Genomic epidemiology of SARS-CoV-2 in the United Arab Emirates reveals novel virus mutation, patterns of co-infection and tissue specific host responses (preprint)

Background: The United Arab Emirates is a major business hub with substantial amount of international travel. Like many other countries, it was greatly affected by the COVID-19 pandemic since late January 2020, with recurring waves of infection. This study aimed at combining genomic and epidemiological data to unravel the source of SARS-CoV-2 introduction, transmission and evolution in the country. Methods: We performed meta-transcriptomic sequencing of 1,067 nasopharyngeal swab samples collected from qRT-PCR positive COVID-19 patients in Abu Dhabi, UAE, between May 9th and June 29th 2020. We investigated the genetic diversity and transmission dynamics of the viral population and analyzed the infection and transmission potential of novel genomic clusters. Within-host SARS-CoV-2 genetic variation was analyzed to determine the occurrence and prevalence of multiple infections. Finally, we evaluated innate host responses during the prolonged period of local infection. Results: All globally known SARS-CoV-2 clades were identified within the UAE sequenced strains, with a higher occurrence of European and East Asian clades. We defined 5 subclades based on 11 unique genetic variants within the UAE strains, which were associated with no significantly different viral loads. Multiple infection of different SARS-CoV-2 strains was observed for at least 5% of the patients. We also discovered an enrichment of cytosine-to-uracil mutation among the viral population collected from the nasopharynx, that is different from the adenosine-to-inosine change previously observed in the bronchoalveolar lavage fluid samples. This observation is accompanied with an upregulation of APOBEC4, an under-studied putative cytidine-uridine editing enzyme in the infected nasopharynx. Conclusions: The genomic epidemiological and molecular biological knowledge obtained in the study provides new insights for the SARS-CoV-2 evolution and transmission. We highlight the importance of sustained surveillance of the virus mutation using genomic sequencing as a public health strategy. Keywords: SARS-CoV-2, meta-transcriptomic sequencing, novel mutations and subclades, co-infection, cyosine depletion, host RNA editing

Genomic Epidemiology of SARS-CoV-2 in the United Arab Emirates Reveals Novel Insights into the Virus Mutation, Co-Infection and Host-Dependent RNA Editing (preprint)

Background: The United Arab Emirates is a major business hub with substantial amount of international travel. Like many other countries, it was greatly affected by the COVID-19 pandemic since late January 2020, with recurring waves of infection. This study aimed at combining genomic and epidemiological data to unravel the source of SARS-CoV-2 introduction, transmission and evolution in the country.Methods: We performed meta-transcriptomic sequencing of 1,067 nasopharyngeal swab samples collected from qRT-PCR positive COVID-19 patients in Abu Dhabi, UAE, between May 9th and June 29th 2020. We investigated the genetic diversity and transmission dynamics of the viral population and analyzed the infection and transmission potential of novel genomic clusters. Within-host SARS-CoV-2 genetic variation was analyzed to determine the occurrence and prevalence of multiple infections. Finally, we evaluated innate host responses during the prolonged period of local infection.Findings: All globally known SARS-CoV-2 clades were identified within the UAE sequenced strains, with a higher occurrence of European and East Asian clades. We defined 5 subclades based on 11 unique genetic variants within the UAE strains, which were associated with higher viral loads (p<0.001). Multiple infection of different SARS-CoV-2 strains was observed for at least 5% of the patients. We also observed a host-defense mechanism via RNA editing, likely mediated by APOBEC3 rather than ADAR in nasopharyngeal samples.Interpretation: The SARS-CoV-2 epidemic in the UAE was founded by international importation followed by local transmission, leading to prevalent multiple infection and large subclade descendances. While RNA editing mechanisms mutate the viral population, newly arisen genetic variation can contribute to a heavier viral burden. Meta-transcriptomic sequencing can help to determine the transmission patterns of SARS-CoV-2.Funding: Department of Health of Abu Dhabi, UAE and National Natural Science Foundation of China.Declaration of Interests: None to declareEthics Approval Statement: The study was approved by the Abu Dhabi COVID19 Research IRB Committee (approval number DOH/CVDC/2020/1945).

