PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification

Oliveira, Renato R. M.; Negri, Tatianne; Nunes, Gisele; Medeiros, Inácio Gomes; Araujo, G.; Silva, Fabrício de Oliveira; Souza, Jorge Estefano Santana de; Alves, Ronnie; Oliveira, Guilherme

doi:10.7717/peerj.13300

Cited by 8 publications

(7 citation statements)

References 23 publications

(30 reference statements)

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“…The quality treatment, mapping, assembly, and variants identifications were performed using the PipeCoV pipeline ( 20 ). First, FASTQ files were trimmed using the Phred score (−q 20) as parameters with small reads discarded (−l 20).…”

Section: Methodsmentioning

confidence: 99%

Transmission dynamics of SARS-CoV-2 variants in the Brazilian state of Pará

Pinho,

Vidal,

Negri Rocha

et al. 2023

Front. Public Health

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IntroductionAfter three years since the beginning of the pandemic, the new coronavirus continues to raise several questions regarding its infectious process and host response. Several mutations occurred in different regions of the SARS-CoV-2 genome, such as in the spike gene, causing the emergence of variants of concern and interest (VOCs and VOIs), of which some present higher transmissibility and virulence, especially among patients with previous comorbidities. It is essential to understand its spread dynamics to prevent and control new biological threats that may occur in the future. In this population_based retrospective observational study, we generated data and used public databases to understand SARS-CoV-2 dynamics.MethodsWe sequenced 1,003 SARS-CoV-2 genomes from naso-oropharyngeal swabs and saliva samples from Pará from May 2020 to October 2022. To gather epidemiological data from Brazil and the world, we used FIOCRUZ and GISAID databases.ResultsRegarding our samples, 496 (49.45%) were derived from female participants and 507 (50.55%) from male participants, and the average age was 43 years old. The Gamma variant presented the highest number of cases, with 290 (28.91%) cases, followed by delta with 53 (5.28%). Moreover, we found seven (0.69%) Omicron cases and 651 (64.9%) non-VOC cases. A significant association was observed between sex and the clinical condition (female, p = 8.65e-08; male, p = 0.008961) and age (p = 3.6e-10).DiscussionAlthough gamma had been officially identified only in December 2020/January 2021, we identified a gamma case from Belém (capital of Pará State) dated May 2020 and three other cases in October 2020. This indicates that this variant was circulating in the North region of Brazil several months before its formal identification and that Gamma demonstrated its actual transmission capacity only at the end of 2020. Furthermore, the public data analysis showed that SARS-CoV-2 dispersion dynamics differed in Brazil as Gamma played an important role here, while most other countries reported a new infection caused by the Delta variant. The genetic and epidemiological information of this study reinforces the relevance of having a robust genomic surveillance service that allows better management of the pandemic and that provides efficient solutions to possible new disease-causing agents.

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Section: Methodsmentioning

confidence: 99%

Transmission dynamics of SARS-CoV-2 variants in the Brazilian state of Pará

Pinho,

Vidal,

Negri Rocha

et al. 2023

Front. Public Health

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“…The approach provides the alignment of DNA fragments (reads) to a reference genome, while reads are mapped based on the best match and alignment to the reference genome [122]. The majority of pipelines developed for the genome assembly of SARS-CoV-2, such as Viralrecon, V-pipe and SIGNAL provide a reference-based strategy [123]. De novo assemblies are performed without the necessity of a reference genome.…”

Section: Sars-cov-2 Genome Sequencing Methodsmentioning

confidence: 99%

“…On the other hand, de novo assemblies are useful when the pathogen is unknown/poorly understood and also when a suitable reference is absent in the database [125]. A recently reported de novo assembly pipeline developed for the genome assembly of SARS-CoV-2 is PipeCoV [123].…”

