Insights in Virus Transmission Using Genomic Epidemiology

Brazil has experienced some of the highest numbers of COVID-19 infections and deaths globally and made Latin America a pandemic epicenter from May 2021. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of local virus transmission dynamics. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and an adjacent country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed, the absence of effective restriction measures led to the local emergence and international spread of Variants of Concern (VOC) and under monitoring (VUM), including the Gamma (P.1) and Zeta (P.2) variants. In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring and providing a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

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Genomic Epidemiology of the First Wave of SARS-CoV-2 in Italy

Viruses ◽

10.3390/v12121438 ◽

2020 ◽

Vol 12 (12) ◽

pp. 1438

Author(s):

Francesca Di Giallonardo ◽

Sebastian Duchene ◽

Ilaria Puglia ◽

Valentina Curini ◽

Francesca Profeta ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Severe Acute Respiratory Syndrome ◽

Genome Sequence ◽

Sequence Data ◽

Central Italy ◽

Virus Transmission ◽

Virus Genome ◽

Extensive Study ◽

Genomic Epidemiology ◽

Italian Regions

Italy was one of the first countries to experience a major epidemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with >1000 cases confirmed by 1 March 2020. However, virus genome sequence data is sparse and there has been only limited investigation of virus transmission across the country. Here, we provide the most extensive study to date of the genomic epidemiology of SARS-CoV-2 in Italy covering the first wave of infection. We generated 191 new full-length genomes, largely sampled from central Italy (Abruzzo), before, during, and after the enforcement of a nationwide “lockdown” (8 March–3 June). These were combined with 460 published SARS-CoV-2 sequences sampled across Italy. Phylogenetic analysis including global sequence data revealed multiple independent introductions into Italy, with at least 124 instances of sequence clusters representing longer chains of transmission. Eighteen of these transmission clusters emerged before the nation-wide lockdown was implemented on 8 March, and an additional 18 had evidence for transmission between different Italian regions. Extended transmission periods between infections of up to 104 days were observed in five clusters. In addition, we found seven clusters that persisted throughout the lockdown period. Overall, we show how importations were an important driver of the first wave of SARS-CoV-2 in Italy.

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Genomic epidemiology of SARS-CoV-2 in Colombia

10.1101/2020.06.26.20135715 ◽

2020 ◽

Cited By ~ 5

Author(s):

Katherine Laiton-Donato ◽

Christian Julián Villabona-Arenas ◽

José A. Usme-Ciro ◽

Carlos Franco-Muñoz ◽

Diego A. Álvarez-Díaz ◽

...

Keyword(s):

Genome Sequencing ◽

Human Mobility ◽

Virus Transmission ◽

Genetic Data ◽

Air Travel ◽

Transmission Dynamics ◽

Clinical Samples ◽

Epidemiological Investigation ◽

Multiple Introductions ◽

Genomic Epidemiology

AbstractCoronavirus disease 2019 (COVID-19) was first diagnosed in Colombia from a traveler arriving from Italy on February 26, 2020. To date, available data on the origins and number or introductions of SARS-CoV-2 into the country are limited. Here, we sequenced SARS-CoV-2 from 43 clinical samples and—together with another 73 genomes sequences available from the country—we investigated the emergence and the routes of importation of COVID-19 into Colombia using epidemiological, historical air travel and phylogenetic observations. Our study provided evidence of multiple introductions, mostly from Europe, with at least 12 lineages being documented. Phylogenetic findings validated the linkage of epidemiologically-linked transmission chains. Our results demonstrate the advantages of genome sequencing to complement COVID-19 outbreak investigation and underscores that human mobility and genetic data are relevant to complete epidemiological investigation and better characterize virus transmission dynamics at local scales.

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Molecular Analysis of SARS-CoV-2 Circulating in Bangladesh during 2020 Revealed Lineage Diversity and Potential Mutations

Microorganisms ◽

10.3390/microorganisms9051035 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1035

Author(s):

Rokshana Parvin ◽

Sultana Zahura Afrin ◽

Jahan Ara Begum ◽

Salma Ahmed ◽

Mohammed Nooruzzaman ◽

...