Discovery of Pre-Existing Drugs that Suppress the Replication of SARS-CoV-2 in Vitro (preprint)

SARS-CoV-2, the causative agent of coronavirus disease 19 (COVID 19), is responsible for the ongoing pandemic but still lacks approved antivirals. Repurposing pre-existing FDA approved drugs presents a rapid approach for new therapeutic options. In the present study, we report that three pre-existing FDA-approved drugs, i.e., vapreotide, grazoprevir, and simeprevir, inhibit the replication of SARS-CoV-2 in cells. The E50 values of vapreotide, grazoprevir, and simeprevir against SARS-CoV-2 in Vero E6 cells was 3.98 ± 0.35 μM, 2.08 ± 0.13 μM, and 1.41 ± 0.12 μM, respectively. In vitro biochemical experiments further revealed that vapreotide, grazoprevir, and simeprevir efficiently inhibits the unwinding activity of the Nsp13 helicase of SARS-CoV-2 with IC50 values of ⁓10, ⁓2.5, and ⁓1.25 µM, respectively, providing signs for understanding their antiviral mechanism of action. Given their good safety profiles in their original indications, our study offices new insights in repurposing these drugs alone or in combination with other antivirals in the global fighting against SARS-CoV-2.Funding: This work was financially supported by the Youth Innovation Promotion Association CAS (to H.Y.), and the National Natural Science Foundation of China (No. 31770192 and No. 32070187 to H.Y.).Conflict of Interest: The authors declare no competing interests.

Safety and immunogenicity of a recombinant tandem-repeat dimeric RBD protein vaccine against COVID-19 in adults: pooled analysis of two randomized, double-blind, placebo-controlled, phase 1 and 2 trials (preprint)

BackgroundA safe and effective coronavirus disease 2019 (COVID-19) vaccine is urgently needed to control the ongoing pandemic. Although progress has been made recently with several candidates reporting positive efficacy results, COVID-19 vaccines developed so far cannot meet the global vaccine demand. We developed a protein subunit vaccine against COVID-19, using dimeric form of receptor-binding domain (RBD) as the antigen. We aimed to assess the safety and immunogenicity of this vaccine in humans and determine the appropriate dose and schedule for an efficacy study. MethodsWe did two randomized, double-blind, placebo-controlled, phase 1 and 2 trials for an RBD-based protein subunit vaccine, ZF2001. In phase 1 study, 50 healthy adults aged 18-59 years were enrolled and randomly allocated to three groups to receive three doses of vaccine (25 g or 50 g RBD-dimer, with adjuvant) or placebo (adjuvant-only) intramuscularly, 30 days apart. In phase 2 study, 900 healthy adults aged 18-59 years were enrolled and randomly allocated to six groups to receive vaccine (25 g or 50 g RBD-dimer, with adjuvant) or placebo (adjuvant-only) intramuscularly, with the former 3 groups given two doses and the latter 3 groups given three doses, 30 days apart. For phase 1 trial, the primary outcome was safety, as measured by the occurrence of adverse events and serious adverse events. The secondary outcome was immunogenicity as measured by the seroconversion rate and magnitude of antigen-binding antibodies, neutralizing antibodies and T-cell cytokine production. For phase 2 trial, the primary outcome included both safety and immunogenicity. These trials are registered with ClinicaTrials.gov, NCT04445194 and NCT04466085. FindingsBetween June 22 and September 15, 2020, 50 participants were enrolled to the phase 1 study (mean age 32.6 years) and 900 participants were enrolled to phase 2 study (mean age 43.5 years), to receive vaccine or placebo with a two-dose or three-dose schedule. For both trials, local and systemic adverse reactions were absent or mild in most participants. There were no serious adverse events related to vaccine in either trial. After three doses, neutralizing antibodies were detected in all participants receiving either 25 g or 50 g dose of vaccine in phase 1 study, and in 97% (the 25 g group) and 93% (the 50 g group) of participants, respectively, in phase 2 study. The SARS-CoV-2-neutralizing geometric mean titres (GMTs) were 94.5 for the 25 g group and 117.8 for the 50 g group in phase 1, and 102.5 for the 25 g group and 69.1 for the 50 g group in phase 2, exceeding the level of a panel of COVID-19 convalescent samples (GMT, 51). Vaccine induced balanced TH1 and TH2 responses. The 50 g group did not show enhanced immunogenicity compared with the 25 g group. InterpretationThe protein subunit vaccine ZF2001 is well-tolerated and immunogenic. The safety and immunogenicity data from phase 1 and 2 trials for ZF2001 support the use of 25 g vaccine dose with three-dose schedule to an ongoing phase 3 large-scale evaluation for safety and efficacy. FundingNational Program on Key Research Project of China, National Science and Technology Major Projects of Drug Discovery, Strategic Priority Research Program of the Chinese Academy of Sciences, and Anhui Zhifei Longcom Biopharmaceutical.

