, a gedunin analogue, can behave as an orthopoxvirus. The study found that these bioactive natural drug candidates could potentially work as monkeypox virus inhibitors. We recommended further experimental validation to confirm the promising findings of the study.
{"title":"Therapeutic Promises of Plant Metabolites against Monkeypox Virus: An In Silico Study.","authors":"Anik Banik, Sheikh Rashel Ahmed, Sonia Binte Shahid, Tufayel Ahmed, Hafaza Khandaker Tamanna, Hlamrasong Marma","doi":"10.1155/2023/9919776","DOIUrl":"https://doi.org/10.1155/2023/9919776","url":null,"abstract":"<p><p>The monkeypox virus was still spreading in May 2022, with the first case identified in a person with travel ties to Nigeria. Using molecular docking-based techniques, we evaluated the efficiency of different bioactive chemicals obtained from plants against the monkeypox virus. A total of 56 plant compounds were evaluated for antimonekypox capabilities, with the top four candidates having a higher binding affinity than the control. We targeted the monkeypox profilin-like protein, which plays a key role in viral replication and assembly. Among the metabolites, curcumin showed the strongest binding affinity with a value of -37.43 kcal/mol, followed by gedunin (-34.89 kcal/mol), piperine (-34.58 kcal/mol), and coumadin (-34.14 kcal/mol). Based on ADME and toxicity assessments, the top four substances had no negative impacts. Furthermore, four compounds demonstrated resistance to deformability, which was corroborated by normal mode analysis. According to the bioactivity prediction study, the top compound target class was an enzyme, membrane receptor, and oxidoreductase. Furthermore, the study discovered that wortmannin, a gedunin analogue, can behave as an orthopoxvirus. The study found that these bioactive natural drug candidates could potentially work as monkeypox virus inhibitors. We recommended further experimental validation to confirm the promising findings of the study.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"9919776"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10492655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10225164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Khalid Edderdouri, Hakima Kabbaj, Leila Laamara, Noureddine Lahmouddi, Oumayma Lamdarsi, Amal Zouaki, Ghizlane El Amin, Jalila Zirar, Myriam Seffar
Respiratory viruses are the most involved pathogens in acute respiratory infections. During the COVID-19 pandemic, new elements have been brought to this topic, especially at the diagnostic and therapeutic level. The objective of this work is to describe the epidemiology of respiratory viruses in patients admitted to the Ibn Sina University Hospital of Rabat during a period characterized by the emergence and spread of SARS-CoV-2. We conducted a retrospective study from January 1 to December 31. We included all patients treated for acute respiratory infection and for whom a multiplex respiratory panel PCR was requested. Virus detection was performed using a FilmArray RP 2.1 plus BioFire multiplex respiratory panel. The study population was relatively adults with a mean age of 39 years. The sex ratio M/F was 1.20. The survey revealed a high prevalence of 42.3% of patients hospitalized in the adult intensive care unit whose respiratory distress was the most common reason for hospitalization (58%). The positivity rate was 48.1%. This rate was higher in the pediatric population 83.13% compared to adults 29.7%. Monoinfection was found in 36.4% of cases, and codetection in 11.7% of cases. This survey revealed that a total of 322 viruses were detected, HRV being the most incriminated virus (48.7%), followed by RSV in 13.8% of patients. Considering the five most detected viruses in our study (HRV, RSV, PIV3, ADV, and hMPV), we found that the incidence was significantly higher in the pediatric population. SARS-CoV-2 was detected only in adult's population. In our study, we found that influenza A and B viruses, PIV2, MERS, and all bacteria were not detected by this kit during the study period. Regarding the seasonal distribution, RSV and hMPV showed a significantly high incidence during autumn and summer and SARS-CoV-2 and CoV OC43 showed a high peak during winter. In this study, we found a lack of detection of influenza virus and a shift in the usual winter peak of RSV to the summer, while the detection of ADV and HRV was less affected. This difference in detection could be due on the one hand to the difference in stability between enveloped and nonenveloped viruses and on the other hand to the escape of certain viruses to the different sanitary measures introduced after the declaration of the COVID-19 pandemic. These same measures were effective against enveloped viruses such as RSV and influenza viruses. The emergence of SARS-CoV-2 has modified the epidemiology of other respiratory viruses, either directly by viral interference or indirectly by the preventive measures taken.
