Genomic analysis of SARS-CoV-2 reveals local viral evolution in Ghana

The confirmed case fatality rate for the coronavirus disease 2019 (COVID-19) in Ghana has dropped from a peak of 2% in March to be consistently below 1% since May 2020. Globally, case fatality rates have been linked to the strains/clades of circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a specific country. Here we present 46 whole genomes of SARS-CoV-2 circulating in Ghana, from two separate sequencing batches: 15 isolates from the early epidemic (March 12–April 1 2020) and 31 from later time-points ( 25–27 May 2020). Sequencing was carried out on an Illumina MiSeq system following an amplicon-based enrichment for SARS-CoV-2 cDNA. After genome assembly and quality control processes, phylogenetic analysis showed that the first batch of 15 genomes clustered into five clades: 19A, 19B, 20A, 20B, and 20C, whereas the second batch of 31 genomes clustered to only three clades 19B, 20A, and 20B. The imported cases (6/46) mapped to circulating viruses in their countries of origin, namely, India, Hungary, Norway, the United Kingdom, and the United States of America. All genomes mapped to the original Wuhan strain with high similarity (99.5–99.8%). All imported strains mapped to the European superclade A, whereas 5/9 locally infected individuals harbored the B4 clade, from the East Asian superclade B. Ghana appears to have 19B and 20B as the two largest circulating clades based on our sequence analyses. In line with global reports, the D614G linked viruses seem to be predominating. Comparison of Ghanaian SARS-CoV-2 genomes with global genomes indicates that Ghanaian strains have not diverged significantly from circulating strains commonly imported into Africa. The low level of diversity in our genomes may indicate lower levels of transmission, even for D614G viruses, which is consistent with the relatively low levels of infection reported in Ghana.     

Genetic tracing of HCoV-19 for the re-emerging outbreak of COVID-19 in Beijing,China

The ongoing pandemic of coronavirus disease 2019(COVID-19)caused by a novel severe acute respiratory syndrome coronavirus 2(SARS-CoV-2,also named as 2019-nCoV or HCoV-19)poses an unprecedented threat to public health(Zhu et al.,2020;Wang et al.,2020;Jiang et al.,2020).The novel HCoV-19 virus has rapidly spread into multiple countries across the world since it was first reported in December 2019.The World Health Organization(WHO)declared COVID-19 as a pandemic on 11th March 2020.As of 4th July,over 10 million confirmed COVID-19 cases have been reported in over 200 countries/regions with more than 0.5 million deaths,including 85,287 documented cases and 4,648 deaths in China(WHO,2020a).     

Molecular deconvolution of the neutralizing antibodies induced by an inactivated SARS-CoV-2 virus vaccine

Dear Editor, The rapid emergence and persistence of the pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) has had enormous impacts on global health and the economy.Effective vaccines against SARS-CoV-2 are urgently needed to control the coronavirus disease 2019(COVID-19) pandemic,and multiple vaccines have been found to be efficacious in preventing symptomatic COVID-19(Polack et al.,2020;Wu et al.,2020;Jones and Roy,2021).We have developed a traditional beta-propiolactone-inacti-vated aluminum hydroxide-adjuvanted whole-virion SARS-CoV-2 vaccine (BBIBP-CorV),which elicited protective immune responses in clinical trials (Wang et al.,2020;Xia et al.,2021).The vaccine has been granted conditional approvals or emergency use authorizations (EUAs) in China and other countries.     

SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event

The first case of SARS-CoV-2 in Basel, Switzerland was detected on February 26^th 2020. We present a phylogenetic study to explore viral introduction and evolution during the exponential early phase of the local COVID-19 outbreak from February 26^th until March 23^rd. We sequenced SARS-CoV-2 naso-oropharyngeal swabs from 746 positive tests that were performed at the University Hospital Basel during the study period. We successfully generated 468 high quality genomes from unique patients and called variants with our COVID-19 Pipeline (COVGAP), and analysed viral genetic diversity using PANGOLIN taxonomic lineages. To identify introduction and dissemination events we incorporated global SARS-CoV-2 genomes and inferred a time-calibrated phylogeny. Epidemiological data from patient questionnaires was used to facilitate the interpretation of phylogenetic observations. The early outbreak in Basel was dominated by lineage B.1 (83·6%), detected first on March 2^nd, although the first sample identified belonged to B.1.1. Within B.1, 68·2% of our samples fall within a clade defined by the SNP C15324T (‘Basel cluster’), including 157 identical sequences at the root of the ‘Basel cluster’, some of which we can specifically trace to regional spreading events. We infer the origin of B.1-C15324T to mid-February in our tri-national region. The other genomes map broadly over the global phylogenetic tree, showing several introduction events from and/or dissemination to other regions of the world via travellers. Family transmissions can also be traced in our data. A single lineage variant dominated the outbreak in the Basel area while other lineages, such as the first (B.1.1), did not propagate. A mass gathering event was the predominant initial source of cases, with travel returners and family transmissions to a lesser extent. We highlight the importance of adding specific questions to epidemiological questionnaires, to obtain data on attendance of large gatherings and their locations, as well as travel history, to effectively identify routes of transmissions in up-coming outbreaks. This phylogenetic analysis in concert with epidemiological and contact tracing data, allows connection and interpretation of events, and can inform public health interventions.Trial Registration: ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT04351503","term_id":"NCT04351503"}}NCT04351503.     

SARS-CoV-2 signaling pathway map: A functional landscape of molecular mechanisms in COVID-19

Coronavirus disease (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 has been declared a pandemic by WHO. The clinical manifestation and disease progression in COVID-19 patients varies from minimal symptoms to severe respiratory issues with multiple organ failure. Understanding the mechanism of SARS-CoV-2 interaction with host cells will provide key insights into the effective molecular targets for the development of novel therapeutics. Recent studies have identified virus-mediated phosphorylation or activation of some major signaling pathways, such as ERK1/2, JNK, p38, PI3K/AKT and NF-κB signaling, that potentially elicit the cytokine storm that serves as a major cause of tissue injuries. Several studies highlight the aggressive inflammatory response particularly ‘cytokine storm’ in SARS-CoV-2 patients. A depiction of host molecular dynamics triggered by SARS-CoV-2 in the form of a network of signaling molecules will be helpful for COVID-19 research. Therefore, we developed the signaling pathway map of SARS-CoV-2 infection using data mined from the recently published literature. This integrated signaling pathway map of SARS-CoV-2 consists of 326 proteins and 73 reactions. These include information pertaining to 1,629 molecular association events, 30 enzyme catalysis events, 43 activation/inhibition events, and 8,531 gene regulation events. The pathway map is publicly available through WikiPathways: https://www.wikipathways.org/index.php/Pathway:WP5115.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12079-021-00632-4.     

SARS-CoV-2 Does Not Replicate in Aedes Mosquito Cells nor Present in Field-Caught Mosquitoes from Wuhan

With the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and growing fear, people have become very concerned about whether this novel coronavirus could be transmitted by mosquitoes. We evaluate the infectivity of SARS-CoV-2 in Aedes albopictus and Aedes aegypti derived cell lines. The results indicated that SARS-CoV-2 could not replicate in both C6/36, Sf9 and Aag2 cells. Further, no SARS-CoV-2 RNA was detected in the field collected Culex, and Anopheles mosquitoes during the months of April and May in Wuhan in 2020. Our findings highlight the restricted replication of SARS-CoV-2 in mosquito cells and field-caught mosquitoes.     

The impact of COVID-19 on pregnancy outcomes: a systematic review and meta-analysis

Background:The impact of coronavirus disease 2019 (COVID-19) on maternal and newborn health is unclear. We aimed to evaluate the association between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection during pregnancy and adverse pregnancy outcomes.METHODS:We conducted a systematic review and meta-analysis of observational studies with comparison data on SARS-CoV-2 infection and severity of COVID-19 during pregnancy. We searched for eligible studies in MEDLINE, Embase, ClinicalTrials.gov, medRxiv and Cochrane databases up to Jan. 29, 2021, using Medical Subject Headings terms and keywords for “severe acute respiratory syndrome coronavirus 2 OR SARS-CoV-2 OR coronavirus disease 2019 OR COVID-19” AND “pregnancy.” We evaluated the methodologic quality of all included studies using the Newcastle–Ottawa Scale. Our primary outcomes were preeclampsia and preterm birth. Secondary outcomes included stillbirth, gestational diabetes and other pregnancy outcomes. We calculated summary odds ratios (ORs) or weighted mean differences with 95% confidence intervals (CI) using random-effects meta-analysis.RESULTS:We included 42 studies involving 438 548 people who were pregnant. Compared with no SARS-CoV-2 infection in pregnancy, COVID-19 was associated with preeclampsia (OR 1.33, 95% CI 1.03 to 1.73), preterm birth (OR 1.82, 95% CI 1.38 to 2.39) and stillbirth (OR 2.11, 95% CI 1.14 to 3.90). Compared with mild COVID-19, severe COVID-19 was strongly associated with preeclampsia (OR 4.16, 95% CI 1.55 to 11.15), preterm birth (OR 4.29, 95% CI 2.41 to 7.63), gestational diabetes (OR 1.99, 95% CI 1.09 to 3.64) and low birth weight (OR 1.89, 95% CI 1.14 to 3.12).INTERPRETATION:COVID-19 may be associated with increased risks of preeclampsia, preterm birth and other adverse pregnancy outcomes.