Developing multiplex ddPCR assays for SARS-CoV-2 detection based on probe mix and amplitude based multiplexing (preprint)

Multiplexing has been highlighted to save on costs, increase sample throughput, and maximize on the number of targets that can be sensitively detected within a small sample. With the ongoing SARS-CoV-2 pandemic, different articles have been published highlighting the superiority of droplet digital PCR (ddPCR) over the gold reverse transcription PCR (RT-PCR) in SARS-CoV-2 detection. However, few studies have been reported on developing multiplex ddPCR assays for SARS-CoV-2 detection and their performance. In this study, we developed simplex (1 target), duplex (2 targets), triplex probe mix (3 targets), and fourplex (4 targets) assays based on a two color ddPCR system for SARS-CoV-2 detection. Results showed that the fourplex assay had the similar limits of detection and accuracy to the lower multiplex assays. Analyzing 94 clinical isolates demonstrated that the ddPCR triplex probe mix assay had better sensitivity than the RT-qPCR assay. Additionally, the ddPCR multiplex assay showed that remdesivir could inhibit the growth of SARS-CoV-2 in vitro while another testing drug couldn't. Conclusively, our research shows that developing multiplex ddPCR assays is possible by combing probe mix and amplitude based multiplexing, which will help in developing multiplexed ddPCR assays for different SARS-CoV-2 applications.

Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients (preprint)

Summary Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. Method Between January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection rates, the prevalence and abundance of microbial communities in these COVID-19 patients were determined. Findings Notably, respiratory microbial co-infections were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death one month after ICU admission. Interpretation Our findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2. Funding National Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.

Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2 (preprint)

The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions. Author summaryIn this study, we compared SARS-CoV-2 populations of 13 Chinese COVID-19 patients. Those viral populations contained a considerable proportion of viral sub-genomic messenger RNAs (sgmRNA), reflecting an active viral replication activity in the respiratory tract tissues. The comparison of 66 identified intra-host variants further showed a low viral genetic distance between intra-household patients and a narrow transmission bottleneck size. Despite the co-existence of genetically distinct viruses within the same host, most intra-host minor variants were not shared between transmission pairs, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions. Furthermore, the narrow bottleneck and active viral activity in the respiratory tract show that the passage of a small number of virions can cause infection. Our data have therefore delivered a key genomic resource for the SARS-CoV-2 transmission research and enhanced our understanding of the evolutionary dynamics of SARS-CoV-2.

A path towards SARS-CoV-2 attenuation: metabolic pressure on CTP synthesis rules the virus evolution (preprint)

Fighting the COVID-19 epidemic summons deep understanding of the way SARS-CoV-2 taps into its host cell metabolic resources. We describe here the singular metabolic background that creates a bottleneck constraining coronaviruses to evolve towards likely attenuation in the long term. Cytidine triphosphate (CTP) is at the crossroad of the biosynthetic processes that allow the virus to multiply. This is because CTP is in demand for three essential steps. It is a building block of the virus genome, it is required for synthesis of the cytosine-based liponucleotide precursors of the viral envelope and, finally, it is a critical building block of the host transfer RNAs synthesis. The CCA 3-end of all the transfer RNAs required to translate the RNA genome and further transcripts into the proteins used to build active virus copies is not coded in the human genome. It must be synthesized de novo from CTP and ATP. Furthermore, intermediary metabolism is built on compulsory steps of synthesis and salvage of cytosine-based metabolites via uridine triphosphate (UTP) that keep limiting CTP availability. As a consequence, accidental replication errors tend to replace cytosine by uracil in the genome, unless recombination events allow the sequence to return to its ancestral sequences. We document some of the consequences of this situation in the function of viral proteins. We also highlight and provide a raison detre to viperin, an enzyme of innate antiviral immunity, which synthesizes 3-deoxy-3',4-didehydro-CTP (ddhCTP) as an extremely efficient antiviral nucleotide.

