Genetic diversity of SARS-CoV-2 in South America: demographic history and structuration signals

Buitrago, Sindy P.; Garzón‐Ospina, Diego

doi:10.1007/s00705-021-05258-w

Cited by 4 publications

(6 citation statements)

References 78 publications

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“…Moreover, other minor forces are expected to increase diversity, such as co-circulation and population genetic admixture. These results are in congruence with other studies that showed statistically significantly negative values for neutrality tests [ 51 ].…”

Section: Discussionsupporting

confidence: 93%

“…The genetic distance between the three SARS-CoV-2 clusters (Fst > 0.25) and low to intermediate gene flow (Nm) supports the clustering of the genetic diversity, with signs of gene flow between cluster A and B (Nm = 0.57) and between I and C (Nm = 0.36), but with low transfer of genetic diversity (Nm = 0.21) between cluster B and C due to extensive movement of hosts. A study in South America showed statistically significant values, indicating slight genetic differentiation [ 51 ]. Unlike the Fst, the other genetic differentiation estimators, Gst and Da, were underestimated due to the high mutation rate [ 33 , 52 ].…”

Section: Discussionmentioning

confidence: 99%

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Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine

Ereqat,

Alikhan,

Al-Jawabreh

et al. 2024

Pathogens

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The emergence of new SARS-CoV-2 variants in Palestine highlights the need for continuous genetic surveillance and accurate screening strategies. This case series study aimed to investigate the geographic distribution and genetic variation of the SARS-CoV-2 Delta Variant in Palestine in August 2021. Samples were collected at random in August 2021 (n = 571) from eight districts in the West Bank, Palestine. All samples were confirmed as positive for COVID-19 by RT-PCR. The samples passed the quality control test and were successfully sequenced using the ARTIC protocol. The Delta Variant was revealed to have four dominant lineages: B.1.617 (19%), AY.122 (18%), AY.106 (17%), and AY.121 (13%). The study revealed eight significant purely spatial clusters (p < 0.005) distributed in the northern and southern parts of Palestine. Phylogenetic analysis of SARS-CoV-2 genomes (n = 552) showed no geographically specific clades. The haplotype network revealed three haplogroups without any geographic distribution. Chronologically, the Delta Variant peak in Palestine was shortly preceded by the one in the neighboring Israeli community and shortly followed by the peak in Jordan. In addition, the study revealed an extremely intense transmission network of the Delta Variant circulating between the Palestinian districts as hubs (SHR ≈ 0.5), with Al-Khalil, the district with the highest prevalence of COVID-19, witnessing the highest frequency of transitions. Genetic diversity analysis indicated closely related haplogroups, as haplotype diversity (Hd) is high but has low nucleotide diversity (π). However, nucleotide diversity (π) in Palestine is still higher than the global figures. Neutrality tests were significantly (p < 0.05) low, including Tajima’s D, Fu-Li’s F, and Fu-Li’s D, suggesting one or more of the following: population expansion, selective sweep, and natural negative selection. Wright’s F-statistic (Fst) showed genetic differentiation (Fst > 0.25) with low to medium gene flow (Nm). Recombination events were minimal between clusters (Rm) and between adjacent sites (Rs). The study confirms the utility of the whole genome sequence as a surveillance system to track the emergence of new SARS-CoV-2 variants for any possible geographical association and the use of genetic variation analysis and haplotype networking to delineate any minimal change or slight deviation in the viral genome from a reference strain.

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Section: Discussionsupporting

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine

Ereqat,

Alikhan,

Al-Jawabreh

et al. 2024

Pathogens

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“…These already-characterized mutations are present in variants being monitored, such as Mu and Zeta ( 7 , 30 , 31 ). It is important to mention that, given the variability of the amplified regions, we expect to detect more relevant mutations in future VoCs ( 16 , 44 – 47 ).…”

Section: Resultsmentioning

confidence: 99%

A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing

Burgos,

Ambuludí,

Morales-Jadán

et al. 2023

Microbiol Spectr

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.

