Remdesivir, Molnupiravir and Nirmatrelvir remain active against SARS-CoV-2 Omicron and other variants of concern.

The in vitro effect of GS-441524, remdesivir, EIDD-1931, molnupiravir and nirmatrelvir against the various SARS-CoV-2 VOCs, including Omicron, was determined. VeroE6-GFP cells were pre-treated overnight with serial dilutions of the compounds before infection. The number of fluorescent pixels of GFP signal, determined by high-content imaging on day 4 post-infection, was used as read-out, and the EC50 of each compound on a viral isolate of each VOC was calculated. These experiments were performed in the presence of the Pgp-inhibitor CP-100356 in order to limit compound efflux. A SARS-CoV-2 strain grown from the first Belgian patient sample was used as ancestral strain. All the other isolates were obtained from patients in Belgium as well. Our results indicate that GS-441524, remdesivir, EIDD-1931, molnupiravir and nirmatrelvir retain their activity against the VOCs Alpha, Beta, Gamma, Delta and Omicron. This is in accordance with the observation that the target proteins of these antivirals are highly conserved.

Receptor binding and escape from Beta antibody responses drive Omicron-B.1.1.529 evolution

On the 24th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced. Omicron contains a total of 30 substitutions plus deletions and an insertion in Spike, far more than any previously reported variant. The mutations include those previously identified by In-vitro evolution to contribute to high-affinity binding to ACE2, including mutations Q498R and N501Y critical in forming additional interactions in the interface. Together with increased charge complementarity between the RBD and ACE2, these substantially increase affinity and potentially virus transmissibility through increased syncytia formation. Further mutations promote immune evasion. We have studied the binding of a large panel of potent monoclonal antibodies generated from early pandemic or Beta infected cases. Mutations in Omicron will likely compromise the binding of many of these and additionally, the binding of antibodies under commercial development, however residual binding should provide protection from severe disease.

Emerging Mutations Potentially Related to SARS-CoV-2 Immune Escape: The Case of a Long-Term Patient

SARS-CoV-2 isolates from long-term COVID-19 patients play a significant role in understanding the mechanisms of infection and virus persistence. This study describes a SARS-CoV-2 isolate from a 53-year-old woman from Apulia (Italy), who was COVID-19 positive for approximately four months. In this paper we aimed to investigate any potential correlation between genetic mutations and clinical features of this case of infection. The viral isolate was assigned to lineage B.1.177.51 through whole-genome sequencing (WGS) and harbored a novel set of mutations on the Spike protein (V143D, del144/145 and E484K); furthermore, seroneutralization assays showed impaired response of the surveyed strain to BNT162b2 (Comirnaty) Pfizer/BioNTech vaccine-induced (average reduction of 70%) and convalescent sera (average reduction of 19.04%), when compared to VOC P.1. This study highlights the importance of genomic surveillance for the management of the COVID-19 pandemic, the relevance of monitoring of emerging SARS-CoV-2 mutations in all lineages, and the necessity of testing the response of emerging variants to available therapies and vaccines.

ONTdeCIPHER: An amplicon-based nanopore sequencing pipeline for tracking pathogen variants

Motivation: Amplicon-based nanopore sequencing is increasingly used for molecular surveillance during epidemics (e.g. ZIKA, EBOLA) or pandemics (e.g. SARS-CoV-2). However, there is still a lack of versatile and easy-to-use tools that allow users with minimal bioinformatics skills to perform the main steps of downstream analysis, from quality testing to SNPs effect to phylogenetic analysis. Results: Here, we present ONTdeCIPHER, an amplicon-based Oxford Nanopore Technology (ONT) sequencing pipeline to analyze the genetic diversity of SARS-CoV-2 and other pathogenes. Our pipeline integrates 13 bioinformatics tools. With a single command line and a simple configuration file, users can pre-process their data and obtain the sequencing statistics, reconstruct the consensus genome, identify variants and their effects for each viral isolate, infer lineage and, finally perform multi-sequence alignments and phylogenetic analyses.

COMPARATIVE STUDY BETWEEN ROTA VIRUSES ISOLATED FROM DIARRHEATIC INFANT BABIES AND NEWLY BORN CALVES

Rota viruses were isolated in vero continuous cell line from infant babies and newly borne calves affected by diarrhea after treatment in every passage with 10 mg/ml of trypsin and adding 0.5 mg/ml of trypsin in the maintenance media. The isolated viruses induced distinctive and progressive type of cytopatheic effect in infected cells and highest titer was 2x10 6. TCID,50/0.1 for bovine viral isolate. The isolated 50/0.1 for human viral isolate and 2x10 » viruses were identified by indirect fluorescent antibody technique by using reference calf rotavirus antisera. Comparative study were conducted on both human and bovine viral isolate including growth in different cell culture, vero cell line was very sensitive to support growth of both viruses than secondary embryonic calf kidney cell culture, lamb testes and primary embryonic chicken fibroblast cell culture. Both viruses induced morphologically similar kind or plaques in vero cell line but plaqes formed by human isolate were larger in size about 1.5 - 2.5 mm in diameter than those of bovine isolate 1.5 - 2 mm. Cross reactive viral antigens were detected between the isolated viruses in indirect fluorescent antibody technique but not in serum neutralization test by using reference bovine rotavirus antisera.