Risk Factors and Outcomes of Acute Kidney Injury in Critically Ill Patients With Coronavirus Disease 2019 (preprint)

Background: Coronavirus disease 2019 (COVID-19) has emerged as a major global health threat with a great number of deaths worldwide. Acute kidney injury (AKI) is a common complication in patients admitted to the intensive care unit. We aimed toassess the incidence, risk factors and in-hospital outcomes of AKI in COVID-19 patients admitted to intensive care unitMethods: we conducted a retrospective observational study in intensive care unit of Tongji hospital, which was assigned responsibility for the treatments of severe COVID-19 patients by Wuhan government. The AKI was defined and staged based onKidney Disease: Improving Global Outcomes (KDIGO) criteria. Mild AKI was defined as stage 1, and severe AKI was defined as stage 2 or stage 3. We used logistic regression analysis to evaluate AKI risk factors and the association between AKI and in-hospital mortality.Results: A total of 150 patients with COVID-19 were included in our study. The median age of patients was 70 (interquartile range, 60-80) years and 62.7% were male. 70 (46.7%) patients developed AKI during hospitalization, corresponding to the 17.3% in stage 1 and 9.3% in stage 2 and 20.0% in stage 3, respectively. Compared to patients without AKI, patients with AKI had higher proportion of mechanical ventilation mortality and higher in-hospital mortality. 95.5% patients with severe AKI received mechanical ventilation and in-hospital mortality was up to 79.5%. Severe AKI was independently associated with high in-hospital mortality (OR: 4.30; 95% CI: 1.83-10.10). Logistic regression analysis demonstrated that high serum interleukin-6 (OR: 2.54; 95%CI: 1.00-6.42) and interleukin-10 (OR: 3.02; 95%CI: 1.17-7.82) were risk factors for severe AKI development.Conclusions: severe AKI was associated with high in-hospital mortality and inflammatory response may play a role in AKI development in critically ill patients with COVID-19. 

Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients (preprint)

As of middle May 2020, the causative agent of COVID-19, SARS-CoV-2, has infected over 4 million people with more than 300 thousand death as official reports1,2. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. Here, using deep sequencing data, we achieved and characterized consensus genomes and intra-host genomic variants from 32 serial samples collected from eight patients with COVID-19. The 32 consensus genomes revealed the coexistence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparison of allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events among intra-host transmissions. Nonetheless, we observed a maintained viral genetic diversity within GIT, showing an increased population with accumulated mutations developed in the tissue-specific environments. The iSNVs identified here not only show spatial divergence of intra-host viral populations, but also provide new insights into the complex virus-host interactions.

Clinical characteristics of 10 children with COVID-19 outside of Wuhan in Hubei Province (preprint)

Background：An outbreak of coronavirus disease 2019 (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) began in Wuhan, Hubei Province, China in December 2019. This study aims to report the clinical characteristics of children COVID-19 in Xiangyang, a city outside of Wuhan within Hubei Province.Methods：We retrospectively investigated the clinical manifestations, Chest CT imaging, and laboratory characteristics of confirmed cases of children with COVID-19 with WHO interim guidance in Xiangyang Central Hospital from Feb 1 to Mar 10, 2020. 10 children cases were confirmed by real-time RT-PCR and were analyzed for epidemiological, demographic, clinical, radiological features and laboratory data. Outcomes were followed up until Mar 10, 2020.Results：6 cases (60%) had never been to Wuhan but closely contacted with family members with confirmed COVID-19, and 4 cases (40%) had made short term trips to Wuhan alone without familial clustering. The most common symptoms were cough (50%) followed by fever (40%), 4 cases (40%) showed asymptomatic characteristics including 2 cases (20%) with abnormal chest computed tomograms (CT) image. 9 cases (90%) were mild type, only 1 case (10%) was moderate type, none of them progressed in severe or critical disease. 4 (40%) cases showed leucopenia but none lymphopenia. Abnormalities on chest CT were detected among 8 cases (80%), 2 of 4 cases without obvious symptoms had abnormal chest CT.Conclusions: Children's infection is mainly caused by family clusters. No transmission to other individuals from children was found in our observation. The clinical manifestations in children with COVID-19 are non-specific with milder symptoms and good outcomes.

