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1.
Science ; : eabp8337, 2022 Jul 26.
Article in English | MEDLINE | ID: covidwho-1962060

ABSTRACT

Understanding the circumstances that lead to pandemics is important for their prevention. Here, we analyze the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October-8 December), while the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans prior to November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.

2.
Nat Commun ; 13(1): 3645, 2022 06 25.
Article in English | MEDLINE | ID: covidwho-1908172

ABSTRACT

Recombination is an evolutionary process by which many pathogens generate diversity and acquire novel functions. Although a common occurrence during coronavirus replication, detection of recombination is only feasible when genetically distinct viruses contemporaneously infect the same host. Here, we identify an instance of SARS-CoV-2 superinfection, whereby an individual was infected with two distinct viral variants: Alpha (B.1.1.7) and Epsilon (B.1.429). This superinfection was first noted when an Alpha genome sequence failed to exhibit the classic S gene target failure behavior used to track this variant. Full genome sequencing from four independent extracts reveals that Alpha variant alleles comprise around 75% of the genomes, whereas the Epsilon variant alleles comprise around 20% of the sample. Further investigation reveals the presence of numerous recombinant haplotypes spanning the genome, specifically in the spike, nucleocapsid, and ORF 8 coding regions. These findings support the potential for recombination to reshape SARS-CoV-2 genetic diversity.


Subject(s)
COVID-19 , Superinfection , Genome, Viral/genetics , Humans , New York City/epidemiology , Recombination, Genetic , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics
3.
J Infect Dis ; 2022 Jun 30.
Article in English | MEDLINE | ID: covidwho-1908839

ABSTRACT

BACKGROUND: Monitoring the emergence and spread of SARS-CoV-2 variants is an important public health objective. We investigated how the Gamma variant was established in New York City (NYC) in early 2021 in the presence of travel restrictions that aimed to prevent viral spread from Brazil, the country where the variant was first identified. METHODS: We performed phylogeographic analysis on 15,967 Gamma sequences sampled between March 10th through May 1st, 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC. RESULTS: We identified 16 phylogenetically-distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes); most of them were introduced from Florida and Illinois and only one directly from Brazil. By the time the first Gamma case was reported by genomic surveillance in NYC on March 10th, the majority (57%) of circulating Gamma lineages had already been established in the city for at least two weeks. CONCLUSIONS: Although travel from Brazil to the US was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.

5.
Nat Commun ; 12(1): 4886, 2021 08 09.
Article in English | MEDLINE | ID: covidwho-1349666

ABSTRACT

Wide-scale SARS-CoV-2 genome sequencing is critical to tracking viral evolution during the ongoing pandemic. We develop the software tool, Variant Database (VDB), for quickly examining the changing landscape of spike mutations. Using VDB, we detect an emerging lineage of SARS-CoV-2 in the New York region that shares mutations with previously reported variants. The most common sets of spike mutations in this lineage (now designated as B.1.526) are L5F, T95I, D253G, E484K or S477N, D614G, and A701V. This lineage was first sequenced in late November 2020. Phylodynamic inference confirmed the rapid growth of the B.1.526 lineage. In concert with other variants, like B.1.1.7, the rise of B.1.526 appears to have extended the duration of the second wave of COVID-19 cases in NYC in early 2021. Pseudovirus neutralization experiments demonstrated that B.1.526 spike mutations adversely affect the neutralization titer of convalescent and vaccinee plasma, supporting the public health relevance of this lineage.


Subject(s)
COVID-19/virology , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , COVID-19/epidemiology , Genome, Viral , Humans , Models, Molecular , Mutation , New York/epidemiology , Phylogeny , SARS-CoV-2/genetics , Software , Spike Glycoprotein, Coronavirus/genetics
6.
Science ; 371(6530): 708-712, 2021 02 12.
Article in English | MEDLINE | ID: covidwho-1066806

ABSTRACT

The United Kingdom's COVID-19 epidemic during early 2020 was one of world's largest and was unusually well represented by virus genomic sampling. We determined the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes, including 26,181 from the UK sampled throughout the country's first wave of infection. Using large-scale phylogenetic analyses combined with epidemiological and travel data, we quantified the size, spatiotemporal origins, and persistence of genetically distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whereas lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.


Subject(s)
COVID-19/epidemiology , COVID-19/virology , Genome, Viral , SARS-CoV-2/genetics , COVID-19/prevention & control , COVID-19/transmission , Chain of Infection , Communicable Disease Control , Communicable Diseases, Imported/epidemiology , Communicable Diseases, Imported/virology , Epidemics , Humans , Phylogeny , Travel , United Kingdom/epidemiology
7.
J Int AIDS Soc ; 23(7): e25583, 2020 07.
Article in English | MEDLINE | ID: covidwho-665828

ABSTRACT

INTRODUCTION: In light of the COVID-19 pandemic, considerable effort is going into identifying and protecting those at risk. Criminalization, stigmatization and the psychological, physical, behavioural and economic consequences of substance use make people who inject drugs (PWID) extremely vulnerable to many infectious diseases. While relationships between drug use and blood-borne and sexually transmitted infections are well studied, less attention has been paid to other infectious disease outbreaks among PWID. DISCUSSION: COVID-19 is likely to disproportionally affect PWID due to a high prevalence of comorbidities that make the disease more severe, unsanitary and overcrowded living conditions, stigmatization, common incarceration, homelessness and difficulties in adhering to quarantine, social distancing or self-isolation mandates. The COVID-19 pandemic also jeopardizes essential for PWID services, such as needle exchange or substitution therapy programmes, which can be affected both in a short- and a long-term perspective. Importantly, there is substantial evidence of other infectious disease outbreaks in PWID that were associated with factors that enable COVID-19 transmission, such as poor hygiene, overcrowded living conditions and communal ways of using drugs. CONCLUSIONS: The COVID-19 crisis might increase risks of homelessnes, overdoses and unsafe injecting and sexual practices for PWID. In order to address existing inequalities, consultations with PWID advocacy groups are vital when designing inclusive health response to the COVID-19 pandemic.


Subject(s)
Betacoronavirus , Coronavirus Infections/complications , Pneumonia, Viral/complications , Substance Abuse, Intravenous/complications , Adult , COVID-19 , Disease Outbreaks , Drug Overdose/epidemiology , HIV Infections/complications , HIV Infections/epidemiology , Homeless Persons/statistics & numerical data , Humans , Injections/adverse effects , Male , Pandemics , Risk Factors , SARS-CoV-2 , Unsafe Sex/statistics & numerical data
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