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1.
JAMA Netw Open ; 5(2): e2146805, 2022 02 01.
Article in English | MEDLINE | ID: covidwho-1669327

ABSTRACT

Importance: The COVID-19 pandemic led many higher education institutions to close campuses during the 2020-2021 academic year. As campuses prepared for a return to in-person education, many institutions were mandating vaccines for students and considering the same for faculty and staff. Objective: To determine the association between vaccination coverage and the levels and spread of SARS-CoV-2, even in the presence of highly-transmissible variants and congregate living, at a midsized university in the US. Design, Setting, and Participants: This case series was conducted at a midsized Midwestern university during the spring 2021 semester. The university developed a saliva-based surveillance program capable of high-throughput SARS-CoV-2 polymerase chain reaction testing and genomic sequencing with the capacity to deliver results in less than 24 hours. On April 7, 2021, the university announced a vaccine requirement for all students for the fall 2021 semester and announced the same requirement for faculty and staff on May 20, 2021. The university hosted an onsite mass vaccination clinic using the 2-dose Pfizer-BioNTech vaccine during April 8 to 15 and April 29 to May 6, 2021. Data were analyzed for 14 894 individuals from the university population who were tested for COVID-19 on campus from January 6 to May 20, 2021. Main Outcomes and Measures: Positive SARS-CoV-2 diagnosis was confirmed by quantitative reverse transcription-polymerase chain reaction of saliva specimens, and variant identity was assessed by quantitative reverse transcription-polymerase chain reaction and next-generation sequencing of viral genomes. Results: Between January 6 and May 20, 2021, the university conducted 196 185 COVID-19 tests for 14 894 individuals and identified 1603 positive cases. Within those positive cases, 950 individuals (59.3%) were male, 644 (40.2%) were female, 1426 (89.0%) were students, and 1265 (78.9%) were aged 17 to 22 years. Among the 1603 positive cases, 687 were identified via polymerase chain reaction of saliva specimens. The Alpha (B.1.1.7) variant constituted 218 of the 446 total positives sequenced (48.9%). By May 20, 2021, 10 068 of 11 091 students (90.8%), 814 of 883 faculty (92.2%), and 2081 of 2890 staff (72.0%) were vaccinated. The 7-day rolling average of positive cases peaked at 37 cases on February 17 but declined to zero by May 14, 2021. The 7-day moving average of positive cases was inversely associated with cumulative vaccination coverage, with a statistically significant Pearson correlation coefficient of -0.57 (95% CI, -0.68 to -0.44). Conclusions and Relevance: This case series study elucidated the association of a robust vaccination program with a statistically significant decrease in positive COVID-19 cases among the study population even in the presence of highly transmissible variants and congregate living.


Subject(s)
COVID-19/diagnosis , COVID-19/prevention & control , Mass Screening/methods , Mass Vaccination/methods , Return to School , SARS-CoV-2 , Universities , Adolescent , COVID-19 Nucleic Acid Testing , Faculty , Female , High-Throughput Nucleotide Sequencing , Humans , Male , Sequence Analysis , Students , Vaccination Coverage , Young Adult
3.
PLoS One ; 17(1): e0261014, 2022.
Article in English | MEDLINE | ID: covidwho-1622333

ABSTRACT

High viral transmission in the COVID-19 pandemic has enabled SARS-CoV-2 to acquire new mutations that may impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from fifteen COVID-19 positive patients. ARTIC data covered 94.47% of the virus genome fraction in the positive control and patient samples. Variant analysis in the ARTIC data detected 217 mutations, including 209 single nucleotide variants (SNVs) and eight insertions & deletions. On the other hand, long-amplicon data detected 156 mutations, of which 80% were concordant with ARTIC data. Combined analysis of ARTIC + MRL data improved the genomic coverage to 97.03% and identified 214 high confidence mutations. The combined final set of 214 mutations included 203 SNVs, 8 deletions and 3 insertions. Analysis showed 26 SARS-CoV-2 lineage defining mutations including 4 known variants of concern K417N, E484K, N501Y, P618H in spike gene. Hybrid analysis identified 7 nonsynonymous and 5 synonymous mutations across the genome that were either ambiguous or not called in ARTIC data. For example, G172V mutation in the ORF3a protein and A2A mutation in Membrane protein were missed by the ARTIC assay. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.


