Rapid longitudinal SARS-CoV-2 intra-host emergence of novel haplotypes regardless of immune deficiencies

  1. Laura Manuto
  2. Marco Grazioli
  3. Andrea Spitaleri
  4. Paolo Fontana
  5. Luca Bianco
  6. Luigi Bertolotti
  7. Martina Bado
  8. Giorgia Mazzotti
  9. Federico Bianca
  10. Francesco Onelia
  11. Giovanni Lorenzin
  12. Fabio Simeoni
  13. Dejan Lazarevic
  14. Elisa Franchin
  15. Claudia Del Vecchio
  16. Ilaria Dorigatti
  17. Giovanni Tonon
  18. Daniela Cirillo
  19. Enrico Lavezzo
  20. Andrea Crisanti
  21. Stefano Toppo

Reviewed by

Read the full article

Listed in

Log in to save this article

Abstract

On February 2020, the municipality of Vo’, a small town near Padua (Italy), was quarantined due to the first coronavirus disease 19 (COVID-19)-related death detected in Italy. The entire population was swab tested in two sequential surveys. Here we report the analysis of the viral genomes, which revealed that the unique ancestor haplotype introduced in Vo’ belongs to lineage B and, more specifically, to the subtype found at the end of January 2020 in two Chinese tourists visiting Rome and other Italian cities, carrying mutations G11083T and G26144T . The sequences, obtained for 87 samples, allowed us to investigate viral evolution while being transmitted within and across households and the effectiveness of the non-pharmaceutical interventions implemented in Vo’. We report, for the first time, evidence that novel viral haplotypes can naturally arise intra-host within an interval as short as two weeks, in approximately 30% of the infected individuals, regardless of symptoms severity or immune system deficiencies. Moreover, both phylogenetic and minimum spanning network analyses converge on the hypothesis that the viral sequences evolved from a unique common ancestor haplotype, carried by an index case. The lockdown extinguished both viral spread and the emergence of new variants, confirming the efficiency of this containment strategy. The information gathered from household was used to reconstructs possible transmission events.

AUTHOR SUMMARY

It is of great interest and importance to understand SARS-CoV-2 ability to mutate generating new viral strains, and to assess the impact of containment strategies on viral transmission. In this study we highlight the rapid intra-host haplotype evolution regardless of symptom severity and immune deficiencies that we observed during the first wave of the pandemic in the municipality of Vo’ in Italy. The confirmation that all the haplotypes found in this small community derive from a common ancestor haplotype, has allowed us to track the rapid emergence of new variants but lockdown and mass testing efficiently prevented their spread elsewhere.

Article activity feed

  1. ScreenIT

    SciScore for 10.1101/2021.12.22.473949: (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
    SentencesResources
    Viral genome assembly: quality check and mapping of the reads: Raw sequences were filtered for length and quality with Trimmomatic v0.40 according to the following parameters: ILLUMINACLIP:TruSeq3-PE-2:2:30:10 LEADING:30 TRAILING:30 SLIDINGWINDOW:4:20 MINLEN:90.
    Trimmomatic
    suggested: (Trimmomatic, RRID:SCR_011848)
    High quality reads were aligned on the SARS-CoV-2 reference genome (genbank ACC: NC_045512) with BWA-MEM v0.7.1.
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    Duplicated reads were then removed with Picard tool v2.25.0 (http://broadinstitute.github.io/picard/).
    Picard
    suggested: (Picard, RRID:SCR_006525)
    Consensus sequence were generated using a combination of SAMtools v1.11 and VarScan v2.4.1 variant caller.
    SAMtools
    suggested: (SAMTOOLS, RRID:SCR_002105)
    Consensus sequences were reconstructed from VarScan output with an in-house script that automatically introduces ‘N’ in low quality or uncertain/uncovered regions of the reference sequence.
    VarScan
    suggested: (VARSCAN, RRID:SCR_006849)
    The first 20 most similar genomes of every cluster were used as input of MAFFT (33) to produce a multiple alignment with the Wuhan genome (GenBank ID MN908947.3) as reference.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Phylogenetic trees were constructed using RAxML (35) software.
    RAxML
    suggested: (RAxML, RRID:SCR_006086)

    Results from OddPub: Thank you for sharing your data.

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    To sum up, this study sheds light around the effectiveness of contact tracing based on interviews, which showed limitations in the coverage and traceability of the contacts among the identified infections. For these reasons, in the absence of effective digital contact tracing, mass testing followed by case isolation represents the best approach, when applicable, for identifying and isolating infections thus giving the best chances to achieve epidemic control (28–30). As a matter of fact, the variants generated in the Vo’ population, did not spread outside Vo’ showing that effective control strategies not only curb transmission, but also control the emergence and spread of new variants. The number of mutations observed in the Vo’ population over just two weeks should warn about the velocity of adaptation that may be occurring in different subjects and the potential ability of SARS-CoV-2 to develop immune evasion.

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  2. Version published to 10.1101/2021.12.22.473949v1 on bioRxiv