Keyword(s):

Virus Transmission ◽

Genomic Diversity ◽

Evolutionary Analysis ◽

Multiple Introductions ◽

Genomic Epidemiology ◽

Community Transmission ◽

Amino Acid Diversity ◽

Significant Amino Acid ◽

Mutation Analyses ◽

Lineage Diversity

Virus evolution and mutation analyses are crucial for tracing virus transmission, the potential variants, and other pathogenic determinants. Despite continuing circulation of the SARS-CoV-2, very limited studies have been conducted on genetic evolutionary analysis of the virus in Bangladesh. In this study, a total of 791 complete genome sequences of SARS-CoV-2 from Bangladesh deposited in the GISAID database during March 2020 to January 2021 were analyzed. Phylogenetic analysis revealed circulation of seven GISAID clades G, GH, GR, GRY, L, O, and S or five Nextstrain clades 20A, 20B, 20C, 19A, and 19B in the country during the study period. The GISAID clade GR or the Nextstrain clade 20B or lineage B.1.1.25 is predominant in Bangladesh and closely related to the sequences from India, USA, Canada, UK, and Italy. The GR clade or B.1.1.25 lineage is likely to be responsible for the widespread community transmission of SARS-CoV-2 in the country during the first wave of infection. Significant amino acid diversity was observed among Bangladeshi SARS-CoV-2 isolates, where a total of 1023 mutations were detected. In particular, the D614G mutation in the spike protein (S_D614G) was found in 97% of the sequences. However, the introduction of lineage B.1.1.7 (UK variant/S_N501Y) and S_E484K mutation in lineage B.1.1.25 in a few sequences reported in late December 2020 is of particular concern. The wide genomic diversity indicated multiple introductions of SARS-CoV-2 into Bangladesh through various routes. Therefore, a continuous and extensive genome sequence analysis would be necessary to understand the genomic epidemiology of SARS-CoV-2 in Bangladesh.

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Longitudinal Surveillance for SARS-CoV-2 RNA Among Asymptomatic Staff in Five Colorado Skilled Nursing Facilities: Epidemiologic, Virologic and Sequence Analysis

10.1101/2020.06.08.20125989 ◽

2020 ◽

Cited By ~ 11

Author(s):

Kendra Quicke ◽

Emily Gallichotte ◽

Nicole Sexton ◽

Michael Young ◽

Ashley Janich ◽

...

Keyword(s):

Infectious Virus ◽

Virus Transmission ◽

Asymptomatic Infection ◽

Skilled Nursing Facilities ◽

Nursing Facilities ◽

Term Care ◽

Skilled Nursing ◽

Genomic Epidemiology ◽

Short Period ◽

Asymptomatic Individuals

AbstractSARS-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 also has been notable due to its impacts on individuals residing within skilled nursing facilities (SNFs) such as rehabilitation centers and nursing homes. SNF residents tend to possess several risk factors for the most severe outcomes of SARS-CoV-2 infection, including advanced age and the presence of multiple comorbidities. Indeed, residents of long-term care facilities represent approximately 40 percent of US SARS-CoV-2 deaths. To assess the prevalence and incidence of SARS-CoV-2 among SNF workers, determine the extent of asymptomatic infection by SARS-CoV-2, and provide information on the genomic epidemiology of the virus within these unique care settings, we sampled workers weekly at five SNFs in Colorado using nasopharyngeal swabs, determined the presence of viral RNA and infectious virus among these workers, and sequenced 48 nearly complete genomes. This manuscript reports results from the first five to six weeks of observation. Our data reveal a strikingly high degree of asymptomatic infection, a strong correlation between RNA detection and the presence of infectious virus in NP swabs, persistent RNA in a subset of individuals, and declining incidence over time. Our data suggests that asymptomatic individuals infected by SARS-CoV-2 may contribute to virus transmission within the workplace.

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Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab665 ◽

2022 ◽

Author(s):

Sebastian Duchene ◽

Leo Featherstone ◽

Birgitte Freiesleben de Blasio ◽

Edward C Holmes ◽

Jon Bohlin ◽

...

Keyword(s):

Virus Transmission ◽

Positive Association ◽

Intervention Strategies ◽

Nordic Countries ◽

Contact Tracing ◽

Response Measure ◽

Significant Positive Association ◽

Genomic Epidemiology ◽

Rapid Deployment ◽

Country Specific

Abstract We explored how the duration, size and number of virus transmission clusters, defined as country-specific monophyletic groups in a SARS-CoV-2 phylogenetic tree, differed between the Nordic countries of Norway, Sweden, Denmark, Finland and Iceland. Our results suggest that although geographical connectivity, population density and openness influence the spread and the size of SARS-CoV-2 transmission clusters, the differing country-specific intervention strategies had the largest impact. We also found a significant positive association between the size and duration of transmission clusters in the Nordic countries, suggesting that the rapid deployment of contact tracing is a key response measure in reducing virus transmission.

