We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)–associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.

Chronic hepatitis B virus (HBV) infection can result in severe liver disease with eventual progression to cirrhosis and hepatocellular carcinoma. 1 Roughly 5% of the world' s population (over 350 million persons) are chronically infected with HBV. 2 Although interferon alfa remains the only licensed drug for the treatment of chronic HBV infection, the overall response rate to this immunotherapy is less than 40%. 3 Therefore, other effective antiviral therapies for patients with HBV infection are needed.Lamivudine [(-)2Ј-deoxy-3Ј-thiacytidine, 3TC] is a member of a class of antiviral nucleoside analogs that inhibit hepadnavirus replication specifically by terminating viral DNA synthesis. 4 Lamivudine is currently being evaluated in Phase III clinical trials for the treatment of both patients chronically infected with HBV and patients with HBV reinfection of an allograft after orthotopic liver transplantation.In Phase II trials, 5-7 lamivudine treatment was shown to rapidly reduce serum HBV DNA to levels below the detection limit of standard commercial assays, and to be well tolerated with no major toxicities. However, as with other antivirals, 7-11 resistance to lamivudine therapy can emerge in some patients. Recent investigations have reported the development of lamivudine-resistant HBV in six orthotopic liver transplantation patients on therapy. [12][13][14] In each patient, sequence analysis of serum HBV DNA revealed the presence of specific mutations in the tyrosine, methionine, aspartate, aspartate (YMDD) amino acid motif of the viral polymerase. This YMDD motif is a conserved domain of all reverse transcriptases (RT) and is required for polymerization activity. However, various other amino acid changes in the polymerase were also described in these reports.To determine the significance of various mutations in the development of lamivudine-resistant HBV, a more comprehensive study was undertaken. In this study, DNA sequences were determined from HBV isolates from 20 patients experiencing breakthrough HBV reactivation while on lamivudine therapy. From this larger series of 20 clinical HBV isolates, the database of lamivudine-resistant HBV sequences was expanded to confirm viral DNA mutations associated with lamivudine resistance in vivo. To explore the biological significance of the key observed mutations, putative resis-

By analysis of a single, variable, and short DNA sequence of 447 bp located within open reading frame 22 (ORF22), we discriminated three major varicella-zoster virus (VZV) genotypes. VZV isolates from all six inhabited continents that showed nearly complete homology to ORF22 of the European reference strain Dumas were assigned to the European (E) genotype. All Japanese isolates, defined as the Japanese (J) genotype, were identical in the respective genomic region and proved the most divergent from the E strains, carrying four distinct variations. The remaining isolates carried a combination of E-and J-specific variations in the target sequence and thus were collectively termed the mosaic (M) genotype. Three hundred twenty-six isolates collected in 27 countries were genotyped. A distinctive longitudinal distribution of VZV genotypes supports this approach. Among 111 isolates collected from European patients, 96.4% were genotype E. Consistent with this observation, approximately 80% of the VZV strains from the United States were also genotype E. Similarly, genotype E viruses were dominant in the Asian part of Russia and in eastern Australia. M genotype viruses were strongly dominant in tropical regions of Africa, Indochina, and Central America, and they were common in western Australia. However, genotype M viruses were also identified as a minority in several countries worldwide. Two major intertypic variations of genotype M strains were identified, suggesting that the M genotype can be further differentiated into subgenotypes. These data highlight the direction for future VZV genotyping efforts. This approach provides the first simple genotyping method for VZV strains in clinical samples.Varicella-zoster virus (VZV) is a human herpesvirus that commonly causes chicken pox (varicella), usually in young children. Following primary infection a lifelong latent infection is established, and the virus often reactivates in adulthood or senescence to cause shingles (zoster). The VZV genome consists of 125 kb of linear, double-stranded DNA comprising one long and one short unique region, each flanked by inverted repeats (10), and five internal repeat regions (R1 to R5) have been identified. The VZV genome contains at least 71 open reading frames (ORFs), and the functions of many of the proteins they encode have been characterized (10).During the past 2 decades, several groups attempted to evaluate VZV phylogeny. Early efforts in VZV typing used DNA restriction fragment length polymorphism (RFLP) analysis (13,37,38), an approach that confirmed the identity of the VZV strain that causes varicella on primary infection and later reactivates to cause zoster. Relatively consistent restriction enzyme digestion profiles for different VZV strains were observed, providing the first evidence that VZV has a highly conserved genome. Intrastrain variation in restriction enzyme fragment profiles among wild-type VZV isolates was observed (22,36,37). However, the most prominent differences were linked to variation in the number and composi...

