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Strategies for monitoring the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are crucial for combating the pandemic. Detection and mutation surveillance of SARS-CoV-2 and other respiratory viruses require separate and complex workflows that rely on highly-specialized facilities, personnel, and reagents. To date, no method can rapidly diagnose multiple viral infections and determine variants in a high-throughput manner. We describe a method for multiplex isothermal amplification-based sequencing and real-time analysis of multiple viral genomes, termed NIRVANA. It can simultaneously detect SARS-CoV-2, influenza A, human adenovirus, and human coronavirus, and monitor mutations for up to 96 samples in real-time. NIRVANA showed high sensitivity and specificity for SARS-CoV-2 in 70 clinical samples with a detection limit of 20 viral RNA copies per μl of extracted nucleic acid. It also detected the influenza A co-infection in two samples. The variant analysis results of SARS-CoV-2 positive samples mirror the epidemiology of COVID-19. Additionally, NIRVANA could simultaneously detect SARS-CoV-2 and PMMoV (an omnipresent virus and water quality indicator) in municipal wastewater samples. NIRVANA provides high-confidence detection of both SARS-CoV-2 and other respiratory viruses and mutation surveillance of SARS-CoV-2 on the fly. We expect it to offer a promising solution for rapid field-deployable detection and mutational surveillance of pandemic viruses. M.L. is supported by KAUST Office of Sponsored Research (BAS/1/1080-01). This work is supported by KAUST Competitive Research Grant (URF/1/3412-01-01, M.L. and J.C.I.B.) and Universidad Catolica San Antonio de Murcia (J.C.I.B.). A.M.H. is supported by Saudi Ministry of Education (project 436).
Chongwei Bi; Gerardo Ramos-Mandujano; Yeteng Tian; Sharif Hala; Jinna Xu; Sara Mfarrej; Concepcion Rodriguez Esteban; Estrella Nuñez Delicado; Fadwa S. Alofi; Asim Khogeer; Anwar M. Hashem; Naif A.M. Almontashiri; Arnab Pain; Juan Carlos Izpisua Belmonte; Mo Li. Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing. Med 2021, 2, 689 -700.e4.
AMA StyleChongwei Bi, Gerardo Ramos-Mandujano, Yeteng Tian, Sharif Hala, Jinna Xu, Sara Mfarrej, Concepcion Rodriguez Esteban, Estrella Nuñez Delicado, Fadwa S. Alofi, Asim Khogeer, Anwar M. Hashem, Naif A.M. Almontashiri, Arnab Pain, Juan Carlos Izpisua Belmonte, Mo Li. Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing. Med. 2021; 2 (6):689-700.e4.
Chicago/Turabian StyleChongwei Bi; Gerardo Ramos-Mandujano; Yeteng Tian; Sharif Hala; Jinna Xu; Sara Mfarrej; Concepcion Rodriguez Esteban; Estrella Nuñez Delicado; Fadwa S. Alofi; Asim Khogeer; Anwar M. Hashem; Naif A.M. Almontashiri; Arnab Pain; Juan Carlos Izpisua Belmonte; Mo Li. 2021. "Simultaneous detection and mutation surveillance of SARS-CoV-2 and multiple respiratory viruses by rapid field-deployable sequencing." Med 2, no. 6: 689-700.e4.
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to spread globally. Although several rapid commercial serological assays have been developed, little is known about their performance and accuracy in detecting SARS-CoV-2-specific antibodies in COVID-19 patient samples. Here, we have evaluated the performance of seven commercially available rapid lateral flow immunoassays (LFIA) obtained from different manufacturers, and compared them to in-house developed and validated ELISA assays for the detection of SARS-CoV-2-specific IgM and IgG antibodies in RT-PCR-confirmed COVID-19 patients. While all evaluated LFIA assays showed high specificity, our data showed a significant variation in sensitivity of these assays, which ranged from 0% to 54% for samples collected early during infection (3–7 days post symptoms onset) and from 54% to 88% for samples collected at later time points during infection (8–27 days post symptoms onset). Therefore, we recommend prior evaluation and validation of these assays before being routinely used to detect IgM and IgG in COVID-19 patients. Moreover, our findings suggest the use of LFIA assays in combination with other standard methods, and not as an alternative.
