SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity

Siqueira, Juliana D.; Goes, Livia R; Alves, Brunna M.; Carvalho, Pedro S. de; Cicala, Claudia; Arthos, James; Viola, João P. B.; Melo, Andréia Cristina de; Soares, Marcelo A.

doi:10.1093/ve/veab013

Cited by 28 publications

(25 citation statements)

References 32 publications

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“…The present report points out to differences in the distribution of SARS-CoV-2 lineages at the Brazilian National Cancer Institute in the first wave of infections as compared to recent samples from December 2020 to March 2021. We have previously shown that in the first half of 2020 most of the patients and HCW at INCA were infected by lineage B.1.1.28 ( Siqueira et al, 2021 ), however this was not the case for our recent samples where lineages P.1 and P.2 have risen and are now predominant. None of the subjects included in this study had any travel history to Manaus, epicenter of P.1, indicating that the P.1 lineage is circulating at high frequency in Rio de Janeiro.…”

Section: Discussioncontrasting

confidence: 65%

New infections by SARS-CoV-2 variants of concern after natural infections and post-vaccination in Rio de Janeiro, Brazil

Goes

Siqueira

Garrido

et al. 2021

Infection, Genetics and Evolution

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After a one-year rollout of the pandemic caused by SARS-CoV-2, the continuous dissemination of the virus has generated a number of variants with increased transmissibility and infectivity, called variants of concern (VOC), which now predominate worldwide. Concerns about the susceptibility of humans that have already been infected before or those already vaccinated to infection by VOC rise among scientists and clinicians. Herein, we assessed the prevalence of different VOC among recent infections at the Brazilian National Cancer Institute (Rio de Janeiro, Brazil). By using a Sanger-based sequencing approach targeting the viral S gene to identify VOC, we have analyzed 72 recent infections. The overall prevalence of VOC was 97%. Among the subjects analyzed, six had been vaccinated with the ChAdOx1-S/nCoV-19 ( n = 4; one with two doses and three with one dose) or the CoronaVac ( n = 2; both with 2 doses) vaccine, while five subjects represented reinfection cases, being two of them also part of the vaccinated group (each one with one vaccine type). All vaccinated and re-infected subjects carried VOC irrespective of the vaccine type taken, the number of doses taken, IgG titers or being previously infected during the first wave of the Brazilian pandemic. Importantly, all six vaccinees only had mild symptoms. We present here several examples of how natural infections or vaccination may not be fully capable of conferring sterilizing immunity against VOC

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Section: Discussioncontrasting

confidence: 65%

New infections by SARS-CoV-2 variants of concern after natural infections and post-vaccination in Rio de Janeiro, Brazil

Goes

Siqueira

Garrido

et al. 2021

Infection, Genetics and Evolution

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“…The copyright holder for this preprint this version posted March 25, 2021. ; https://doi.org/10.1101/2021.03.21.21253418 doi: medRxiv preprint Convergent mutations seem to play an essential role in the evolutionary dynamics of SARS-CoV-2. Intense selective pressure from the immune system against prolonged infections may promote intrahost variants with higher adaptive value [12,[35][36][37][38][39]. Previous studies have shown that both N501Y and E484K have independently emerged in patients with persistent infection [35,40].…”

Section: Discussionmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Lamarca

Almeida

Francisco

et al. 2021

Preprint

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The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. Novel SARS-CoV-2 lineages P.1 and P.2, first identified respectively in Manaus and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed a whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraiba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) aiming to identify SARS-CoV-2 mutations that could be involved in the surge of COVID19 cases in Brazil. Here, we showed a widespread dispersion of P.1 and P.2 across Brazilian regions. Except for Manaus, P.2 was the predominant lineage identified country-wise. P.2 lineage was estimated to have originated in February, 2020 and has diverged into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December. P.1 origin was inferred to have happened in August 2020. We also confirmed the presence of the variant under investigation (VUI) NP13L recently described in the southernmost region of Brazil to have spread across the Northeastern states. P.1, P.2 and NP13L are descended from the ancient B.1.1.28 strain, although during the first phase of the pandemic in Brazil presence of B.1.1.33 strain was also reported. Here, for the first time, we investigate the possible occurrence of a new variant of concern descending from B.1.1.33 that also carries the E484K mutation. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to early identify novel variants of concern and to monitor for vaccine effectiveness.

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“…Convergent mutations seem to play an essential role in the evolutionary dynamics of SARS-CoV-2. Intense selective pressure from the immune system against prolonged infections may promote intrahost variants with higher adaptive value [25,[54][55][56][57][58]. Previous studies have shown that both N501Y and E484K have independently emerged in patients with persistent infection [54,59].…”

Section: Discussionmentioning

confidence: 99%

“…In this work, a total of 185 participants were selected from Amazonas (4), Rio Grande do Norte (44), Paraiba (43), Bahia (58), and Rio de Janeiro (36) states, representing the Brazilian North, Northeast, and Southeast regions. Samples from Amazonas) were obtained from the four patients transferred to Paraı ´ba in late January 2021 while samples from Rio de Janeiro, Rio Grande do Norte, Paraı ´ba and Bahia were randomly selected among COVID-19 positive cases.…”

Section: Sample Collectionmentioning

confidence: 99%

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

et al. 2021

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The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to identify novel variants of interest and monitor for vaccine effectiveness.

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SARS-CoV-2 genomic analyses in cancer patients reveal elevated intrahost genetic diversity

Cited by 28 publications

References 32 publications

New infections by SARS-CoV-2 variants of concern after natural infections and post-vaccination in Rio de Janeiro, Brazil

New infections by SARS-CoV-2 variants of concern after natural infections and post-vaccination in Rio de Janeiro, Brazil

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

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