Background COVID-19 is diagnosed via detection of SARS-CoV-2 RNA using real time reverse-transcriptase polymerase chain reaction (rtRT-PCR). Performance of many SARS-CoV-2 rtRT-PCR assays is not entirely known due to the lack of a gold standard. We sought to evaluate the false negative rate (FNR) and sensitivity of our laboratory-developed SARS-CoV-2 rtRT-PCR targeting the envelope (E) and RNA-dependent RNA-polymerase (RdRp) genes. Methods SARS-CoV-2 rtRT-PCR results at the Public Health Laboratory (Alberta, Canada) from January 21 to April 18, 2020 were reviewed to identify patients with an initial negative rtRT-PCR followed by a positive result on repeat testing within 14 days (defined as discordant results). Negative samples from these discordant specimens were re-tested using three alternate rtRT-PCR assays (targeting the E gene and N1/N2 regions of the nucleocapsid genes) to assess for false negative (FN) results. Results During the time period specified, 95,919 patients (100,001 samples) were tested for SARS-CoV-2. Of these, 49 patients were found to have discordant results including 49 positive and 52 negative swabs. Repeat testing of 52 negative swabs found five FNs (from five separate patients). Assuming 100% specificity of the diagnostic assay, the FNR and sensitivity in this group of patients with discordant testing was 9.3% (95% CI 1.5–17.0%) and 90.7% (95% CI 82.6–98.9%) respectively. Conclusions Studies to understand the FNR of routinely used assays are important to confirm adequate clinical performance. In this study, most FN results were due to low amounts of SARS-CoV-2 virus concentrations in patients with multiple specimens collected during different stages of infection. Post-test clinical evaluation of each patient is advised to ensure that rtRT-PCR results are not the only factor in excluding COVID-19.

We have developed a single-tube assay for SARS-CoV-2 in patient samples. This assay combined advantages of reverse transcription (RT) loop-mediated isothermal amplification (LAMP) with clustered regularly interspaced short palindromic repeats (CRISPRs) and the CRISPR-associated (Cas) enzyme Cas12a. Our assay is able to detect SARS-CoV-2 in a single tube within 40 min, requiring only a single temperature control (62 °C). The RT-LAMP reagents were added to the sample vial, while CRISPR Cas12a reagents were deposited onto the lid of the vial. After a half-hour RT-LAMP amplification, the tube was inverted and flicked to mix the detection reagents with the amplicon. The sequence-specific recognition of the amplicon by the CRISPR guide RNA and Cas12a enzyme improved specificity. Visible green fluorescence generated by the CRISPR Cas12a system was recorded using a smartphone camera. Analysis of 100 human respiratory swab samples for the N and/or E gene of SARS-CoV-2 produced 100% clinical specificity and no false positive. Analysis of 50 samples that were detected positive using reverse transcription quantitative polymerase chain reaction (RT-qPCR) resulted in an overall clinical sensitivity of 94%. Importantly, this included 20 samples that required 30–39 threshold cycles of RT-qPCR to achieve a positive detection. Integration of the exponential amplification ability of RT-LAMP and the sequence-specific processing by the CRISPR-Cas system into a molecular assay resulted in improvements in both analytical sensitivity and specificity. The single-tube assay is beneficial for future point-of-care applications.