Anwar M. Hashem; Rowa Y. Alhabbab; Abdullah Algaissi; Mohamed A. AlFaleh; Sharif Hala; Turki S. Abujamel; M-Zaki ElAssouli; Afrah A. Al-Somali; Fadwa S. Alofi; Asim A. Khogeer; Almohanad A. Alkayyal; Ahmad Bakur Mahmoud; Naif A. M. Almontashiri; Arnab Pain. Performance of Commercially Available Rapid Serological Assays for the Detection of SARS-CoV-2 Antibodies. Pathogens 2020, 9, 1067 .
AMA StyleAnwar M. Hashem, Rowa Y. Alhabbab, Abdullah Algaissi, Mohamed A. AlFaleh, Sharif Hala, Turki S. Abujamel, M-Zaki ElAssouli, Afrah A. Al-Somali, Fadwa S. Alofi, Asim A. Khogeer, Almohanad A. Alkayyal, Ahmad Bakur Mahmoud, Naif A. M. Almontashiri, Arnab Pain. Performance of Commercially Available Rapid Serological Assays for the Detection of SARS-CoV-2 Antibodies. Pathogens. 2020; 9 (12):1067.
Chicago/Turabian StyleAnwar M. Hashem; Rowa Y. Alhabbab; Abdullah Algaissi; Mohamed A. AlFaleh; Sharif Hala; Turki S. Abujamel; M-Zaki ElAssouli; Afrah A. Al-Somali; Fadwa S. Alofi; Asim A. Khogeer; Almohanad A. Alkayyal; Ahmad Bakur Mahmoud; Naif A. M. Almontashiri; Arnab Pain. 2020. "Performance of Commercially Available Rapid Serological Assays for the Detection of SARS-CoV-2 Antibodies." Pathogens 9, no. 12: 1067.
The Coronavirus Disease 2019 (COVID-19), caused by SARS-CoV-2, continues to spread globally with significantly high morbidity and mortality rates. Antigen-specific responses are of unquestionable value for clinical management of COVID-19 patients. Here, we investigated the kinetics of IgM, IgG against the spike (S) and nucleoproteins (N) proteins and their neutralizing capabilities in hospitalized COVID-19 patients with different disease presentations (i.e., mild, moderate or severe), need for intensive care units (ICU) admission or outcomes (i.e., survival vs death). We show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations. Interestingly, significantly higher levels of nAbs as well as anti-S1 and -N IgG and IgM antibodies were found in patients with more severe symptoms, patients requiring admission to ICU or those with fatal outcomes. More importantly, early after symptoms onset, we found that the levels of anti-N antibodies correlated strongly with disease severity. Collectively, these findings provide new insights into the kinetics of antibody responses in COVID-19 patients with different disease severity.
Anwar M. Hashem; Abdullah Algaissi; Sarah A. Almahboub; Mohamed A. Alfaleh; Turki S. Abujamel; Sawsan S. Alamri; Khalid A. Alluhaybi; Haya I. Hobani; Rahaf H. AlHarbi; Reem M. Alsulaiman; M-Zaki ElAssouli; Sharif Hala; Naif K. Alharbi; Rowa Y. Alhabbab; Ahdab A. AlSaieedi; Wesam H. Abdulaal; Abdullah Bukhari; Afrah A. Al-Somali; Fadwa S. Alofi; Asim A. Khogeer; Arnab Pain; Almohanad A. Alkayyal; Naif A. M. Almontashiri; Ahmad Bakur Mahmoud; Xuguang Li. Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients. Viruses 2020, 12, 1390 .
AMA StyleAnwar M. Hashem, Abdullah Algaissi, Sarah A. Almahboub, Mohamed A. Alfaleh, Turki S. Abujamel, Sawsan S. Alamri, Khalid A. Alluhaybi, Haya I. Hobani, Rahaf H. AlHarbi, Reem M. Alsulaiman, M-Zaki ElAssouli, Sharif Hala, Naif K. Alharbi, Rowa Y. Alhabbab, Ahdab A. AlSaieedi, Wesam H. Abdulaal, Abdullah Bukhari, Afrah A. Al-Somali, Fadwa S. Alofi, Asim A. Khogeer, Arnab Pain, Almohanad A. Alkayyal, Naif A. M. Almontashiri, Ahmad Bakur Mahmoud, Xuguang Li. Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients. Viruses. 2020; 12 (12):1390.