Effect of continuous renal replacement therapy on all-cause mortality in COVID-19 patients undergoing invasive mechanical ventilation: a retrospective cohort study (preprint)

BackgroundFor the coronavirus disease 2019 (COVID-19), critically ill patients had a high mortality rate. We aimed to assess the association between prolonged intermittent renal replacement therapy (PIRRT) and mortality in patients with COVID-19 undergoing invasive mechanical ventilation. MethodsIn this retrospective cohort study, we included all patients with COVID-19 undergoing invasive mechanical ventilation from February 12nd to March 2nd, 2020. All patients were followed until death or March 28th, and all survivors were followed for at least 30 days. ResultsFor 36 hospitalized COVID-19 patients with invasive mechanical ventilation, the mean age was 69.4 ({+/-} 10.8) years, and 30 patients (83.3%) were men. Twenty-two (61.1%) patients received PIRRT (PIRRT group) and 14 cases (38.9%) were managed with conventional strategy (non-PIRRT group). There were no differences in age, sex, comorbidities, complications, treatments and most of the laboratory findings. During median follow-up period of 9.5 (interquartile range 4.3-33.5) days, 13 of 22 (59.1%) patients in the PIRRT group and 11 of 14 (78.6%) patients in the non-PIRRT group died. Kaplan-Meier analysis demonstrated prolonged survival in patients in the PIRRT group compared with that in the non-PIRRT group (P = 0.042). The association between PIRRT and a reduced risk of mortality remained significant in three different models, with adjusted hazard ratios varying from 0.332 to 0.398. Higher levels of IL-2 receptor, TNF-, procalcitonin, prothrombin time, and NT-proBNP were significantly associated with an increased risk of mortality in patients with PIRRT. ConclusionPIRRT may be beneficial for the treatment of COVID-19 patients with invasive mechanical ventilation. Further prospective multicenter studies with larger sample sizes are required.

Multiple approaches for massively parallel sequencing of HCoV-19 genomes directly from clinical samples (preprint)

COVID-19 has caused a major epidemic worldwide, however, much is yet to be known about the epidemiology and evolution of the virus. One reason is that the challenges underneath sequencing HCoV-19 directly from clinical samples have not been completely tackled. Here we illustrate the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19 from clinical samples covering a range of sample types and viral load. We also examine and compare the bias, sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. This is, to date, the first work systematically implements amplicon and capture approaches in sequencing HCoV-19, as well as the first comparative study across methods. Our work offers practical solutions for genome sequencing and analyses of HCoV-19 and other emerging viruses.

Kidney impairment is associated with in-hospital death of COVID-19 patients (preprint)

Background: Information on kidney impairment in patients with coronavirus disease 2019 (COVID-19) is limited. This study aims to assess the prevalence and impact of abnormal urine analysis and kidney dysfunction in hospitalized COVID-19 patients in Wuhan. Method: We conducted a consecutive cohort study of COVID-19 patients admitted in a tertiary teaching hospital with 3 branches following a major outbreak in Wuhan in 2020. Hematuria, proteinuria, serum creatinine concentration and other clinical parameters were extracted from the electronic hospitalization databases and laboratory databases. Incidence rate for acute kidney injury (AKI) was examined during the study period. Association between kidney impairment and in-hospital death was analyzed. Results: We included 710 consecutive COVID19 patients, 89 (12.3%) of whom died in hospital. The median age of the patients was 63 years (inter quartile range, 51-71), including 374 men and 336 women. On admission, 44% of patients have proteinuria hematuria and 26.9% have hematuria, and the prevalence of elevated serum creatinine and blood urea nitrogen were 15.5% and 14.1% respectively. During the study period, AKI occurred in 3.2% patients. Kaplan-Meier analysis demonstrated that patients with kidney impairment have higher risk for in-hospital death. Cox proportional hazard regression confirmed that elevated serum creatinine, elevated urea nitrogen, AKI, proteinuria and hematuria was an independent risk factor for in-hospital death after adjusting for age, sex, disease severity, leukocyte count and lymphocyte count. Conclusion: The prevalence of kidney impairment (hematuria, proteinuria and kidney dysfunction) in hospitalized COVID-19 patients was high. After adjustment for confounders, kidney impairment indicators were associated with higher risk of in-hospital death. Clinicians should increase their awareness of kidney impairment in hospitalized COVID-19 patients.