Section: Sars-cov-2 Genome Sequencing Methodsmentioning

confidence: 99%

Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection

et al. 2022

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COVID-19 emerged in late 2019 in China and quickly spread across the globe, causing over 521 million cases of infection and 6.26 million deaths to date. After 2 years, numerous advances have been made. First of all, the preventive vaccine, which has been implemented in record time, is effective in more than 95% of cases. Additionally, in the diagnostic field, there are numerous molecular and antigenic diagnostic kits that are equipped with high sensitivity and specificity. Real Time-PCR-based assays for the detection of viral RNA are currently considered the gold-standard method for SARS-CoV-2 diagnosis and can be used efficiently on pooled nasopharyngeal, or oropharyngeal samples for widespread screening. Moreover, additional, and more advanced molecular methods such as droplet-digital PCR (ddPCR), clustered regularly interspaced short palindromic repeats (CRISPR) and next-generation sequencing (NGS), are currently under development to detect the SARS-CoV-2 RNA. However, as the number of subjects infected with SARS-CoV-2 continuously increases globally, health care systems are being placed under increased stress. Thus, the clinical laboratory plays an important role, helping to select especially asymptomatic individuals who are actively carrying the live replicating virus, with fast and non-invasive molecular technologies. Recent diagnostic strategies, other than molecular methods, have been adopted to either detect viral antigens, i.e., antigen-based immunoassays, or human anti-SARS-CoV-2 antibodies, i.e., antibody-based immunoassays, in nasal or oropharyngeal swabs, as well as in blood or saliva samples. However, the role of mucosal sIgAs, which are essential in the control of viruses entering the body through mucosal surfaces, remains to be elucidated, and in particular the role of the immune response in counteracting SARS-CoV-2 infection, primarily at the site(s) of virus entry that appears to be promising.

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“…To contribute with SARS-CoV-2 genome sequences from Latin America, seven participant countries (Argentina, Bolivia, Brazil, Costa Rica, Colombia, Mexico, and Peru) were involved in sample processing from COVID-19 patients. Diagnosis using RT-qPCR, genome sequencing and assembly, as well as the genotyping, were implemented using the laboratory protocols and bioinformatic pipelines that are being locally used as part of the genomic surveillance efforts in each country as shown in Table 1 and reported in (Molina-Mora et al, 2021;Oliveira et al, 2022;Resende et al, 2020). Genome sequences were uploaded to the GISAID database (https://www.gisaid.org/).…”

Section: Sample Sequencing and Genome Analysismentioning

confidence: 99%

Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021

Molina-Mora

Reales-González

Camacho

et al. 2022

Preprint

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Latin America is one of the regions in which the COVID-19 pandemic has had a stronger impact, with more than 72 million reported infections and 1.6 million deaths until June 2022. Since this region is ecologically diverse and is affected by enormous social inequalities, efforts to identify genomic patterns of the circulating SARS-CoV-2 genotypes are necessary for the suitable management of the pandemic. To contribute to the genomic surveillance of the SARS-CoV-2 in Latin America, we extended the number of SARS-CoV-2 genomes available from the region by sequencing and analyzing the viral genome from COVID-19 patients from seven countries (Argentina, Brazil, Costa Rica, Colombia, Mexico, Bolivia and Peru). Subsequently, we analyzed the genomes circulating mainly during 2021 including records from GISAID database from Latin America. A total of 1534 genome sequences were generated from seven countries, demonstrating the laboratory and bioinformatics capabilities for genomic surveillance of pathogens that have been developed locally. For Latin America, patterns regarding several variants associated with multiple re-introductions, a relatively low percentage of sequenced samples, as well as an increment in the mutation frequency since the beginning of the pandemic, are in line with worldwide data. Besides, some variants of concern (VOC) and variants of interest (VOI) such as Gamma, Mu and Lambda, and at least 83 other lineages have predominated locally with a country-specific enrichments. This work has contributed to the understanding of the dynamics of the pandemic in Latin America as part of the local and international efforts to achieve timely genomic surveillance of SARS-CoV-2.

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PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification

Cited by 8 publications

References 23 publications

Transmission dynamics of SARS-CoV-2 variants in the Brazilian state of Pará

Transmission dynamics of SARS-CoV-2 variants in the Brazilian state of Pará

Advanced Molecular and Immunological Diagnostic Methods to Detect SARS-CoV-2 Infection

Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021

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