Chicago/Turabian StyleAnwar M. Hashem; Abdullah Algaissi; Sarah A. Almahboub; Mohamed A. Alfaleh; Turki S. Abujamel; Sawsan S. Alamri; Khalid A. Alluhaybi; Haya I. Hobani; Rahaf H. AlHarbi; Reem M. Alsulaiman; M-Zaki ElAssouli; Sharif Hala; Naif K. Alharbi; Rowa Y. Alhabbab; Ahdab A. AlSaieedi; Wesam H. Abdulaal; Abdullah Bukhari; Afrah A. Al-Somali; Fadwa S. Alofi; Asim A. Khogeer; Arnab Pain; Almohanad A. Alkayyal; Naif A. M. Almontashiri; Ahmad Bakur Mahmoud; Xuguang Li. 2020. "Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients." Viruses 12, no. 12: 1390.
The Coronavirus Disease 2019 (COVID-19), caused by the novel SARS-CoV-2, continues to spread globally with significantly high morbidity and mortality rates. Immunological surrogate markers, in particular antigen-specific responses, are of unquestionable value for clinical management of patients with COVID-19. Here, we investigated the kinetics of IgM, IgG against the spike (S) and nucleoproteins (N) proteins and their neutralizing capabilities in hospitalized patients with RT-PCR confirmed COVID-19 infection. Our data show that SARS-CoV-2 specific IgG, IgM and neutralizing antibodies (nAbs) were readily detectable in almost all COVID-19 patients with various clinical presentations. Notably, anti-S and -N IgG, peaked 20-40 day after disease onset, and were still detectable for at least up to 70 days, with nAbs observed during the same time period. Moreover, nAbs titers were strongly correlated with IgG antibodies. Significantly higher levels of nAbs as well as anti-S1 and N IgG and IgM antibodies were found in patients with more severe clinical presentations, patients requiring admission to intensive care units (ICU) or those with fatal outcomes. Interestingly, lower levels of antibodies, particularly anti-N IgG and IgM in the first 15 days after symptoms onset, were found in survivors and those with mild clinical presentations. Collectively, these findings provide new insights into the characteristics and kinetics of antibody responses in COVID-19 patients with different disease severity.
Anwar M Hashem; Abdullah Algaissi; Sarah A Almahboub; Mohamed A Alfaleh; Turki S Abujamel; Sawsan S Alamri; Khalid A Alluhaybi; Haya I Hobani; Rahaf H AlHarbi; Reem M Alsulaiman; M-Zaki ElAssouli; Sharif Hala; Naif K Alharbi; Rowa Y Alhabbab; Ahdab A AlSaieedi; Wesam H Abdulaal; Abdullah Bukhari; Afrah A Al-Somali; Fadwa S Alofi; Asim A Khogeer; Arnab Pain; Almohanad A Alkayyal; Naif Am Almontashiri; Ahmad Bakur Mahmoud; Xuguang Li. Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients. 2020, 1 .
AMA StyleAnwar M Hashem, Abdullah Algaissi, Sarah A Almahboub, Mohamed A Alfaleh, Turki S Abujamel, Sawsan S Alamri, Khalid A Alluhaybi, Haya I Hobani, Rahaf H AlHarbi, Reem M Alsulaiman, M-Zaki ElAssouli, Sharif Hala, Naif K Alharbi, Rowa Y Alhabbab, Ahdab A AlSaieedi, Wesam H Abdulaal, Abdullah Bukhari, Afrah A Al-Somali, Fadwa S Alofi, Asim A Khogeer, Arnab Pain, Almohanad A Alkayyal, Naif Am Almontashiri, Ahmad Bakur Mahmoud, Xuguang Li. Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients. . 2020; ():1.
Chicago/Turabian StyleAnwar M Hashem; Abdullah Algaissi; Sarah A Almahboub; Mohamed A Alfaleh; Turki S Abujamel; Sawsan S Alamri; Khalid A Alluhaybi; Haya I Hobani; Rahaf H AlHarbi; Reem M Alsulaiman; M-Zaki ElAssouli; Sharif Hala; Naif K Alharbi; Rowa Y Alhabbab; Ahdab A AlSaieedi; Wesam H Abdulaal; Abdullah Bukhari; Afrah A Al-Somali; Fadwa S Alofi; Asim A Khogeer; Arnab Pain; Almohanad A Alkayyal; Naif Am Almontashiri; Ahmad Bakur Mahmoud; Xuguang Li. 2020. "Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients." , no. : 1.
