Both simulation and sequencing data reveal coinfections with multiple SARS-CoV-2 variants in the COVID-19 pandemic.

SARS-CoV-2 is a single-stranded RNA betacoronavirus with a high mutation rate. The rapidly emerging SARS-CoV-2 variants could increase transmissibility and diminish vaccine protection. However, whether coinfection with multiple SARS-CoV-2 variants exists remains controversial. This study collected 12,986 and 4,113 SARS-CoV-2 genomes from the GISAID database on May 11, 2020 (GISAID20May11), and Apr 1, 2021 (GISAID21Apr1), respectively. With single-nucleotide variant (SNV) and network clique analyses, we constructed single-nucleotide polymorphism (SNP) coexistence networks and discovered maximal SNP cliques of sizes 16 and 34 in the GISAID20May11 and GISAID21Apr1 datasets, respectively. Simulating the transmission routes and SNV accumulations, we discovered a linear relationship between the size of the maximal clique and the number of coinfected variants. We deduced that the COVID-19 cases in GISAID20May11 and GISAID21Apr1 were coinfections with 3.20 and 3.42 variants on average, respectively. Additionally, we performed Nanopore sequencing on 42 COVID-19 patients and discovered recurrent heterozygous SNPs in twenty of the patients, including loci 8,782 and 28,144, which were crucial for SARS-CoV-2 lineage divergence. In conclusion, our findings reported SARS-CoV-2 variants coinfection in COVID-19 patients and demonstrated the increasing number of coinfected variants.

Mycotic infection as a risk factor for COVID-19: A meta-analysis.

More than 405 million people have contracted coronavirus disease 2019 (COVID-19) worldwide, and mycotic infection may be related to COVID-19 development. There are a large number of reports showing that COVID-19 patients with mycotic infection have an increased risk of mortality. However, whether mycotic infection can be considered a risk factor for COVID-19 remains unknown. We searched the PubMed and Web of Science databases for studies published from inception to December 27, 2021. Pooled effect sizes were calculated according to a random-effects model or fixed-effect model, depending on heterogeneity. We also performed subgroup analyses to identify differences in mortality rates between continents and fungal species. A total of 20 articles were included in this study. Compared with the controls, patients with mycotic infection had an odds ratio (OR) of 2.69 [95% confidence interval (CI): 2.22-3.26] for mortality and an OR of 2.28 (95% CI: 1.65-3.16) for renal replacement therapy (RRT). We also conducted two subgroup analyses based on continent and fungal species, and we found that Europe and Asia had the highest ORs, while Candida was the most dangerous strain of fungi. We performed Egger's test and Begg's test to evaluate the publication bias of the included articles, and the p-value was 0.423, which indicated no significant bias. Mycotic infection can be regarded as a risk factor for COVID-19, and decision makers should be made aware of this risk.

Intranasal Lentiviral Vector-Mediated Antibody Delivery Confers Reduction of SARS-CoV-2 Infection in Elderly and Immunocompromised Mice.

Vaccines for COVID-19 are now a crucial public health need, but the degree of protection provided by conventional vaccinations for individuals with compromised immune systems is unclear. The use of viral vectors to express neutralizing monoclonal antibodies (mAbs) in the lung is an alternative approach that does not wholly depend on individuals having intact immune systems and responses. Here, we identified an anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) monoclonal antibody, NC0321, which can efficiently neutralize a range of SARS-CoV-2 variants, including alpha, beta, delta, and eta. Both prophylactic and therapeutic NC0321 treatments effectively protected mice from SARS-CoV-2 infection. Notably, we adopted viral vector-mediated delivery of NC0321 IgG1 as an attractive approach to prevent SARS-CoV-2 infection. The NC0321 IgG1 expression in the proximal airway, expressed by a single direct in-vivo intranasal (I.N.) administration of a self-inactivating and recombinant lentiviral vector (rSIV.F/HN-NC0321), can protect young, elderly, and immunocompromised mice against mouse-adapted SARS-CoV-2 surrogate challenge. Long-term monitoring indicated that rSIV.F/HN-NC0321 mediated robust IgG expression throughout the airway of young and SCID mice, importantly, no statistical difference in the NC0321 expression between young and SCID mice was observed. A single I.N. dose of rSIV.F/HN-NC0321 30 or 180 days prior to SARS-CoV-2 challenge significantly reduced lung SARS-CoV-2 titers in an Ad5-hACE2-transduced mouse model, reconfirming that this vectored immunoprophylaxis strategy could be useful, especially for those individuals who cannot gain effective immunity from existing vaccines, and could potentially prevent clinical sequelae.

