The Principles of SARS-CoV-2 Intervariant Competition Are Exemplified in the Pre-Omicron Era of the Colombian Epidemic

Orf, Gregory S.; Pérez, Lester J.; Čiuoderis, Karl; Cardona, Andrés Felipe; Villegas, Simon; Hernández-Ortiz, Juan P.; Baele, Guy; Mohaimani, Aurash; Osorio, Jorge E.; Berg, Michael G.; Cloherty, Gavin

doi:10.1128/spectrum.05346-22

Cited by 5 publications

(5 citation statements)

References 70 publications

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“…Third, Mu faced competition from Gamma/Lambda in South American countries and from Delta in Mexico, Central America, and the Caribbean. Delta variant transmissibility was estimated as being the highest among the variants that emerged before it 36 , 40 and this feature might have offered an advantage to Delta over Mu where they co-circulated, as also suggested by 41 . Fourth, dissemination of Mu may have been limited by the “hybrid immunity” generated by the combination of natural infection and vaccination in LAC region 42 – 44 .…”

Section: Discussionmentioning

confidence: 96%

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean

Gräf,

Martinez,

Bello

et al. 2024

Nat Commun

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Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.

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Section: Discussionmentioning

confidence: 96%

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean

Gräf,

Martinez,

Bello

et al. 2024

Nat Commun

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“…In NYC, the introduction of the Alpha variant around the time of Iota emergence [ 7 ] likely prevented Iota from establishing at a level that would make it difficult for Alpha to compete. Unlike previous analyses that focused on competition at a country level [ 23 , 24 ], we were able to decipher competition dynamics between variants at the neighborhood level owing to the granularity of seropositivity data and SARS-CoV-2 genome data. Given the higher transmissibility of the Alpha variant, it might have completely eliminated Iota from NYC if not for the pockets of higher seropositivity left in the wake of the first wave of SARS-CoV-2.…”

Section: Discussionmentioning

confidence: 99%

“…At the same time, the Gamma variant was not able to successfully establish itself in the neighboring Colombia or Peru. This failure is likely due to a founder effect as competing variants, Mu in Colombia and Lambda in Peru, which also have immune-evasive properties, already dominated the Colombian and Peruvian epidemic by the time Gamma reached the country [ 23 , 24 ]. Thus, the time of VOCs emergence and introductions, and mechanisms for increased fitness, is crucial for their success in a location in the presence of other variants.…”

Section: Discussionmentioning

confidence: 99%

The role of socio-economic disparities in the relative success and persistence of SARS-CoV-2 variants in New York City in early 2021

Vasylyeva,

Havens,

Wang

et al. 2024

PLoS Pathog

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Socio-economic disparities were associated with disproportionate viral incidence between neighborhoods of New York City (NYC) during the first wave of SARS-CoV-2. We investigated how these disparities affected the co-circulation of SARS-CoV-2 variants during the second wave in NYC. We tested for correlation between the prevalence, in late 2020/early 2021, of Alpha, Iota, Iota with E484K mutation (Iota-E484K), and B.1-like genomes and pre-existing immunity (seropositivity) in NYC neighborhoods. In the context of varying seroprevalence we described socio-economic profiles of neighborhoods and performed migration and lineage persistence analyses using a Bayesian phylogeographical framework. Seropositivity was greater in areas with high poverty and a larger proportion of Black and Hispanic or Latino residents. Seropositivity was positively correlated with the proportion of Iota-E484K and Iota genomes, and negatively correlated with the proportion of Alpha and B.1-like genomes. The proportion of persisting Alpha lineages declined over time in locations with high seroprevalence, whereas the proportion of persisting Iota-E484K lineages remained the same in high seroprevalence areas. During the second wave, the geographic variation of standing immunity, due to disproportionate disease burden during the first wave of SARS-CoV-2 in NYC, allowed for the immune evasive Iota-E484K variant, but not the more transmissible Alpha variant, to circulate in locations with high pre-existing immunity.

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“…In NYC, the introduction of the Alpha variant around the time of Iota emergence (7) likely prevented Iota from establishing at a level that would make it difficult for Alpha to compete. Unlike previous analyses that focused on competition at a country level (23,24), we were able to decipher competition dynamics between variants at the neighborhood level owing to the granularity of seropositivity data and SARS-CoV-2 genome data. Given the higher transmissibility of the Alpha variant, it might have completely eliminated Iota from NYC if not for the pockets of higher seropositivity left in the wake of the first wave of SARS-CoV-2.…”

Section: Discussionmentioning

confidence: 99%

“…The Gamma variant dominated the Brazilian SARS-CoV-2 epidemic in late 2020/early 2021 due to the high levels of pre-existing immunity in Brazilian population (26,27), but in mid-2021 it was quickly replaced by Delta due to the Delta variant's higher transmissibility (28). At the same time, the Gamma variant was not able to successfully establish itself in the neighboring Colombia or Peru (23,24). This failure is likely due to a founder effect as competing variants, Mu in Colombia and Lambda in Peru, which also have immune-evasive properties, already dominated the Colombian and Peruvian epidemic by the time Gamma reached the country.…”

Section: Discussionmentioning

confidence: 99%

The role of socio-economic disparities in the relative success of SARS-CoV-2 variants in New York City in early 2021

Vasylyeva,

Havens,

Wang

et al. 2023

Preprint

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BackgroundSocio-economic disparities were associated with disproportionate viral incidence between neighborhoods of New York City (NYC) during the first wave of SARS-CoV-2. We investigated how these disparities affected the co-circulation SARS-CoV-2 variants during the second wave in NYC.MethodsWe tested for correlation between the prevalence, in late 2020/early 2021, of Alpha, Iota, Iota with E484K mutation (Iota-E484K), and B.1-like genomes and pre-existing immunity (seropositivity) in NYC neighborhoods. In the context of varying seroprevalence we described socio-economic profiles of neighborhoods and performed migration and lineage persistence analyses using a Bayesian phylogeographical framework.FindingsSeropositivity was greater in areas with high poverty and a larger proportion of Black and Hispanic or Latino residents. Seropositivity was positively correlated with the proportion of Iota-E484K and Iota genomes, and negatively correlated with the proportion of Alpha and B.1-like genomes. The proportion of persisting Alpha lineages declined over time in locations with high seroprevalence, whereas the proportion of persisting Iota-E484K lineages remained the same in high seroprevalence areas.InterpretationDuring the second wave, the geographic variation of standing immunity, due to disproportionate disease burden during the first wave of SARS-CoV-2 in NYC, allowed for the immune evasive Iota-E484K variant, but not the more transmissible Alpha variant, to circulate in locations with high pre-existing immunity.FundingWe acknowledge funding from the National Institutes of Health and the Centers for Disease Control and Prevention.

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The Principles of SARS-CoV-2 Intervariant Competition Are Exemplified in the Pre-Omicron Era of the Colombian Epidemic

Cited by 5 publications

References 70 publications

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean

The role of socio-economic disparities in the relative success and persistence of SARS-CoV-2 variants in New York City in early 2021

The role of socio-economic disparities in the relative success of SARS-CoV-2 variants in New York City in early 2021

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