Varicella-zoster virus (VZV), the cause of chickenpox and zoster, was the first human herpesvirus to be sequenced fully and the first for which vaccines have been licensed and widely used. Three groups have published genotyping schemes based on single nucleotide polymorphisms (SNPs) and, between them, have identified five distinct phylogenetic clades, with an additional two putative clades. Sequencing of over 23 whole VZV genomes from around the world further refined the phylogenetic distinctions between SNP genotypes. Widespread surveillance in countries in which the varicella vaccine is now in use and the difficulties posed by three unique genotyping approaches prompted an international meeting, at which a common nomenclature based on phylogenetic clades was agreed upon. In this paper, we review the original genotyping schemes and discuss the basis for a novel common nomenclature for VZV strains. We propose a minimum set of SNPs that we recommend should be used to genotype these viruses. Finally, we suggest criteria by which novel clades can be recognized.

Background: COVID serological tests are essential to determine the overall seroprevalence of a population, and to facilitate exposure estimates within that population. Methods: We performed a head-to-head assessment of enzyme immunoassays (EIA) and point of care lateral flow assays (POCT) to detect SARS-CoV-2 antibodies. Demographics, symptoms, co-morbidities, treatment, and mortality of patients whose sera was used were also reviewed. Results: Six EIAs (Abbott, Affinity, BioRad, DiaSorin, Euroimmun, and Roche), and six POCTs (BTNX, Biolidics, Deep Blue, Genrui, Getein BioTech, and Innovita) were evaluated for the detection of SARS-CoV-2 antibodies in known COVID-19 infected individuals. Sensitivity of EIAs ranged from 50-100%, with only four assays having overall sensitivities >95% after 21 days post symptom onset. Notably, cross-reactivity with other respiratory viruses (PIV-4 (n=5), hMPV (n=3), rhinovirus/enterovirus (n=1), CoV-229E (n=2), CoV-NL63 (n=2), and CoV-OC43 (n=2) was observed; however, overall specificity for EIAs was good (92-100%; where all but one assay had specificity above 95%). POCTs were 0-100% sensitive >21 days post onset, with specificity ranging from 96-100%. However, many POCTs had faint banding and were often difficult to interpret. Conclusions: Serology assays can detect SARS-CoV-2 antibodies as early as 10 days post onset. Serology assays vary in their sensitivity based on the marker (IgA/M vs. IgG vs. total) and by manufacturer; however, overall only 4 EIA and 4 POCT assays had sensitivities >95% >21 days post symptom onset. Cross-reactivity with other seasonal coronaviruses is of concern. The use of serology assays should not be used for the diagnosis of acute infection, but rather for use in carefully designed serosurveys to facilitate understanding of seroprevalence in a population and to identify previous exposure to SARS-CoV-2.

In order to gain a better perspective on the true variability of varicella-zoster virus (VZV) and to catalogue the location and number of differences, 11 new complete genome sequences were compared with those previously in the public domain (18 complete genomes in total). Three of the newly sequenced genomes were derived from a single strain in order to assess variations that can occur during serial passage in cell culture. The analysis revealed that while VZV is relatively stable genetically it does posses a certain degree of variability. The reiteration regions, origins of replication and intergenic homopolymer regions were all found to be variable between strains as well as within a given strain. In addition, the terminal viral sequences were found to vary within and between strains specifically at the 3' end of the genome. Analysis of single nucleotide polymorphisms (SNPs) identified a total of 557 variable sites, 451 of which were found in coding regions and resulted in 187 different in amino acid substitutions. A comparison of the SNPs present in the two gE mutant strains, VZV-MSP and VZV-BC, suggested that the missense mutation in gE was primarily responsible for the accelerated cell spread phenotype. Some of the variations noted with high passage in cell culture are consistent with variations seen in the IE62 gene of the vaccine strains (S628G, R958G and I1260V) that may help in pinpointing variations essential for attenuation. Although VZV has been considered to be one of the most genetically stable human herpesviruses, this initial assessment of genomic VZV cartography provides insight into ORFs with previously unreported variations.