Critical Review of the Scientific Evidence and Recommendations in COVID-19 Management Guidelines.

BACKGROUND: Little is known about the quality and potential impacts of the guidelines for coronavirus disease 2019 (COVID-19) management. METHODS: We systematically searched PubMed, Web of Science, Cochrane Library, guideline databases, and specialty society websites to evaluate the quality of the retrieved guidelines using the Appraisal of Guidelines for Research and Evaluation II. RESULTS: A total of 66 guidelines were identified. Only 24% were categorized as "recommended" for clinical practice. The 211 identified recommendations for COVID-19 management were classified into 4 topics: respiratory support (27), acute respiratory distress syndrome management (31), antiviral or immunomodulatory therapy (95), or other medicines (58). Only 63% and 56% of recommendations were supported by, respectively, assessment of the strength of the recommendations or level of evidence. There were notable discrepancies between the different guidelines regarding the recommendations on COVID-19 management. CONCLUSIONS: The quality of the guidelines for COVID-19 management is heterogeneous, and the recommendations are rarely supported by evidence.

A Confirmed Case of SARS-CoV-2 Pneumonia With Negative Routine Reverse Transcriptase-Polymerase Chain Reaction and Virus Variation in Guangzhou, China.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia is a newly recognized disease, and its diagnosis is primarily confirmed by routine reverse transcriptase -polymerase chain reaction (RT-PCR) detection of SARS-CoV-2. METHODS: However, we report a confirmed case of SARS-CoV-2 pneumonia with a negative routine RT-PCR. RESULTS: This case was finally diagnosed by nanopore sequencing combined with antibody of SARS-CoV-2. Simultaneously, the ORF and NP gene variations of SARS-CoV-2 were found. CONCLUSIONS: This case highlighted that false-negative results could be present in routine RT-PCR diagnosis, especially with virus variation. Currently, nanopore pathogen sequencing and antibody detection have been found to be effective in clinical diagnosis.

Epidemiological and clinical characteristics of suspected COVID-19 patients in the isolation ward in Guangzhou, China: a cohort study.

BACKGROUND: Since there are reports of cases of 2019-coronavirus disease (COVID-19) asymptomatic carriers in China recently and fever is one of the main symptoms, we aimed to distinguish COVID-19 cases from other febrile patients with clinical examinations in this study. METHODS: A total of 134 suspected COVID-19 patients in the isolation ward of the First Affiliated Hospital of Guangzhou Medical University were recruited from January 23 to May 23, 2020. We analyze the pathogenic form and clinical characteristics. RESULTS: Among them, pathogens were identified in only 84 patients (62.7%), including 23 (17.1%) with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), 30 (22.3%) with other viruses, 31 (25.0%) with other pathogens and 3 (3.5%) with mixed infections. The commonly observed symptoms of COVID-19 patients were cough, fever, fatigue, and muscle aches, which were significantly different than the symptoms of nonviral infections (P<0.05) but from those of other viral infections (P>0.05). Furthermore, lactate dehydrogenase and the neutrophil/lymphocyte were found significantly high in COVID-19 patients compared to non-COVID-19 patients (P<0.05). The most common manifestations of COVID-19 patients were ground-glass opacities (100%) with or without lung consolidation, however, they also often showed involvement of several lobes of both lungs (P<0.05). Due to the clear differential diagnosis, the overall antibiotic use rate was 35.8% (31/87). CONCLUSIONS: When diagnosing COVID-19, infections with other pathogens should not be ignored. Successful pathogen identification will support accurate treatment.

Longitudinal virological changes and underlying pathogenesis in hospitalized COVID-19 patients in Guangzhou, China.

Prolonged viral RNA shedding and recurrence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in coronavirus disease 2019 (COVID-19) patients have been reported. However, the clinical outcome and pathogenesis remain unclear. In this study, we recruited 43 laboratory-confirmed COVID-19 patients. We found that prolonged viral RNA shedding or recurrence mainly occurred in severe/critical patients (P<0.05). The average viral shedding time in severe/critical patients was more than 50 days, and up to 100 days in some patients, after symptom onset. However, chest computed tomography gradually improved and complete absorption occurred when SARS-CoV-2 RT-PCR was still positive, but specific antibodies appeared. Furthermore, the viral shedding time significantly decreased when the A1,430G or C12,473T mutation occurred (P<0.01 and FDR<0.01) and increased when G227A occurred (P<0.05 and FDR<0.05). High IL1R1, IL1R2, and TNFRSF21 expression in the host positively correlated with viral shedding time (P<0.05 and false discovery rate <0.05). Prolonged viral RNA shedding often occurs but may not increase disease damage. Prolonged viral RNA shedding is associated with viral mutations and host factors.