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and was declared a global pandemic in March 2020.¹ Pregnant people and infants may be particularly susceptible to COVID-19 because the physiologic changes of pregnancy involve cardiorespiratory and immune systems, which may result in an altered response to SARS-CoV-2 infection in pregnancy. ² Fetuses may be exposed to SARS-CoV-2 during critical periods of fetal development.³ The nature of the association between COVID-19 and pregnancy outcomes remains unclear, and meta-analyses involving patients with COVID-19 who are pregnant are limited. Previous reviews have focused mostly on prevalence estimates from case reports or case series that are difficult to interpret and potentially biased.^4,5 A 2020 systematic review suggested that people who are pregnant did not have an increased risk of SARS-CoV-2 infection or symptomatic COVID-19, but they were at risk of severe COVID-19 compared with those who were not pregnant.⁵ However, this review included suspected COVID-19 cases in addition to confirmed cases.⁵ Although some recent observational studies have suggested that people with confirmed asymptomatic and symptomatic COVID-19,^6–15 as well as mild and severe infections,^{6,8,9,15–22} may be at risk of adverse pregnancy outcomes, we are unaware of any systematic reviews that have comprehensively evaluated these data.We performed a systematic review and meta-analysis of maternal, fetal and neonatal outcomes among pregnant patients with COVID-19. We aimed to determine the association between SARS-CoV-2 infection and adverse pregnancy outcomes, including preeclampsia, preterm birth and stillbirth.     

Re-detectable positive SARS-CoV-2 RNA tests in patients who recovered from COVID-19 with intestinal infection

Dear Editor,Severe acute respiratory syndrome coronavirus 2(SARSCoV-2),a novel coronavirus that causes Coronavirus Disease 2019(COVID-19)(Yang and Wang,2020),has spread to more than 200 countries and infected more than 9,000,000 people as of Jun 2020.Tens of thousands of patients with COVID-19 have recovered and been discharged from hospital.However,there are reports of recovered patients who subsequently tested positive for SARSCoV-2 after discharge(re-detectable positive,RP)(An et al.,2020;Lan et al.,2020),and this has led to increasing focus on the mechanism(s)underlying RP.     

The Global Landscape of SARS-CoV-2 Genomes,Variants, and Haplotypes in 2019nCoVR

On January 22, 2020, China National Center for Bioinformation (CNCB) released the 2019 Novel Coronavirus Resource (2019nCoVR), an open-access information resource for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). 2019nCoVR features a comprehensive integration of sequence and clinical information for all publicly available SARS-CoV-2 isolates, which are manually curated with value-added annotations and quality evaluated by an automated in-house pipeline. Of particular note, 2019nCoVR offers systematic analyses to generate a dynamic landscape of SARS-CoV-2 genomic variations at a global scale. It provides all identified variants and their detailed statistics for each virus isolate, and congregates the quality score, functional annotation, and population frequency for each variant. Spatiotemporal change for each variant can be visualized and historical viral haplotype network maps for the course of the outbreak are also generated based on all complete and high-quality genomes available. Moreover, 2019nCoVR provides a full collection of SARS-CoV-2 relevant literature on the coronavirus disease 2019 (COVID-19), including published papers from PubMed as well as preprints from services such as bioRxiv and medRxiv through Europe PMC. Furthermore, by linking with relevant databases in CNCB, 2019nCoVR offers data submission services for raw sequence reads and assembled genomes, and data sharing with NCBI. Collectively, SARS-CoV-2 is updated daily to collect the latest information on genome sequences, variants, haplotypes, and literature for a timely reflection, making 2019nCoVR a valuable resource for the global research community. 2019nCoVR is accessible at https://bigd.big.ac.cn/ncov/.     