Subject(s)
Genome, Viral/genetics , Genomics/methods , SARS-CoV-2/genetics , Whole Genome Sequencing/methods , COVID-19/virology , Humans , RNA, Viral/genetics , Sequence Analysis/methods
4.
Microbiol Spectr ; 9(3): e0100321, 2021 12 22.
Article in English | MEDLINE | ID: covidwho-1593461

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 and has become a major global pathogen in an astonishingly short period of time. The emergence of SARS-CoV-2 has been notable due to its impacts on residents in long-term care facilities (LTCFs). LTCF residents tend to possess several risk factors for severe outcomes of SARS-CoV-2 infection, including advanced age and the presence of comorbidities. Indeed, residents of LTCFs represent approximately 40% of SARS-CoV-2 deaths in the United States. Few studies have focused on the prevalence and transmission dynamics of SARS-CoV-2 among LTCF staff during the early months of the pandemic, prior to mandated surveillance testing. To assess the prevalence and incidence of SARS-CoV-2 among LTCF staff, characterize the extent of asymptomatic infections, and investigate the genomic epidemiology of the virus within these settings, we sampled staff for 8 to 11 weeks at six LTCFs with nasopharyngeal swabs from March through June of 2020. We determined the presence and levels of viral RNA and infectious virus and sequenced 54 nearly complete genomes. Our data revealed that over 50% of infections were asymptomatic/mildly symptomatic and that there was a strongly significant relationship between viral RNA (vRNA) and infectious virus, prolonged infections, and persistent vRNA (4+ weeks) in a subset of individuals, and declining incidence over time. Our data suggest that asymptomatic SARS-CoV-2-infected LTCF staff contributed to virus persistence and transmission within the workplace during the early pandemic period. Genetic epidemiology data generated from samples collected during this period support that SARS-CoV-2 was commonly spread between staff within an LTCF and that multiple-introduction events were less common. IMPORTANCE Our work comprises unique data on the characteristics of SARS-CoV-2 dynamics among staff working at LTCFs in the early months of the SARS-CoV-2 pandemic prior to mandated staff surveillance testing. During this time period, LTCF residents were largely sheltering-in-place. Given that staff were able to leave and return daily and could therefore be a continued source of imported or exported infection, we performed weekly SARS-CoV-2 PCR on nasal swab samples collected from this population. There are limited data from the early months of the pandemic comprising longitudinal surveillance of staff at LTCFs. Our data reveal the surprisingly high level of asymptomatic/presymptomatic infections within this cohort during the early months of the pandemic and show genetic epidemiological analyses that add novel insights into both the origin and transmission of SARS-CoV-2 within LTCFs.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/epidemiology , Hospitals , Long-Term Care , SARS-CoV-2/isolation & purification , Sequence Analysis/methods , Adolescent , Adult , Aged , Asymptomatic Infections/epidemiology , COVID-19/virology , Cohort Studies , Diagnostic Tests, Routine , Epidemiological Monitoring , Female , High-Throughput Nucleotide Sequencing , Humans , Male , Middle Aged , Pandemics , Phylogeny , Prevalence , RNA, Viral , SARS-CoV-2/classification , SARS-CoV-2/genetics , Specimen Handling , Young Adult
5.
Nat Microbiol ; 7(1): 108-119, 2022 01.
Article in English | MEDLINE | ID: covidwho-1574813

ABSTRACT

The global spread and continued evolution of SARS-CoV-2 has driven an unprecedented surge in viral genomic surveillance. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine laboratory processes and results. This challenge will increase with the expanding global production of sequences across a variety of laboratories for epidemiological and clinical interpretation, as well as for genomic surveillance of emerging diseases in future outbreaks. We present SDSI + AmpSeq, an approach that uses 96 synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination throughout the sequencing workflow. We apply SDSIs to the ARTIC Consortium's amplicon design, demonstrate their utility and efficiency in a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases and validate them across 6,676 diagnostic samples at multiple laboratories. We establish that SDSI + AmpSeq provides increased confidence in genomic data by detecting and correcting for relatively common, yet previously unobserved modes of error, including spillover and sample swaps, without impacting genome recovery.


Subject(s)
DNA Primers/standards , SARS-CoV-2/genetics , Sequence Analysis/standards , COVID-19/diagnosis , DNA Primers/chemical synthesis , Genome, Viral/genetics , Humans , Quality Control , RNA, Viral/genetics , Reproducibility of Results , Sequence Analysis/methods , Whole Genome Sequencing , Workflow
6.
J Med Virol ; 94(4): 1728-1733, 2022 04.
Article in English | MEDLINE | ID: covidwho-1568200

ABSTRACT

Despite the worldwide vaccination, the COVID-19 pandemic continues as SARS-CoV-2 evolves into numerous variants. Since the first identification of the novel SARS-CoV-2 variant of concern (VOC) Omicron on November 24th, 2021, from an immunocompromised patient in South Africa, the variant has overtaken Delta as the predominant lineage in South Africa and has quickly spread to over 40 countries. Here, we provide an initial molecular characterization of the Omicron variant through analyzing a large number of mutations, especially in the spike protein receptor-binding domain with their potential effects on viral infectivity and host immunity. Our analysis indicates that the Omicron variant has two subclades and may evolve from clade 20B instead of the currently dominant Delta variant. In addition, we have also identified mutations that may affect the ACE2 receptor and/or antibody bindings. Our study has raised additional questions on the evolution, transmission, virulence, and immune escape properties of this new Omicron variant.


Subject(s)
SARS-CoV-2/genetics , Binding Sites , COVID-19/epidemiology , COVID-19/virology , Genome, Viral/genetics , Humans , Mutation , Phylogeny , Sequence Analysis , South Africa/epidemiology , Spike Glycoprotein, Coronavirus/genetics
7.
J Med Virol ; 93(12): 6828-6832, 2021 12.
Article in English | MEDLINE | ID: covidwho-1544316

ABSTRACT

A cluster of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections was found in a cargo ship under repair in Zhoushan, China. Twelve of 20 crew members were identified as SARS-CoV-2 positive. We analyzed four sequences and identified them all in the Delta branch emerging from India with 7-8 amino acid mutation sites in the spike protein.


Subject(s)
COVID-19/virology , SARS-CoV-2/genetics , China , Genome, Viral/genetics , Humans , India , Phylogeny , Sequence Analysis/methods , Ships/methods , Spike Glycoprotein, Coronavirus/genetics
8.
Emerg Infect Dis ; 27(12): 3185-3188, 2021 12.
Article in English | MEDLINE | ID: covidwho-1496967

ABSTRACT

In June 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases surged in Liberia. SARS-CoV-2 sequences from patients hospitalized during March-July 2021 revealed the Delta variant was in Liberia in early March and was dominant in June, irrespective of geography. Mutations and deletions suggest multiple SARS-CoV-2 Delta variant introductions.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Liberia/epidemiology , Sequence Analysis
9.
Genes (Basel) ; 12(9)2021 09 16.
Article in English | MEDLINE | ID: covidwho-1409151

ABSTRACT

A considerable effort has been devoted in all countries to react to the COVID-19 pandemic by tracing infected individuals, containing the spread of the disease, identifying therapies, and producing and distributing vaccines. Currently, a significant concern is the appearance of variants of the virus that may frustrate these efforts by showing increased transmissibility, increased disease severity, reduced response to therapy or vaccines, and ability to escape diagnosis. All countries have therefore devoted a massive attempt to the identification and tracking of these variants, which requires a vast technological effort to sequence a large number of viral genomes. In this paper, we report our experience as one of the Italian laboratories involved in SARS-CoV-2 variant tracing. We summarize the different approaches used, and outline a potential model combining several techniques to increase tracing ability while at the same time minimizing costs.


Subject(s)
COVID-19 Nucleic Acid Testing/methods , COVID-19/virology , SARS-CoV-2/classification , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , COVID-19/diagnostic imaging , Genome, Viral , Humans , Laboratories , Mutation , Pandemics , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Sequence Analysis
11.
MMWR Morb Mortal Wkly Rep ; 69(28): 918-922, 2020 Jul 17.
Article in English | MEDLINE | ID: covidwho-1389847

ABSTRACT

To limit introduction of SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), the United States restricted travel from China on February 2, 2020, and from Europe on March 13. To determine whether local transmission of SARS-CoV-2 could be detected, the New York City (NYC) Department of Health and Mental Hygiene (DOHMH) conducted deidentified sentinel surveillance at six NYC hospital emergency departments (EDs) during March 1-20. On March 8, while testing availability for SARS-CoV-2 was still limited, DOHMH announced sustained community transmission of SARS-CoV-2 (1). At this time, twenty-six NYC residents had confirmed COVID-19, and ED visits for influenza-like illness* increased, despite decreased influenza virus circulation.† The following week, on March 15, when only seven of the 56 (13%) patients with known exposure histories had exposure outside of NYC, the level of community SARS-CoV-2 transmission status was elevated from sustained community transmission to widespread community transmission (2). Through sentinel surveillance during March 1-20, DOHMH collected 544 specimens from patients with influenza-like symptoms (ILS)§ who had negative test results for influenza and, in some instances, other respiratory pathogens.¶ All 544 specimens were tested for SARS-CoV-2 at CDC; 36 (6.6%) tested positive. Using genetic sequencing, CDC determined that the sequences of most SARS-CoV-2-positive specimens resembled those circulating in Europe, suggesting probable introductions of SARS-CoV-2 from Europe, from other U.S. locations, and local introductions from within New York. These findings demonstrate that partnering with health care facilities and developing the systems needed for rapid implementation of sentinel surveillance, coupled with capacity for genetic sequencing before an outbreak, can help inform timely containment and mitigation strategies.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/isolation & purification , Community-Acquired Infections/diagnosis , Community-Acquired Infections/virology , Coronavirus Infections/diagnosis , Coronavirus Infections/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/virology , Sentinel Surveillance , Adolescent , Adult , Aged , COVID-19 , Child , Child, Preschool , Community-Acquired Infections/epidemiology , Coronavirus Infections/epidemiology , Emergency Service, Hospital , Female , Humans , Infant , Male , Middle Aged , New York City/epidemiology , Pandemics , Pneumonia, Viral/epidemiology , SARS-CoV-2 , Sequence Analysis , Travel-Related Illness , Young Adult
12.
Viruses ; 13(4)2021 04 03.
Article in English | MEDLINE | ID: covidwho-1389536

ABSTRACT

Replication of RNA viruses is characterized by exploration of sequence space which facilitates their adaptation to changing environments. It is generally accepted that such exploration takes place mainly in response to positive selection, and that further diversification is boosted by modifications of virus population size, particularly bottleneck events. Our recent results with hepatitis C virus (HCV) have shown that the expansion in sequence space of a viral clone continues despite prolonged replication in a stable cell culture environment. Diagnosis of the expansion was based on the quantification of diversity indices, the occurrence of intra-population mutational waves (variations in mutant frequencies), and greater individual residue variations in mutant spectra than those anticipated from sequence alignments in data banks. In the present report, we review our previous results, and show additionally that mutational waves in amplicons from the NS5A-NS5B-coding region are equally prominent during HCV passage in the absence or presence of the mutagenic nucleotide analogues favipiravir or ribavirin. In addition, by extending our previous analysis to amplicons of the NS3- and NS5A-coding region, we provide further evidence of the incongruence between amino acid conservation scores in mutant spectra from infected patients and in the Los Alamos National Laboratory HCV data banks. We hypothesize that these observations have as a common origin a permanent state of HCV population disequilibrium even upon extensive viral replication in the absence of external selective constraints or changes in population size. Such a persistent disequilibrium-revealed by the changing composition of the mutant spectrum-may facilitate finding alternative mutational pathways for HCV antiviral resistance. The possible significance of our model for other genetically variable viruses is discussed.


Subject(s)
Hepacivirus/genetics , Hepacivirus/physiology , Hepatitis C/virology , Antiviral Agents/pharmacology , COVID-19 , Cell Line , Drug Resistance, Viral/drug effects , Hepacivirus/drug effects , Humans , Mutation , RNA, Viral , Ribavirin/pharmacology , Sequence Analysis , Viral Nonstructural Proteins/genetics , Virus Replication/drug effects
13.
Nat Commun ; 12(1): 4809, 2021 08 10.
Article in English | MEDLINE | ID: covidwho-1351953

ABSTRACT

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Genome, Viral , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/diagnosis , COVID-19/transmission , Child , Child, Preschool , Female , Genetic Variation , Humans , Infant , Kenya/epidemiology , Male , Middle Aged , Pandemics , Phylogeny , Public Health , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Sequence Analysis , Tanzania , Travel , Young Adult
14.
Am J Infect Control ; 49(10): 1232-1236, 2021 10.
Article in English | MEDLINE | ID: covidwho-1347470

ABSTRACT

BACKGROUND: The COVID-19 pandemic poses a particularly high risk for End Stage Renal Disease (ESRD) patients so rapid identification of case clusters in ESRD facilities is essential. Nevertheless, with high community prevalence, a series of ESRD patients may test positive contemporaneously for reasons unrelated to their shared ESRD facility. Here we describe a series of 5 cases detected within 11 days in November 2020 in a hospital-based 32-station ESRD facility in Southwest Wisconsin, the subsequent facility-wide testing, and the use of genetic sequence analysis to evaluate links between cases. METHODS: Four patient cases and one staff case were identified in symptomatic individuals by RT-PCR. Facility-wide screening was conducted using rapid SARS-CoV-2 antigen tests. SARS-CoV-2 genome sequences were obtained from residual diagnostic specimens. RESULTS: Facility-wide screening of 47 staff and 107 patients identified no additional cases. Residual specimens from 4 of 5 cases were available for genetic sequencing. Clear genetic differences proved that these contemporaneous cases were not linked. CONCLUSIONS: With high community prevalence, epidemiological data alone is insufficient to deem a case cluster an outbreak. Cluster evaluation with genomic data, when available with a short turn-around time, can play an important role in infection prevention and control response programs.


Subject(s)
COVID-19 , SARS-CoV-2 , Disease Outbreaks , Humans , Infection Control , Pandemics , Renal Dialysis , Sequence Analysis
15.
Am J Trop Med Hyg ; 105(4): 884-889, 2021 08 09.
Article in English | MEDLINE | ID: covidwho-1348742

ABSTRACT

Evaluating cases of reinfection may offer some insight into areas for further investigation regarding durability of immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sixty cases of reinfection with viral sequencing were identified in PubMed, Embase, Web of Science, and medRxiv before May 1, 2021.Episodes of infection were separated by a median of 116 days. Severity of illness was greater among individuals reinfected within 90 days of initial infection, no asymptomatic initial cases developed severe reinfection, nearly half of cases had suspected escape variants, and nearly all individuals tested following reinfection were found to have detectable levels of anti-SARS-CoV-2 antibodies. This analysis is limited by the heterogeneous methods used among reports. Reinfection continues to be relatively rare. As the case rate presumably increases over time, this review will inform measurements to determine the natural history and causal determinants of reinfection in more rigorous observational cohort studies and other standardized surveillance approaches.


Subject(s)
COVID-19 Nucleic Acid Testing , COVID-19/diagnosis , Reinfection/virology , SARS-CoV-2 , Adult , Aged , Aged, 80 and over , Antibodies, Viral/immunology , Female , Humans , Male , Middle Aged , Sequence Analysis
16.
Brief Bioinform ; 22(2): 924-935, 2021 03 22.
Article in English | MEDLINE | ID: covidwho-1343628

ABSTRACT

In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset. UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction and other preprocessing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, Middle East respiratory syndrome and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv.


Subject(s)
SARS-CoV-2/isolation & purification , Sequence Analysis/methods , Viruses/isolation & purification , Algorithms , Genes, Viral , SARS-CoV-2/genetics , Viruses/genetics
17.
Influenza Other Respir Viruses ; 15(6): 707-710, 2021 11.
Article in English | MEDLINE | ID: covidwho-1341261

ABSTRACT

We describe a Sanger sequencing protocol for SARS-CoV-2 S-gene the Spike (S)-glycoprotein product of which, composed of receptor-binding (S1) and membrane fusion (S2) segments, is the target of vaccines used to combat COVID-19. The protocol can be used in laboratories with basic Sanger sequencing capabilities and allows rapid "at source" screening for SARS-CoV-2 variants, notably those of concern. The protocol has been applied for surveillance, with clinical specimens collected in either nucleic acid preservation lysis-mix or virus transport medium, and research involving cultured viruses, and can yield data of public health importance in a timely manner.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , Sequence Analysis , Spike Glycoprotein, Coronavirus/genetics
18.
J Med Virol ; 93(12): 6828-6832, 2021 12.
Article in English | MEDLINE | ID: covidwho-1326782

ABSTRACT

A cluster of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections was found in a cargo ship under repair in Zhoushan, China. Twelve of 20 crew members were identified as SARS-CoV-2 positive. We analyzed four sequences and identified them all in the Delta branch emerging from India with 7-8 amino acid mutation sites in the spike protein.


Subject(s)
COVID-19/virology , SARS-CoV-2/genetics , China , Genome, Viral/genetics , Humans , India , Phylogeny , Sequence Analysis/methods , Ships/methods , Spike Glycoprotein, Coronavirus/genetics
20.
Curr Opin Virol ; 49: 111-116, 2021 08.
Article in English | MEDLINE | ID: covidwho-1260705

ABSTRACT

The COVID-19 pandemic has entailed simultaneous revolutions in virology diagnostics, clinical trials management, and antiviral therapy and vaccinology. Over the past year, SARS-CoV-2 diagnostic testing has moved from highly centralized laboratories to at-home and even over the-counter. This transition has been lionized for its potential public health impact via isolation, but has been less examined for its effect on individual health and therapeutics. Since early initiation of antiviral therapy routinely has been associated with greater treatment efficacy for viral infections, these diagnostic testing innovations offer new opportunities for both clinical testing as well as clinical trials for antiviral therapy. Given a rapidly growing antiviral therapeutic pipeline and the profound impact of individual beneficiary outcomes on sculpting reimbursement policy, the therapeutic benefits associated with rapid viral testing may lead to significant adoption beyond potential public health impacts.


Subject(s)
COVID-19 Testing , COVID-19/diagnosis , COVID-19/therapy , Point-of-Care Testing , Antiviral Agents/therapeutic use , COVID-19 Testing/economics , COVID-19 Testing/standards , COVID-19 Testing/statistics & numerical data , Clinical Trials as Topic , Early Diagnosis , Humans , Point-of-Care Testing/economics , Point-of-Care Testing/standards , Point-of-Care Testing/statistics & numerical data , SARS-CoV-2/genetics , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Sequence Analysis , Viral Load
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