The use of non-invasive ventilation in COVID-19: A systematic review.

OBJECTIVE: Guidelines from different regions on the use of non-invasive ventilation in COVID-19 have generally been inconsistent. The aim of this systematic review was to appraise the quality and availability of guidelines, and whether non-invasive ventilation in the early stages of the pandemic is of importance. DESIGN AND METHOD: Databases, including PubMed, Web of Science, and Cochrane Library, as well as websites of international organizations and gray literature, were searched up to June 23, 2020. The reference lists of eligible papers were also hand-searched. RESULTS: A total of 26 guidelines met the inclusion criteria. According to the Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument, the guidelines' methodological quality was low. Among six domains, Rigour of Development and Editorial Independence were of the lowest quality. Given the lack of evidence from randomized clinical trials and the great variation between different regions, recommendations for non-invasive ventilation have generated considerable debate regarding the early stages of COVID-19. CONCLUSIONS: Improving the methodological quality of the guidelines should be a goal with regard to future pandemics. Additionally, better-designed randomized clinical trials are needed to resolve contradictions regarding the impact of non-invasive ventilation. PROSPERO REGISTRATION NUMBER: CRD42020198410.

Kinetics of viral load and antibody response in relation to COVID-19 severity.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus 2019 (COVID-19) pneumonia. Little is known about the kinetics, tissue distribution, cross-reactivity, and neutralization antibody response in patients with COVID-19. Two groups of patients with RT-PCR-confirmed COVID-19 were enrolled in this study: 12 severely ill patients in intensive care units who needed mechanical ventilation and 11 mildly ill patients in isolation wards. Serial clinical samples were collected for laboratory detection. Results showed that most of the severely ill patients had viral shedding in a variety of tissues for 20-40 days after onset of disease (8/12, 66.7%), while the majority of mildly ill patients had viral shedding restricted to the respiratory tract and had no detectable virus RNA 10 days after onset (9/11, 81.8%). Mildly ill patients showed significantly lower IgM response compared with that of the severe group. IgG responses were detected in most patients in both the severe and mild groups at 9 days after onset, and remained at a high level throughout the study. Antibodies cross-reactive to SARS-CoV and SARS-CoV-2 were detected in patients with COVID-19 but not in patients with MERS. High levels of neutralizing antibodies were induced after about 10 days after onset in both severely and mildly ill patients which were higher in the severe group. SARS-CoV-2 pseudotype neutralization test and focus reduction neutralization test with authentic virus showed consistent results. Sera from patients with COVID-19 inhibited SARS-CoV-2 entry. Sera from convalescent patients with SARS or Middle East respiratory syndrome (MERS) did not. Anti-SARS-CoV-2 S and N IgG levels exhibited a moderate correlation with neutralization titers in patients' plasma. This study improves our understanding of immune response in humans after SARS-CoV-2 infection.

Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis.

The outbreak of the novel coronavirus disease (COVID-19) quickly spread all over China and to more than 20 other countries. Although the virus (severe acute respiratory syndrome coronavirus [SARS-Cov-2]) nucleic acid real-time polymerase chain reaction (PCR) test has become the standard method for diagnosis of SARS-CoV-2 infection, these real-time PCR test kits have many limitations. In addition, high false-negative rates were reported. There is an urgent need for an accurate and rapid test method to quickly identify a large number of infected patients and asymptomatic carriers to prevent virus transmission and assure timely treatment of patients. We have developed a rapid and simple point-of-care lateral flow immunoassay that can detect immunoglobulin M (IgM) and IgG antibodies simultaneously against SARS-CoV-2 virus in human blood within 15 minutes which can detect patients at different infection stages. With this test kit, we carried out clinical studies to validate its clinical efficacy uses. The clinical detection sensitivity and specificity of this test were measured using blood samples collected from 397 PCR confirmed COVID-19 patients and 128 negative patients at eight different clinical sites. The overall testing sensitivity was 88.66% and specificity was 90.63%. In addition, we evaluated clinical diagnosis results obtained from different types of venous and fingerstick blood samples. The results indicated great detection consistency among samples from fingerstick blood, serum and plasma of venous blood. The IgM-IgG combined assay has better utility and sensitivity compared with a single IgM or IgG test. It can be used for the rapid screening of SARS-CoV-2 carriers, symptomatic or asymptomatic, in hospitals, clinics, and test laboratories.