One-step RT-qPCR is the most widely applied method for COVID-19 diagnostics. Designing in-house one-step RT-qPCR kits is restricted by the patent-rights for the production of enzymes and the lack of information about the components of the commercial kits. Here, we provide a simple, economical, and powerful one-step RT-qPCR kit based on patent-free, specifically-tailored versions of Moloney Murine Leukemia Virus Reverse Transcriptase and Thermus aquaticus DNA polymerase termed the R3T (Rapid Research Response Team) One-step RT-qPCR. Our kit was routinely able to reliably detect as low as 10 copies of the synthetic RNAs of the SARS-CoV-2. More importantly, our kit successfully detected COVID-19 in clinical samples of broad viral titers with similar reliability and selectivity as that of the Invitrogen SuperScript III Platinum One-step RT-qPCR and TaqPath 1-Step RT-qPCR kits. Overall, our kit has shown robust performance in both of laboratory settings and the Saudi Ministry of Health-approved testing facility.
Masateru Takahashi; Muhammad Tehseen; Rahul Salunke; Etsuko Takahashi; Sara Mfarrej; Mohamed A. Sobhy; Fatimah Alhamlan; Sharif Hala; Gerardo R. Mandujano; Ahmed A. Al-Qahtani; Fadwa S. Alofi; Afrah Alsomali; Anwar M. Hashem; Asim Khogeer; Naif A. M. Almontashiri; Jae Man Lee; Hiroaki Mon; Kosuke Sakashita; Mo Li; Takahiro Kusakabe; Arnab Pain; Samir M. Hamdan. R3T (Rapid Research Response Team) One-step RT-qPCR kit for COVID-19 diagnostic using in-house enzymes. 2020, 1 .
AMA StyleMasateru Takahashi, Muhammad Tehseen, Rahul Salunke, Etsuko Takahashi, Sara Mfarrej, Mohamed A. Sobhy, Fatimah Alhamlan, Sharif Hala, Gerardo R. Mandujano, Ahmed A. Al-Qahtani, Fadwa S. Alofi, Afrah Alsomali, Anwar M. Hashem, Asim Khogeer, Naif A. M. Almontashiri, Jae Man Lee, Hiroaki Mon, Kosuke Sakashita, Mo Li, Takahiro Kusakabe, Arnab Pain, Samir M. Hamdan. R3T (Rapid Research Response Team) One-step RT-qPCR kit for COVID-19 diagnostic using in-house enzymes. . 2020; ():1.
Chicago/Turabian StyleMasateru Takahashi; Muhammad Tehseen; Rahul Salunke; Etsuko Takahashi; Sara Mfarrej; Mohamed A. Sobhy; Fatimah Alhamlan; Sharif Hala; Gerardo R. Mandujano; Ahmed A. Al-Qahtani; Fadwa S. Alofi; Afrah Alsomali; Anwar M. Hashem; Asim Khogeer; Naif A. M. Almontashiri; Jae Man Lee; Hiroaki Mon; Kosuke Sakashita; Mo Li; Takahiro Kusakabe; Arnab Pain; Samir M. Hamdan. 2020. "R3T (Rapid Research Response Team) One-step RT-qPCR kit for COVID-19 diagnostic using in-house enzymes." , no. : 1.
As the coronavirus disease 2019 (COVID-19), which is caused by the novel SARS-CoV-2, continues to spread rapidly around the world, there is a need for well validated serological assays that allow the detection of viral specific antibody responses in COVID-19 patients or recovered individuals. In this study, we established and used multiple indirect Enzyme Linked Immunosorbent Assay (ELISA)-based serological assays to study the antibody response in COVID-19 patients. In order to validate the assays we determined the cut off values, sensitivity and specificity of the assays using sera collected from pre-pandemic healthy controls, COVID-19 patients at different time points after disease-onset, and seropositive sera to other human coronaviruses. The developed SARS-CoV-2 S1 subunit of the spike glycoprotein and nucleocapsid (N)-based ELISAs not only showed high specificity and sensitivity but also did not show any cross-reactivity with other CoVs. We also show that all RT-PCR confirmed COVID-19 patients tested in our study developed both virus specific IgM and IgG antibodies as early as week one after disease onset. Our data also suggest that the inclusion of both S1 and N in serological testing would capture as many potential SARS-CoV-2 positive cases as possible than using any of them alone. This is specifically important for tracing contacts and cases and conducting large-scale epidemiological studies to understand the true extent of virus spread in populations.