呼吸道病毒是急性呼吸道感染中最常见的病原体。在2019冠状病毒病大流行期间,这一主题被纳入了新的内容,特别是在诊断和治疗层面。这项工作的目的是描述在以SARS-CoV-2的出现和传播为特征的时期,拉巴特伊本西纳大学医院收治的患者呼吸道病毒的流行病学。我们从1月1日至12月31日进行了回顾性研究。我们纳入了所有因急性呼吸道感染而接受治疗并要求多重呼吸面板PCR的患者。采用FilmArray RP 2.1 + BioFire多路呼吸面板进行病毒检测。研究人群相对成年,平均年龄39岁。性别比M/F为1.20。调查显示,在成人重症监护病房住院的患者中,呼吸窘迫是最常见的住院原因(58%),患病率高达42.3%。阳性率为48.1%。这一比例在儿科人群中较高,为83.13%,而成人为29.7%。单例感染占36.4%,共检占11.7%。本次调查共检出322种病毒,HRV是最常见的病毒(48.7%),其次是RSV(13.8%)。考虑到我们研究中检测最多的五种病毒(HRV、RSV、PIV3、ADV和hMPV),我们发现儿科人群的发病率明显更高。SARS-CoV-2仅在成人人群中检测到。在我们的研究中,我们发现该试剂盒在研究期间未检测到甲型流感病毒和乙型流感病毒、PIV2病毒、MERS病毒和所有细菌。从季节分布来看,RSV和hMPV在秋季和夏季高发,SARS-CoV-2和CoV OC43在冬季高发。在本研究中,我们发现流感病毒检测不足,RSV通常的冬季高峰转移到夏季,而ADV和HRV的检测受影响较小。这种检测结果的差异,一方面是因为包膜病毒和非包膜病毒的稳定性不同,另一方面是因为在宣布为新冠肺炎大流行后,采取了不同的卫生措施,某些病毒得以逃脱。同样的措施对诸如RSV和流感病毒等包膜病毒也有效。SARS-CoV-2的出现或通过病毒的直接干扰,或通过采取预防措施间接改变了其他呼吸道病毒的流行病学。
{"title":"Contribution of the FilmArray BioFire® Technology in the Diagnosis of Viral Respiratory Infections during the COVID-19 Pandemic at Ibn Sina University Hospital Center in Rabat: Epidemiological Study about 503 Cases.","authors":"Khalid Edderdouri, Hakima Kabbaj, Leila Laamara, Noureddine Lahmouddi, Oumayma Lamdarsi, Amal Zouaki, Ghizlane El Amin, Jalila Zirar, Myriam Seffar","doi":"10.1155/2023/2679770","DOIUrl":"https://doi.org/10.1155/2023/2679770","url":null,"abstract":"<p><p>Respiratory viruses are the most involved pathogens in acute respiratory infections. During the COVID-19 pandemic, new elements have been brought to this topic, especially at the diagnostic and therapeutic level. The objective of this work is to describe the epidemiology of respiratory viruses in patients admitted to the Ibn Sina University Hospital of Rabat during a period characterized by the emergence and spread of SARS-CoV-2. We conducted a retrospective study from January 1 to December 31. We included all patients treated for acute respiratory infection and for whom a multiplex respiratory panel PCR was requested. Virus detection was performed using a FilmArray RP 2.1 plus BioFire multiplex respiratory panel. The study population was relatively adults with a mean age of 39 years. The sex ratio M/F was 1.20. The survey revealed a high prevalence of 42.3% of patients hospitalized in the adult intensive care unit whose respiratory distress was the most common reason for hospitalization (58%). The positivity rate was 48.1%. This rate was higher in the pediatric population 83.13% compared to adults 29.7%. Monoinfection was found in 36.4% of cases, and codetection in 11.7% of cases. This survey revealed that a total of 322 viruses were detected, HRV being the most incriminated virus (48.7%), followed by RSV in 13.8% of patients. Considering the five most detected viruses in our study (HRV, RSV, PIV3, ADV, and hMPV), we found that the incidence was significantly higher in the pediatric population. SARS-CoV-2 was detected only in adult's population. In our study, we found that influenza A and B viruses, PIV2, MERS, and all bacteria were not detected by this kit during the study period. Regarding the seasonal distribution, RSV and hMPV showed a significantly high incidence during autumn and summer and SARS-CoV-2 and CoV OC43 showed a high peak during winter. In this study, we found a lack of detection of influenza virus and a shift in the usual winter peak of RSV to the summer, while the detection of ADV and HRV was less affected. This difference in detection could be due on the one hand to the difference in stability between enveloped and nonenveloped viruses and on the other hand to the escape of certain viruses to the different sanitary measures introduced after the declaration of the COVID-19 pandemic. These same measures were effective against enveloped viruses such as RSV and influenza viruses. The emergence of SARS-CoV-2 has modified the epidemiology of other respiratory viruses, either directly by viral interference or indirectly by the preventive measures taken.