In vitro evaluation of antiviral efficacy of a Siddha Formulation against SARS-CoV-2

Introduction: SARS-CoV-2 virus caused COVID-19 pandemic with 218 million cases and 45 million deaths world over. It has challenged the already overburdened healthcare systems and created an urgent need to investigate solutions present in other healthcare systems. In this study Kabasura Kudineer is investigated as an intervention to influence the immune response which is beneficial for the host and stop the viral replication. Methods: Kabasura Kudineer is a polyherbal formulation containing 15 herbal drugs mixed in equal quantity. It is an official Siddha formulation, used for phlegmatic fevers and flu-like symptoms. To conduct this study Vero E6 (CL1008), the African monkey kidney epithelial cell line was taken and infected with SARS-CoV-2 viral isolate. The Kabasura Kudineer was added in different concentrations; 0.5 mg/mL, 0.25 mg/mL, 0.12 mg/mL, 0.06 mg/mL and 0.03 mg/mL to the infected cells respectively. These cell plates were incubated for 3 days in 5% CO2 incubator. Remdesivir was used as a positive control. The cells were fixed with formaldehyde, stained with crystal violet and plaques were visualised. Plaques were counted as PFU/ml. Result: Kabasura Kudineer was found to exhibit good antiviral activity against SARS-CoV-2. The highest antiviral activity was 81.5% at a concentration of 0.5 mg/ml. The IC-50 value was found to be 0.2 mg/mL. Conclusion: The antiviral efficacy of Kabasura Kudineer in our study showed reduction in the viral load which supports the results of clinical studies. Kabasura Kudineer can be used widely in a clinical setting as a treatment for COVID-19.

Near-Complete Genome Sequence of Ndumu Virus from Garissa, Kenya, 1997

We report a nearly complete genome sequence of Ndumu virus (NDUV) identified using a metagenomics approach. The sequence was derived from a viral isolate obtained from a bovine calf following a diagnostic investigation of the 1997 to 1998 Rift Valley fever (RVF) outbreak in the Garissa District of northeastern Kenya.

Caprine Arthritis Encephalitis Virus Is Associated with Renal Lesions

Caprine arthritis encephalitis virus (CAEV) is a monocyte/macrophage-tropic lentivirus that primarily infects goats resulting in a well-recognized set of chronic inflammatory syndromes focused on the joint synovium, tissues of the central nervous system, pulmonary interstitium and mammary gland. Clinically affected animals generally manifest with one or more of these classic CAEV-associated tissue lesions; however, CAEV-associated renal inflammation in goats has not been reported in the peer-reviewed literature. Here we describe six goats with chronic, multisystemic CAEV infections in conjunction with CAEV-associated renal lesions. One of the animals had CAEV antigen-associated thrombotic arteritis resulting in infarction of both the kidney and heart. These goats had microscopic evidence of inflammatory renal injury (interstitial nephritis) with detectable renal immunolabeling for CAEV antigen in three of six animals and amplifiable proviral sequences consistent with CAEV in all six animals. Cardiac lesions (vascular, myocardial or endocardial) were also identified in four of six animals. Within the viral promoter (U3) region, known transcription factor binding sites (TFBSs) were generally conserved, although one viral isolate had a duplication of the U3 A region encoding a second gamma-activated site (GAS). Despite the TFBS conservation, the isolates demonstrated a degree of phylogenetic diversity. At present, the clinical consequence of CAEV-associated renal injury is not clear.

The plasmablast response to SARS-CoV-2 mRNA vaccination is dominated by non-neutralizing antibodies that target both the NTD and the RBD

SummaryIn this study we profiled vaccine-induced polyclonal antibodies as well as plasmablast derived mAbs from subjects who received SARS-CoV-2 spike mRNA vaccine. Polyclonal antibody responses in vaccinees were robust and comparable to or exceeded those seen after natural infection. However, that the ratio of binding to neutralizing antibodies after vaccination was greater than that after natural infection and, at the monoclonal level, we found that the majority of vaccine-induced antibodies did not have neutralizing activity. We also found a co-dominance of mAbs targeting the NTD and RBD of SARS-CoV-2 spike and an original antigenic-sin like backboost to seasonal human coronaviruses OC43 and HKU1 spike proteins. Neutralizing activity of NTD mAbs but not RBD mAbs against a clinical viral isolate carrying E484K as well as extensive changes in the NTD was abolished, suggesting that a proportion of vaccine induced RBD binding antibodies may provide substantial protection against viral variants carrying E484K.