Abdullah Algaissi; Mohamed A. AlFaleh; Sherif Hala; Turki S. Abujamel; Sawsan S. Alamri; Sarah A Almahboub; Khalid A. Alluhaybi; Haya I. Hobani; Reem M. Alsulaiman; Rahaf H. Alharbi; M-Zaki El-Assouli; Rowa Y Alhabbab; Ahdab A. AlSaieedi; Wesam H. Abdulaal; Afrah A. Al-Somali; Fadwa S. Alofi; Asim A. Khogeer; Ahmad Bakur Mahmoud; Almohanad A Alkayyal; Naif A.M. Almontashiri; Arnab Pain; Anwar M. Hashem. SARS-CoV-2 S1 and N-Based Serological Assays Reveal Rapid Seroconversion and Induction of Specific Antibody Response in COVID-19 Patients. 2020, 1 .
AMA StyleAbdullah Algaissi, Mohamed A. AlFaleh, Sherif Hala, Turki S. Abujamel, Sawsan S. Alamri, Sarah A Almahboub, Khalid A. Alluhaybi, Haya I. Hobani, Reem M. Alsulaiman, Rahaf H. Alharbi, M-Zaki El-Assouli, Rowa Y Alhabbab, Ahdab A. AlSaieedi, Wesam H. Abdulaal, Afrah A. Al-Somali, Fadwa S. Alofi, Asim A. Khogeer, Ahmad Bakur Mahmoud, Almohanad A Alkayyal, Naif A.M. Almontashiri, Arnab Pain, Anwar M. Hashem. SARS-CoV-2 S1 and N-Based Serological Assays Reveal Rapid Seroconversion and Induction of Specific Antibody Response in COVID-19 Patients. . 2020; ():1.
Chicago/Turabian StyleAbdullah Algaissi; Mohamed A. AlFaleh; Sherif Hala; Turki S. Abujamel; Sawsan S. Alamri; Sarah A Almahboub; Khalid A. Alluhaybi; Haya I. Hobani; Reem M. Alsulaiman; Rahaf H. Alharbi; M-Zaki El-Assouli; Rowa Y Alhabbab; Ahdab A. AlSaieedi; Wesam H. Abdulaal; Afrah A. Al-Somali; Fadwa S. Alofi; Asim A. Khogeer; Ahmad Bakur Mahmoud; Almohanad A Alkayyal; Naif A.M. Almontashiri; Arnab Pain; Anwar M. Hashem. 2020. "SARS-CoV-2 S1 and N-Based Serological Assays Reveal Rapid Seroconversion and Induction of Specific Antibody Response in COVID-19 Patients." , no. : 1.
Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method calledMagnetic-nanoparticle-AidedViralRNAIsolation ofContagiousSamples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. MAVRICS is scalable and thus could become an enabling technology for widespread community testing and wastewater monitoring in the current and future pandemics.
Gerardo Ramos-Mandujano; Rahul Salunke; Sara Mfarrej; Andri Rachmadi; Sharif Hala; Jinna Xu; Fadwa S. Alofi; Asim Khogeer; Anwar M. Hashem; Naif A.M. Almontashiri; Afrah Alsomali; Samir Hamdan; Peiying Hong; Arnab Pain; Mo Li. A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples. 2020, 1 .
AMA StyleGerardo Ramos-Mandujano, Rahul Salunke, Sara Mfarrej, Andri Rachmadi, Sharif Hala, Jinna Xu, Fadwa S. Alofi, Asim Khogeer, Anwar M. Hashem, Naif A.M. Almontashiri, Afrah Alsomali, Samir Hamdan, Peiying Hong, Arnab Pain, Mo Li. A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples. . 2020; ():1.
Chicago/Turabian StyleGerardo Ramos-Mandujano; Rahul Salunke; Sara Mfarrej; Andri Rachmadi; Sharif Hala; Jinna Xu; Fadwa S. Alofi; Asim Khogeer; Anwar M. Hashem; Naif A.M. Almontashiri; Afrah Alsomali; Samir Hamdan; Peiying Hong; Arnab Pain; Mo Li. 2020. "A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples." , no. : 1.