Gene Presence/Absence Variation analysis of coronavirus family displays its pan-genomic diversity

SARS-CoV-2 belongs to the coronavirus family. Comparing genomic features of viral genomes of coronavirus family can improve our understanding about SARS-CoV-2. Here we present the first pan-genome analysis of 3,932 whole genomes of 101 species out of 4 genera from the coronavirus family. We found that a total of 181 genes in the pan-genome of coronavirus family, among which only 3 genes, the S gene, M gene and N gene, are highly conserved. We also constructed a pan-genome from 23,539 whole genomes of SARS-CoV-2. There are 13 genes in total in the SARS-CoV-2 pan-genome. All of the 13 genes are core genes for SARS-CoV-2. The pan-genome of coronaviruses shows a lower level of diversity than the pan-genomes of other RNA viruses, which contain no core gene. The three highly conserved genes in coronavirus family, which are also core genes in SARS-CoV-2 pan-genome, could be potential targets in developing nucleic acid diagnostic reagents with a decreased possibility of cross-reaction with other coronavirus species.     

Symptoms associated with a positive result for a swab for SARS-CoV-2 infection among children in Alberta

BACKGROUND:Research involving children with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has primarily focused on those presenting to emergency departments. We aimed to determine the symptoms most commonly associated with a positive result for a SARS-CoV-2 swab among community-based children.METHODS:We conducted an observational study among children tested and followed for SARS-CoV-2 infection using nasal, nasopharyngeal, throat or other (e.g., nasopharyngeal aspirate or tracheal secretions, or unknown) swabs between Apr. 13 and Sept. 30, 2020, in Alberta. We calculated positive likelihood ratios (LRs) for self-reported symptoms and a positive SARS-CoV-2 swab result in the entire cohort and in 3 sensitivity analyses: all children with at least 1 symptom, all children tested because of contact tracing whether they were symptomatic or not and all children 5 years of age or older.RESULTS:We analyzed results for 2463 children who underwent testing for SARS-CoV-2 infection; 1987 children had a positive result and 476 had a negative result. Of children with a positive test result for SARS-CoV-2, 714 (35.9%) reported being asymptomatic. Although cough (24.5%) and rhinorrhea (19.3%) were 2 of the most common symptoms among children with SARS-CoV-2 infection, they were also common among those with negative test results and were not predictive of a positive test (positive LR 0.96, 95% confidence interval [CI] 0.81–1.14, and 0.87, 95% CI 0.72–1.06, respectively). Anosmia/ageusia (positive LR 7.33, 95% CI 3.03–17.76), nausea/vomiting (positive LR 5.51, 95% CI 1.74–17.43), headache (positive LR 2.49, 95% CI 1.74– 3.57) and fever (positive LR 1.68, 95% CI 1.34–2.11) were the symptoms most predictive of a positive result for a SARS-CoV-2 swab. The positive LR for the combination of anosmia/ageusia, nausea/vomiting and headache was 65.92 (95% CI 49.48–91.92).INTERPRETATION:About two-thirds of the children who tested positive for SARS-CoV-2 infection reported symptoms. The symptoms most strongly associated with a positive SARS-CoV-2 swab result were anosmia/ageusia, nausea/vomiting, headache and fever.

The refrain that “children are not small adults” certainly seems to apply in the context of coronavirus disease 2019 (COVID-19). Children are less likely to become infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) than adults and seem to experience less severe symptoms and have better prognoses.^1–4 However, some studies have suggested that reduced disease severity in children leads to them being less likely to undergo testing.⁵ Three 2020 studies highlighted that COVID-19 symptoms in children are similar to those of other acute respiratory illnesses, with fever, cough, nasal congestion, fatigue and runny nose predominating. ^6–8 On Sept. 15, 2020, the Centers for Disease Control and Prevention reported death to be an uncommon outcome in people younger than 21 years of age (0.08% of all deaths).⁹Beyond an understanding of what symptoms most commonly present in children, health care professionals and public health policy-makers could benefit from knowing which presenting symptoms are most likely to be associated with SARS-CoV-2 infection. Many jurisdictions have implemented screening questionnaires for pediatric-dominated settings such as schools. We hypothesized that some symptoms in children are more likely than others to be associated with a positive result for a test for SARS-CoV-2. We therefore assessed symptom patterns among children in Alberta who were followed by Alberta Public Health and who had swabs taken for possible SARS-CoV-2 infection, comparing those with positive results and those with negative results to estimate symptom frequencies and prognostic import of symptoms in a large cohort and in 3 subgroups.     