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"2679770"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10299880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9734942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The rising cases of human papillomavirus (HPV) infection and cervical cancer cases in Nigeria are alarming. Only a few studies have looked at secondary school students in Nigeria's understanding of HPV infection and vaccine acceptance, whereas earlier studies have mostly focused on screening. In this study, 400 students from two secondary schools in Kano State, Nigeria, were engaged with the aim of assessing their level of knowledge and attitudes regarding HPV infection. The study further seeks to understand the respondent's opinion on HPV vaccination and sensitize them to the health effects of HPV infection, thereby communicating the findings to the authorities concerned with policy making. The study revealed that only 128 (32%) and 142 (35.5%) respondents have knowledge about HPV and cervical cancer, respectively. Furthermore, none of the respondents were administered the HPV vaccine, with 81% of them not ready to take the vaccine. It was observed that the majority of the respondents (91%) believed that early hospital visits could help in mitigating HPV or cervical cancer cases. Following their sensitization, the respondents were observed to have different levels of satisfaction, ranging from very satisfied and satisfied to not satisfied. Effective awareness creation amongst students as well as parents is therefore essential in HPV vaccination projects, as well as in reducing the burden of cervical cancer in Nigeria.
{"title":"Knowledge and Attitude towards Human Papilloma Virus Infection, Vaccines, and Cervical Cancer Prevention among School Students in Kano, Nigeria.","authors":"Ismail Rabiu, Zainab Yahuza","doi":"10.1155/2023/2803420","DOIUrl":"https://doi.org/10.1155/2023/2803420","url":null,"abstract":"<p><p>The rising cases of human papillomavirus (HPV) infection and cervical cancer cases in Nigeria are alarming. Only a few studies have looked at secondary school students in Nigeria's understanding of HPV infection and vaccine acceptance, whereas earlier studies have mostly focused on screening. In this study, 400 students from two secondary schools in Kano State, Nigeria, were engaged with the aim of assessing their level of knowledge and attitudes regarding HPV infection. The study further seeks to understand the respondent's opinion on HPV vaccination and sensitize them to the health effects of HPV infection, thereby communicating the findings to the authorities concerned with policy making. The study revealed that only 128 (32%) and 142 (35.5%) respondents have knowledge about HPV and cervical cancer, respectively. Furthermore, none of the respondents were administered the HPV vaccine, with 81% of them not ready to take the vaccine. It was observed that the majority of the respondents (91%) believed that early hospital visits could help in mitigating HPV or cervical cancer cases. Following their sensitization, the respondents were observed to have different levels of satisfaction, ranging from very satisfied and satisfied to not satisfied. Effective awareness creation amongst students as well as parents is therefore essential in HPV vaccination projects, as well as in reducing the burden of cervical cancer in Nigeria.</p>","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":"2023 ","pages":"2803420"},"PeriodicalIF":2.2,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9833909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10527343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mpho Magwalivha, J. K. Ngandu, A. Traoré, N. Potgieter
Background Viral diarrhoea is a concern in acute gastroenteritis cases among children younger than 5 years of age. Sapovirus has been noted as an emerging causative agent of acute gastroenteritis worldwide. Objective/Study Design. The aim of this study was to characterize human sapoviruses targeting the VP1 (NVR and N-terminal) region. Twenty-five samples were randomly selected from 40 sapovirus-positive samples previously detected and analyzed for the VP1 region using the One-Step RT-PCR assay. The PCR products were subjected to Sanger sequencing analysis. Results The polyprotein segment (NVR and N-terminal) was successfully amplified from 10/25 samples. Sapovirus GI.1 was the most predominant strain (6/10; 60%), followed by SV-GII.1 (2/10; 20%) and 10% of each GI.3 and GII.3. Conclusion Through the partial analysis of the VP1 region, this study provides more data to add on the human sapovirus genetic characterization of circulating strains in South Africa, with the proposition of further analysis of sapovirus VP1 fragments for the viral structure and function.
{"title":"Partial Analysis of the Capsid Protein (VP1) of Human Sapovirus Isolated from Children with Diarrhoea in Rural Communities of South Africa","authors":"Mpho Magwalivha, J. K. Ngandu, A. Traoré, N. Potgieter","doi":"10.1155/2022/9928378","DOIUrl":"https://doi.org/10.1155/2022/9928378","url":null,"abstract":"Background Viral diarrhoea is a concern in acute gastroenteritis cases among children younger than 5 years of age. Sapovirus has been noted as an emerging causative agent of acute gastroenteritis worldwide. Objective/Study Design. The aim of this study was to characterize human sapoviruses targeting the VP1 (NVR and N-terminal) region. Twenty-five samples were randomly selected from 40 sapovirus-positive samples previously detected and analyzed for the VP1 region using the One-Step RT-PCR assay. The PCR products were subjected to Sanger sequencing analysis. Results The polyprotein segment (NVR and N-terminal) was successfully amplified from 10/25 samples. Sapovirus GI.1 was the most predominant strain (6/10; 60%), followed by SV-GII.1 (2/10; 20%) and 10% of each GI.3 and GII.3. Conclusion Through the partial analysis of the VP1 region, this study provides more data to add on the human sapovirus genetic characterization of circulating strains in South Africa, with the proposition of further analysis of sapovirus VP1 fragments for the viral structure and function.","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47688527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
O. Morais, Manuel Rui Azevedo Alves, Paulo Fernandes
The use of saliva directly as a specimen to detect viral RNA by RT-PCR has been tested for a long time as its advantages are relevant in terms of convenience and costs. However, as other body fluids, its proven inhibition effect on the amplification reaction can be troublesome and compromise its use in the detection of viral particles. The aim of the present work is to demonstrate that saliva pretreatment may influence the RT-PCR amplification of three gene targets of SARS-CoV-2 significantly. A pool of RNA from confirmed COVID-19 patients was used to test the influence of heat pretreatment of saliva samples at 95°C for 5, 10, 15 and 20 min on the amplification performance of ORF1ab, E, and N SARS-CoV-2 genes. Prolonged heating at 95°C significantly improves the Ct value shift, usually observed in the presence of saliva, increasing the limit of detection of viral genes ORF1ab, E, and N. When tested using a cohort of COVID-19 patients' saliva, the increased time of heat pretreatment resulted in a significant increase in the detection sensitivity.
{"title":"Impact of Thermal Pretreatment of Saliva on the RT-PCR Detection of SARS-CoV-2","authors":"O. Morais, Manuel Rui Azevedo Alves, Paulo Fernandes","doi":"10.1155/2022/7442907","DOIUrl":"https://doi.org/10.1155/2022/7442907","url":null,"abstract":"The use of saliva directly as a specimen to detect viral RNA by RT-PCR has been tested for a long time as its advantages are relevant in terms of convenience and costs. However, as other body fluids, its proven inhibition effect on the amplification reaction can be troublesome and compromise its use in the detection of viral particles. The aim of the present work is to demonstrate that saliva pretreatment may influence the RT-PCR amplification of three gene targets of SARS-CoV-2 significantly. A pool of RNA from confirmed COVID-19 patients was used to test the influence of heat pretreatment of saliva samples at 95°C for 5, 10, 15 and 20 min on the amplification performance of ORF1ab, E, and N SARS-CoV-2 genes. Prolonged heating at 95°C significantly improves the Ct value shift, usually observed in the presence of saliva, increasing the limit of detection of viral genes ORF1ab, E, and N. When tested using a cohort of COVID-19 patients' saliva, the increased time of heat pretreatment resulted in a significant increase in the detection sensitivity.","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44553794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Tazi, H. Kabbaj, Jalila Zirar, Amal Zouaki, Ghizlane El Amin, Othman El Himeur, M. Seffar
Background RT-PCR is the gold standard for COVID-19 diagnosis, but the lack of standardization of assays, whose diagnostic performance may widely vary, complicates the interpretation of the discrepancies that may be encountered. Study design. We conducted a retrospective study over a ten-month period at the Central Laboratory of Virology of Ibn Sina University Hospital of Rabat. We included nasopharyngeal swabs, positive and negative for SARS-CoV-2 on FilmArray BioFire® Respiratory Panel 2.1 Plus, which were subjected to our laboratory's reference test, MAScIR SARS-CoV-2 M kit 2.0, initially or after a freeze-thaw cycle. The results were compared, and each discrepant sample with sufficient volume underwent the third test, using ARGENE® SARS-CoV-2 R-GENE kit. Results Of 80 SARS-CoV-2 negative samples on FilmArray, there were no discordant results, whereas of 80 SARS-CoV-2 positive samples on FilmArray, 21 had discordant results on MAScIR, and only 11 could be tested on ARGENE, revealing positive results in 6 cases. 12.7% and 76.5% correspond to the discordance rates for MAScIR (with one or both targets detected on FilmArray), while 14.3% and 100% correspond to those of ARGENE. As the estimated sensitivity and specificity of FilmArray, compared with MAScIR, were 100% and 79.2%, respectively, its lower limit of detection, and ARGENE assay results, made it difficult to distinguish between false positives on FilmArray and false negatives on MAScIR without further investigations. Conclusion The implementation of a new assay in our laboratory revealed discrepancies suggesting a lack of sensitivity of our laboratory's reference test, leading us consequently to retain the SARS-CoV-2 positive result of these discordant samples on FilmArray, regardless of the detection of one or both targets. Our study, which is, to our knowledge, the first comparing FilmArray RP2.1 and MAScIR 2.0 assays for SARS-CoV-2 detection, highlights the urgent need to standardize RT-PCR assays for COVID-19 diagnosis.
{"title":"Comparative Performance Evaluation of FilmArray BioFire RP2.1 and MAScIR 2.0 Assays for SARS-CoV-2 Detection","authors":"S. Tazi, H. Kabbaj, Jalila Zirar, Amal Zouaki, Ghizlane El Amin, Othman El Himeur, M. Seffar","doi":"10.1155/2022/4510900","DOIUrl":"https://doi.org/10.1155/2022/4510900","url":null,"abstract":"Background RT-PCR is the gold standard for COVID-19 diagnosis, but the lack of standardization of assays, whose diagnostic performance may widely vary, complicates the interpretation of the discrepancies that may be encountered. Study design. We conducted a retrospective study over a ten-month period at the Central Laboratory of Virology of Ibn Sina University Hospital of Rabat. We included nasopharyngeal swabs, positive and negative for SARS-CoV-2 on FilmArray BioFire® Respiratory Panel 2.1 Plus, which were subjected to our laboratory's reference test, MAScIR SARS-CoV-2 M kit 2.0, initially or after a freeze-thaw cycle. The results were compared, and each discrepant sample with sufficient volume underwent the third test, using ARGENE® SARS-CoV-2 R-GENE kit. Results Of 80 SARS-CoV-2 negative samples on FilmArray, there were no discordant results, whereas of 80 SARS-CoV-2 positive samples on FilmArray, 21 had discordant results on MAScIR, and only 11 could be tested on ARGENE, revealing positive results in 6 cases. 12.7% and 76.5% correspond to the discordance rates for MAScIR (with one or both targets detected on FilmArray), while 14.3% and 100% correspond to those of ARGENE. As the estimated sensitivity and specificity of FilmArray, compared with MAScIR, were 100% and 79.2%, respectively, its lower limit of detection, and ARGENE assay results, made it difficult to distinguish between false positives on FilmArray and false negatives on MAScIR without further investigations. Conclusion The implementation of a new assay in our laboratory revealed discrepancies suggesting a lack of sensitivity of our laboratory's reference test, leading us consequently to retain the SARS-CoV-2 positive result of these discordant samples on FilmArray, regardless of the detection of one or both targets. Our study, which is, to our knowledge, the first comparing FilmArray RP2.1 and MAScIR 2.0 assays for SARS-CoV-2 detection, highlights the urgent need to standardize RT-PCR assays for COVID-19 diagnosis.","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46257292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abdeally Mohammed, T. R. Chibssa, Waktole Terfa, F. Aklilu, Delesa Damena, Redeat Belayneh, Menbere Kidane
Peste des petits ruminants (PPR) is one of the most important transboundary diseases of small ruminants. In this study, nasal and oral swabs (n = 24) were collected from sheep (n = 7) and goats (n = 17) with clinical signs in southern Ethiopia in March 2020. PPR virus was isolated on Vero dog cells expressing the signaling lymphocyte activation molecule (VDS) and screened using RT-qPCR. Positive samples were confirmed by conventional RT-PCR followed by sequencing of a partial nucleoprotein (N) gene segment. Results revealed that 54% (n = 13/24) of the tested samples were PPRV-positive Phylogenetic analysis revealed that the viruses belonged to lineage IV and lineage II. The lineage IV viruses were similar, although not identical, to other lineage IV viruses previously reported in Ethiopia and other East African countries while the lineage II viruses have been reported for the first time in Ethiopia showed a high nucleotide identity (99.06%) with the vaccine (Nigeria 75/1) that is currently used in Ethiopia for the prevention of PPR. Further investigations are therefore recommended in order to fully understand the true nature of the lineage II PPRVs in Ethiopia.
{"title":"Isolation and Molecular Characterization of Peste des Petits Ruminants Virus from Outbreaks in Southern Ethiopia, 2020","authors":"Abdeally Mohammed, T. R. Chibssa, Waktole Terfa, F. Aklilu, Delesa Damena, Redeat Belayneh, Menbere Kidane","doi":"10.1155/2022/5329898","DOIUrl":"https://doi.org/10.1155/2022/5329898","url":null,"abstract":"Peste des petits ruminants (PPR) is one of the most important transboundary diseases of small ruminants. In this study, nasal and oral swabs (n = 24) were collected from sheep (n = 7) and goats (n = 17) with clinical signs in southern Ethiopia in March 2020. PPR virus was isolated on Vero dog cells expressing the signaling lymphocyte activation molecule (VDS) and screened using RT-qPCR. Positive samples were confirmed by conventional RT-PCR followed by sequencing of a partial nucleoprotein (N) gene segment. Results revealed that 54% (n = 13/24) of the tested samples were PPRV-positive Phylogenetic analysis revealed that the viruses belonged to lineage IV and lineage II. The lineage IV viruses were similar, although not identical, to other lineage IV viruses previously reported in Ethiopia and other East African countries while the lineage II viruses have been reported for the first time in Ethiopia showed a high nucleotide identity (99.06%) with the vaccine (Nigeria 75/1) that is currently used in Ethiopia for the prevention of PPR. Further investigations are therefore recommended in order to fully understand the true nature of the lineage II PPRVs in Ethiopia.","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49464019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shaoqiu Chen, Zitong Gao, Ling Hu, Y. Zuo, Yuanyuan Fu, Meilin Wei, Emory Zitello, G. Huang, Youping Deng
Purpose Septic shock is a severe complication of COVID-19 patients. We aim to identify risk factors associated with septic shock and mortality among COVID-19 patients. Methods A total of 212 COVID-19 confirmed patients in Wuhan were included in this retrospective study. Clinical outcomes were designated as nonseptic shock and septic shock. Log-rank test was conducted to determine any association with clinical progression. A prediction model was established using random forest. Results The mortality of septic shock and nonshock patients with COVID-19 was 96.7% (29/30) and 3.8% (7/182). Patients taking hypnotics had a much lower chance to develop septic shock (HR = 0.096, p=0.0014). By univariate logistic regression analysis, 40 risk factors were significantly associated with septic shock. Based on multiple regression analysis, eight risk factors were shown to be independent risk factors and these factors were then selected to build a model to predict septic shock with AUC = 0.956. These eight factors included disease severity (HR = 15, p < 0.001), age > 65 years (HR = 2.6, p=0.012), temperature > 39.1°C (HR = 2.9, p=0.047), white blood cell count > 10 × 10⁹ (HR = 6.9, p < 0.001), neutrophil count > 75 × 10⁹ (HR = 2.4, p=0.022), creatine kinase > 5 U/L (HR = 1.8, p=0.042), glucose > 6.1 mmol/L (HR = 7, p < 0.001), and lactate > 2 mmol/L (HR = 22, p < 0.001). Conclusions We found 40 risk factors were significantly associated with septic shock. The model contained eight independent factors that can accurately predict septic shock. The administration of hypnotics could potentially reduce the incidence of septic shock in COVID-19 patients.
目的感染性休克是新冠肺炎患者的严重并发症。我们的目的是确定与COVID-19患者感染性休克和死亡率相关的危险因素。方法对武汉市212例新冠肺炎确诊患者进行回顾性研究。临床结果分为非感染性休克和感染性休克。进行Log-rank检验以确定是否与临床进展相关。利用随机森林建立预测模型。结果感染性休克和非休克患者病死率分别为96.7%(29/30)和3.8%(7/182)。服用催眠药的患者发生感染性休克的几率较低(HR = 0.096, p=0.0014)。经单因素logistic回归分析,有40个危险因素与脓毒性休克显著相关。经多元回归分析,8个危险因素为独立危险因素,选取这些危险因素建立预测脓毒性休克的模型,AUC = 0.956。这八个因素包括疾病严重程度(HR = 15, p < 0.001),年龄> 65岁(HR = 2.6, p = 0.012),温度> 39.1°C (HR = 2.9, p = 0.047),白细胞计数> 10×10⁹(HR = 6.9, p < 0.001),中性粒细胞计数> 75×10⁹(HR = 2.4, p = 0.022),肌酸激酶> 5 U / L (HR = 1.8, p = 0.042),葡萄糖> 6.1更易/ L (HR = 7, p < 0.001),和乳酸> 2更易与L (HR = 22, p < 0.001)。结论发现有40种危险因素与脓毒性休克显著相关。该模型包含8个独立因素,可准确预测感染性休克。催眠药的使用可能会降低COVID-19患者感染性休克的发生率。
{"title":"Association of Septic Shock with Mortality in Hospitalized COVID-19 Patients in Wuhan, China","authors":"Shaoqiu Chen, Zitong Gao, Ling Hu, Y. Zuo, Yuanyuan Fu, Meilin Wei, Emory Zitello, G. Huang, Youping Deng","doi":"10.1155/2022/3178283","DOIUrl":"https://doi.org/10.1155/2022/3178283","url":null,"abstract":"Purpose Septic shock is a severe complication of COVID-19 patients. We aim to identify risk factors associated with septic shock and mortality among COVID-19 patients. Methods A total of 212 COVID-19 confirmed patients in Wuhan were included in this retrospective study. Clinical outcomes were designated as nonseptic shock and septic shock. Log-rank test was conducted to determine any association with clinical progression. A prediction model was established using random forest. Results The mortality of septic shock and nonshock patients with COVID-19 was 96.7% (29/30) and 3.8% (7/182). Patients taking hypnotics had a much lower chance to develop septic shock (HR = 0.096, p=0.0014). By univariate logistic regression analysis, 40 risk factors were significantly associated with septic shock. Based on multiple regression analysis, eight risk factors were shown to be independent risk factors and these factors were then selected to build a model to predict septic shock with AUC = 0.956. These eight factors included disease severity (HR = 15, p < 0.001), age > 65 years (HR = 2.6, p=0.012), temperature > 39.1°C (HR = 2.9, p=0.047), white blood cell count > 10 × 10⁹ (HR = 6.9, p < 0.001), neutrophil count > 75 × 10⁹ (HR = 2.4, p=0.022), creatine kinase > 5 U/L (HR = 1.8, p=0.042), glucose > 6.1 mmol/L (HR = 7, p < 0.001), and lactate > 2 mmol/L (HR = 22, p < 0.001). Conclusions We found 40 risk factors were significantly associated with septic shock. The model contained eight independent factors that can accurately predict septic shock. The administration of hypnotics could potentially reduce the incidence of septic shock in COVID-19 patients.","PeriodicalId":7473,"journal":{"name":"Advances in Virology","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2022-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42832709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}