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A38 Genomic epidemiology quantifies gaps in Aedes-borne virus transmission in the Americas

Virus Evolution ◽

10.1093/ve/vez002.037 ◽

2019 ◽

Vol 5 (Supplement_1) ◽

Author(s):

Darlan da Silva Cândido ◽

Oliver G Pybus ◽

Nuno Rodrigues Faria

Keyword(s):

Virus Transmission ◽

Genetic Data ◽

Geographic Region ◽

Sequence Evolution ◽

Viral Pathogens ◽

Genomic Epidemiology ◽

Geographic Spread ◽

Rapid Spread ◽

Phylogenetic Framework ◽

Geographic Regions

Abstract The rapid spread and severity of pathogens, such as Zika (ZIKV) and Chikungunya (CHIKV) viruses in the Americas, demonstrate the need for a better understanding of when and where outbreaks emerge. Sequence evolution of these viral pathogens occurs simultaneously with geographic spread, which allows phylodynamic processes to be recovered from genomic data. Here, we used time-calibrated phylogeographic analyses implemented in a Bayesian phylogenetic framework to characterize the date of introduction of ZIKV, CHIKV, dengue, and yellow fever viruses in different geographic regions of the Americas. To estimate ‘surveillance gaps’, we compared the estimated dates of introduction of these pathogens to the first confirmations of virus circulation in the region. Datasets included all publicly available geo-referenced and time-stamped genetic data from the Americas. A series of environmental and ecological covariates will be tested to infer what factors are associated with the delayed detection of arbovirus transmission in each geographic region. These results will provide important information on where to concentrate surveillance strengthening measures in order to prevent future mosquito-borne virus epidemics.

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Treatment of Hemophilia A with a Highly Purified Factor VIII Concentrate Prepared by Anti-FVIIIc Immunoaffinity Chromatography

Thrombosis and Haemostasis ◽

10.1055/s-0038-1648373 ◽

1992 ◽

Vol 67 (01) ◽

pp. 019-027 ◽

Cited By ~ 47

Author(s):

Joseph E Addiego ◽

Edward Gomperts ◽

Liu Shu-Len ◽

Patricia Bailey ◽

Suzanne G Courter ◽

...

Keyword(s):

Factor Viii ◽

Hemophilia A ◽

Virus Transmission ◽

Human Albumin ◽

Immunoaffinity Chromatography ◽

Exchange Chromatography ◽

Pharmacokinetic Studies ◽

Enveloped Viruses ◽

Clinically Significant ◽

Detergent Mixture

SummaryTo reduce the risk of pathogenic virus transmission associated with the therapeutic administration of plasma-derived antihemophilic factor (FVIIIc), a process utilizing anti-FVIIIc immunoaffinity chromatography to isolate FVIIIc has been developed. In addition, the starting cryoprecipitate solution has been treated with an organic solvent/detergent mixture to inactivate lipid-enveloped viruses. A final ion exchange chromatography step is used to further remove contaminants, e.g., anti-FVIIIc antibody, potentially leached with FVIIIc during the immunoaffinity step. The purified FVTII is stabilized for lyophili-zation and storage by the addition of human albumin. The monoclonal anti-FVIIIc antibody used in the immunoaffinity step of the process is not detectable in the final preparation. Viral reduction studies performed at specific steps of the process demonstrate that 11 logs of human immunodeficiency virus (HIV) and greater than 4-5 logs of other lipid-enveloped viruses are inactivated within the first 30 s of exposure to the solvent/ detergent mixture and 4-5 logs of various model viruses, e. g. Endomyocarditis virus (EMC), are physically removed during washing of the immunoaffinity column. The lyophilized product is reconstituted using sterile water in a matter of seconds.The pharmacokinetics of Hemofil® M were compared to those obtained using a standard heat-treated concentrate (Hemofil® CT) in five severe factor VIII deficient hemophiliacs in a randomized, cross-over study. No statistically significant differences were observed in mean half life (p >0.6) or median recovery (p = 0.4) between the two preparations. No clinically significant adverse effects were observed in patients receiving either FVIII preparation.In addition, 43 patients at 18 different centers underwent pharmacokinetic studies, with a nominal dose of 50 u/kg FVIIIc Hemofil® M. The mean recovery was 103.6%, and the t 1/2 was 14.6 h. The recovery of FVIII in this group was as expected, providing an increase of assayed FVIII of approximately 2% per unit of FVTII/kg infused.Clinical trials using Hemofil® M have been initiated in 124 hemophilia A patients. The safety and efficacy of Hemofil® M has been established. To date, 0 of 60 patients tested have seroconverted to HIV. None of the previously untreated patients show clinical or laboratory evidence of Non-A, Non-B hepatitis (NANB), with 21 patients remaining negative as far as presence of antibodies to the Hepatitis C virus (a-HCV negative) at least 6 months after the initial infusion. There is no evidence of neoantigenicity, evidenced by seroconversion to murine antibody. An 8.7% (2 of 23) prevalence of anti-FVIIIc inhibitor development has been observed in previously untreated patients with FVIIIc⩽3%, receiving only the monoclonally purified solvent/ detergent treated FVIII concentrate while on study and on poststudy surveillance. All patients demonstrated clinical hemostasis following product use for either on demand bleeding or surgical prophylaxis.

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