IL-15 immunotherapy is a viable strategy for COVID-19

Coronavirus disease 2019 (COVID-19) is a pulmonary inflammatory disease induced by a newly recognized coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 infection was detected for the first time in the city of Wuhan in China and spread all over the world at the beginning of 2020. Several millions of people have been infected with SARS-CoV-2, and almost 382,867 human deaths worldwide have been reported so far. Notably, there has been no specific, clinically approved vaccine or anti-viral treatment strategy for COVID-19. Herein, we review COVID-19, the viral replication, and its effect on promoting pulmonary fibro-inflammation via immune cell-mediated cytokine storms in humans. Several clinical trials are currently ongoing for anti-viral drugs, vaccines, and neutralizing antibodies against COVID-19. Viral clearance is the result of effective innate and adaptive immune responses. The pivotal role of interleukin (IL)-15 in viral clearance involves maintaining the balance of induced inflammatory cytokines and the homeostatic responses of natural killer and CD8⁺ T cells. This review presents supporting evidence of the impact of IL-15 immunotherapy on COVID-19.     

Fish ACE2 is not susceptible to SARS-CoV-2

The ongoing pandemic of coronavirus disease 2019 (COVID-19) has reshaped our daily life and caused > 4 million deaths worldwide (https://covid19.who.int/). Although lockdown and vaccination have improved the situation in many countries, imported cases and sporadic outbreaks pose a constant stress to the prevention and control of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent responsible for COVID-19, has a positive-sense single-stranded RNA genome of 30 kb (Coronaviridae Study Group of the International Committee on Taxonomy of Viruses, 2020). We and other groups have demonstrated that the SARS-CoV-2 could use the angiotensin-converting enzyme 2 (ACE2) as cell receptor, including orthologs of a broad range of animal species such as human, bats, ferrets, pigs, cats, and dogs (Hoffmann et al., 2020; Zhou et al., 2020; Liu et al., 2021). Although the evolutionary origin of SARS-CoV-2 can be linked to the discoveries of diverse coronaviruses related to SARS-CoV-2 in wild animals such as bats (Zhou et al., 2020; Wacharapluesadee et al., 2021) and pangolins (Liu et al., 2019; Lam et al., 2020), the direct origin of SARS-CoV-2 in humans remains unknown. In China, several sporadic outbreaks of COVID-19 in 2020 were linked to food in cold chain sold at trade markets, including salmon meat (http://www.nhc.gov.cn/xcs/yqtb/list_gzbd.shtml) (Yang et al., 2020). The detection of SARS-CoV-2 RNA on the surface of frozen meat for as long as 20 days has also been reported (Feng et al., 2021). A concern regarding the potential role of fish in SARS-CoV-2 transmission has also been raised. Therefore, we investigated the susceptibility of fish ACE2 to SARS-CoV-2.     

Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic

The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here, I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’s Sequence Read Archive. I recover the deleted files from the Google Cloud and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data further supports the idea that the Huanan Seafood Market sequences are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of currently known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2’s bat coronavirus relatives.     

新型冠状病毒的相关研究进展

2019年12月出现于湖北武汉的一种新型冠状病毒(SARS-CoV-2)感染所致肺炎疫情,给人类生命安全造成威胁。迄今为止,对2019年出现的SARS-CoV-2的研究仍处于起步阶段,本文就其相关研究进展进行综述,重点阐述了目前关于SARS-CoV-2的病原学与致病机制方面的研究成果,同时对其流行病学以及该病毒引发的肺炎临床特点加以总结,有助于读者及时了解SARS-CoV-2最新的研究动态,并为今后开展治疗药物及疫苗研发提供方向。     

De novo 3D models of SARS-CoV-2 RNA elements from consensus experimental secondary structures

The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosetta''s FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5′ UTR; the reverse complement of the 5′ UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3′ UTR. For eleven of these elements (the stems in SL1–8, reverse complement of SL1–4, FSE, s2m and 3′ UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets (‘FARFAR2-SARS-CoV-2’, https://github.com/DasLab/FARFAR2-SARS-CoV-2; and ‘FARFAR2-Apo-Riboswitch’, at https://github.com/DasLab/FARFAR2-Apo-Riboswitch’) include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules.