Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
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Abstract
Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.
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SciScore for 10.1101/2021.05.04.21256637: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Samples of this particular lineage were sequenced by ECDC using in-house protocols, infrastructure and assembly methods, VUHSK using Illumina COVIDSeq reagents, Illumina MiSeq platform, and assembled with covid-19-signal (Nasir et al., 2020), HLUHSKC using Twist SARS-CoV-2 Research Panel reagents, Illumina NextSeq550 platform, and assembled with V-pipe (Posada-Céspedes et al., 2021), LUHS using ARTIC protocol, Oxford Nanopore Technologies MinION platform, and assembled using ARTIC bioinformatics protocol for SARS-CoV-2, and VULSC using ARTIC V3 protocol combined with Invitrogen Collibri … SciScore for 10.1101/2021.05.04.21256637: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Samples of this particular lineage were sequenced by ECDC using in-house protocols, infrastructure and assembly methods, VUHSK using Illumina COVIDSeq reagents, Illumina MiSeq platform, and assembled with covid-19-signal (Nasir et al., 2020), HLUHSKC using Twist SARS-CoV-2 Research Panel reagents, Illumina NextSeq550 platform, and assembled with V-pipe (Posada-Céspedes et al., 2021), LUHS using ARTIC protocol, Oxford Nanopore Technologies MinION platform, and assembled using ARTIC bioinformatics protocol for SARS-CoV-2, and VULSC using ARTIC V3 protocol combined with Invitrogen Collibri reagents, Illumina MiniSeq platform, Illumina DRAGEN COVID Lineage combined with an in-house BLAST v2.10.18-based assembly protocol. Oxford Nanoporesuggested: (Oxford Nanopore Technologies, RRID:SCR_003756)MinIONsuggested: (MinION, RRID:SCR_017985)MiniSeqsuggested: NoneBLASTsuggested: (BLASTX, RRID:SCR_001653)These sequences were aligned in MAFFT (FFT-NS-2 setting; Katoh and Standley (2013)) with insertions relative to reference removed, and 5’ and 3’ untranslated regions of the genome that were susceptible to sequencing and assembly error trimmed. MAFFTsuggested: (MAFFT, RRID:SCR_011811)We employed TempEst (Rambaut et al., 2016) to inspect the data set for any data quality issues that could result in an excess or shortage of private mutations in any sequences, or would point to assembly or any other type of sequencing issues. TempEstsuggested: (TempEst, RRID:SCR_017304)We subsequently performed a discrete Bayesian phylogeographic analysis in BEAST 1.10.5 (Suchard et al., 2018) using a recently developed model that is able to incorporate available individual travel history information associated with the collected samples (Lemey et al., 2020; Hong et al., 2021). BEASTsuggested: (BEAST, RRID:SCR_010228)A maximum likelihood phylogeny was inferred from this dataset using PhyML (Guindon et al., 2010) under the HKY+Γ4 model of nucleotide substitution (Hasegawa et al., 1985; Yang, 1994) which was then rooted on the reference sequence and shown in Figure S4. PhyMLsuggested: (PhyML, RRID:SCR_014629)To occupy less space in Figure 1 the number of B.1.620 genomes was reduced down to a representative set of 27, and a phylogeny was inferred using MrBayes v3.2 (Ronquist et al., 2012) under the HKY+Γ4 model of nucleotide substitution (Hasegawa et al., 1985; Yang, 1994) and rooted on the reference sequence. MrBayessuggested: (MrBayes, RRID:SCR_012067)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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