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“…Si bien el pelaje de la mascota podría ser un vector pasivo (fómite), por adhesión de partículas virales expulsadas por una persona infectada en estornudos o saliva, aún no se ha reportado este tipo de transmisión. No obstante, la infección natural de SARS-CoV-2 en un nuevo huésped podría ocasionar cambios nucleotídicos de adaptabilidad evolutiva (44) que produzca posibles impactos negativos emergentes del virus (45), por lo cual es importante incluir estas secuencias encontradas en animales, dentro de la Red Regional de Vigilancia Genómica de COVID-19 para vigilar o predecir posibles variantes de interés (VOI) o variantes de preocupación (VOC) que llegasen a evolucionar en estos nuevos huéspedes a medida que aumenta su prevalencia (43,46) La mutación NSP12 S647I se ha eportado en secuencias de humanos en 80 países (47), incluido Colombia y particularmente Antioquia. Esta mutación, al estar extendida en la población humana, probablemente sea una adaptación evolutiva del virus en humanos y no una adaptación específica del virus en las células del gato, como se reportó con la mutación P323L presente en una secuencia de un gato infectado naturalmente en el Reino Unido (48).…”

Section: Discussionunclassified

“…Esta mutación, al estar extendida en la población humana, probablemente sea una adaptación evolutiva del virus en humanos y no una adaptación específica del virus en las células del gato, como se reportó con la mutación P323L presente en una secuencia de un gato infectado naturalmente en el Reino Unido (48). Además, esta mutación puede corresponder a una sustitución natural evolutiva, ya que la tasa de cambio de nucleótidos estimada para el SARS-CoV-2 varía entre 10 -3 y 10 -4 sustituciones por sitio y por año (46). Es necesario realizar estudios en otras regiones del genoma como la región codificante de la proteína S, en la cual, por ejemplo, la mutación D614G (compartida por los genomas felinos) confiere adaptabilidad en humanos y, por consiguiente, favorece la capacidad infecciosa del virus (49).…”

Section: Discussionunclassified

Infección natural por SARS-CoV-2 en gatos y perros domésticos de personas con diagnóstico de COVID-19 en el Valle de Aburrá, Antioquia

Cabrera

González-Álvarez

Gutiérrez³

et al. 2022

biomedica

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Introducción. El síndrome respiratorio agudo grave causado por el nuevo coronavirus SARSCoV-2 es causa de la emergencia sanitaria por la pandemia de COVID-19. Si bien el humano es el el principal huésped vulnerable, en estudios experimentales y reportes de infección natural, se han encontrado casos de zoonosis inversa de SARS-CoV-2 en animales.Objetivo. Evaluar la infección natural por SARS-CoV-2 en gatos y perros de propietarios con diagnóstico de COVID-19 en el Valle de Aburrá, Antioquia, Colombia.Materiales y métodos. La circulación del SARS-CoV-2 se evaluó por RT-qPCR y RT-PCR en muestras de frotis nasofaríngeos y orofaríngeos de gatos y perros cuyos propietarios se encontraban dentro del periodo de los 14 días de aislamiento. Los casos positivos se verificaron amplificando fragmentos de los genes RdRp, N y E; se secuenció el gen RdRp y se analizó filogenéticamente.Resultados. De 80 animales evaluados, seis gatos y tres perros fueron casos confirmados de infección natural por SARS-CoV-2. Los animales no presentaron signos clínicos y sus propietarios, que padecían la infección, reportaron únicamente signos leves de la enfermedad sin complicaciones clínicas. En el análisis de una de las secuencias, se encontró un polimorfismo de un solo nucleótido (SNP) con un cambio en la posición 647, con sustitución del aminoácido serina (S) por una isoleucina (I). Los casos se presentaron en los municipios de Caldas, Medellín y Envigado.Conclusiones. Se infiere que la infección natural en los gatos y perros se asocia al contacto directo con un paciente con COVID-19. No obstante, no es posible determinar la virulencia del virus en este huésped, ni su capacidad de transmisión zoonótica o entre especie.

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Genetic diversity of SARS-CoV-2 in South America: demographic history and structuration signals

Cited by 4 publications

References 78 publications

Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine

Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine

A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing

Infección natural por SARS-CoV-2 en gatos y perros domésticos de personas con diagnóstico de COVID-19 en el Valle de Aburrá, Antioquia

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