Invest Clin 65(2): 169 - 178, 2024 https://doi.org/10.54817/IC.v65n2a04

Autor de Correspondencia Francisco Álvarez-Nava. Carrera de Biología. Facultad de Ciencias Biológicas. Universi-

dad Central del Ecuador. Quito, Ecuador. Tel: +593-252-8810. Fax: +593-252-8810. E-mail: fjalvarez@uce.edu.ec

Genetic association study of the rs10774671

variant of the OAS1 gene with the severity

of COVID-19 in an Ecuadorian population.

Kathya Pilataxi

, Thalía Balarezo

, Erik Chávez, Camila Acosta

, Ivonne Z. Peña

Katherin Narváez

and Francisco Álvarez-Nava

Facultad de Ciencias Biológicas, Universidad Central del Ecuador, Quito, Ecuador.

Hospital Quito Sur del Instituto Ecuatoriano de Seguridad Social, Quito, Ecuador.

Keywords: complex trait; COVID-19; genetic association study; genetic variant;

Hardy-Weinberg equilibrium; innate immune processes.

Abstract. COVID-19 exhibits a wide range of phenotypic manifestations,

from asymptomatic to severe phenotypes with fatal complications. The exis-

tence of risk factors cannot entirely explain the variance in the phenotypic vari-

ability of COVID-19. Genome-wide association analyses have identified target

human genes related to virus transmission and the clinical phenotype observed

in COVID-19 patients. Genetic variants on the OAS1 gene have been associ-

ated with innate immune processes (entry phase and viral replication in host

cells). The A or G alleles of rs10774671 in OAS1 encode isoforms with different

antiviral activities. One hundred COVID-19 patients were genotyped for the

rs10774671 using RFLP-PCR (severe form, n = 43; asymptomatic-mild, n =

57). The susceptibility of the two groups to the severe phenotype of COVID-19

was compared. The allele frequency for A was 0.8. The genotypic frequencies

for AA and GG homozygotes were 0.62 and 0.02, respectively. A Hardy-Weinberg

equilibrium deviation was found in both groups. No statistically significant as-

sociations were found in genetic models adjusted for sex (for the additive model

OR = 1.18, 95% CI = (0.53-2.61), p = 0.69). A relatively recent mix of different

ethnic groups and sample size may influence these findings.

170 Pilataxi et al.

Investigación Clínica 65(2): 2024

Estudio de asociación genética de la variante rs10774671

del gen OAS1 con la severidad de COVID-19 en una población

ecuatoriana.

Invest Clin 2024; 65 (2): 169 – 178

Palabras clave: estudio de asociación genética; equilibrio Hardy-Weinberg; rasgo

complejo; variante genética; procesos inmunes innatos.

Resumen. La COVID-19 presenta una amplia gama de manifestaciones clí-

nicas, desde asintomáticas hasta formas graves con complicaciones mortales.

La variabilidad fenotípica de la COVID-19 no puede explicarse totalmente por

la existencia de factores de riesgo. Se han identificado genes humanos diana

relacionados con la transmisión del virus y el fenotipo clínico observado en

pacientes con COVID-19 mediante análisis de asociación de genoma completo.

Las variantes genéticas del gen OAS1 se han asociado con procesos inmunita-

rios innatos (fase de entrada y replicación viral en las células hospedadoras).

Los alelos A o G de rs10774671 en OAS1 codifican isoformas con diferentes

actividades antivirales. Cien pacientes con COVID-19 fueron genotipados para

el rs10774671 mediante RFLP-PCR (forma grave, n = 43; asintomática-leve, n

= 57). Se comparó la susceptibilidad de los dos grupos al fenotipo severo de

COVID-19. La frecuencia alélica para A fue de 0,8. Las frecuencias genotípicas

para los homocigotos AA y GG fueron 0,62 y 0,02, respectivamente. Se observó

una desviación del equilibrio de Hardy-Weinberg en ambos grupos. No se encon-

traron asociaciones estadísticamente significativas en los modelos genéticos

ajustados por sexo (para el modelo aditivo OR = 1,18, IC 95% = (0,53-2,61),

p = 0,69). La mezcla relativamente reciente de diferentes grupos étnicos y el

tamaño de la muestra pueden influir en estos resultados.

Received: 24-06-2023 Accepted: 13-02-2024

INTRODUCTION

COVID-19 is a human-to-human trans-

missible viral infectious disease

. Until the

beginning of 2023, it had been responsible

for about 7 million deaths worldwide

. Sub-

jects infected with SARS-CoV-2, the etiologi-

cal agent of COVID-19, have a wide range of

phenotypic variability, from asymptomatic

to severe forms of the disease

. This broad

clinical variability is partially explained by

risk factors that include age (> 65 years),

male sex, and the presence of comorbidi-

ties such as obesity, cardiovascular diseases,

diabetes mellitus, and respiratory disorders,

among others

. Therefore, the variance in

the clinical phenotype of COVID-19 may be

caused by additional host-specific factors

Genome-wide association studies have

reported associations between the severe

form of COVID-19 and chromosomal re-

gions, including 12q24.13, which harbors

a gene cluster encoding antiviral restric-

tion enzyme activators (OAS1, OAS2, and

OAS3). These activators are involved in vi-

ral RNA degradation and viral replication

inhibition

6,7

. The OAS1 gene encodes the

enzyme 2′-5′ oligoadenylate synthetase 1

COVID-19 and OAS1 Gene in Ecuadorian Population 171

Vol. 65(2): 169 - 178, 2024

(2-5A), an activator of the ribonuclease L

(RNaseL), which degrades viral RNA within

the host cell, blocks viral replication and

inhibits viral protein synthesis. The genetic

variant rs10774671 is a G→A transition in

the last nucleotide of intron 5 of the OAS1

gene, which affects the nonsense-mediated

decay and the splicing site and controls

the differential expression of isoforms with

lesser enzymatic activity

7,8

. Different allele

and genotype frequencies have been report-

ed in studies, including those of European,

African, and Latin American Afro-Caribbe-

an populations, likely due to the influence

of the ancestral factor

9,10

. Despite being a

multiethnic society composed of different

communities with South American, West

Eurasian, and Sub-Saharan ancestries, the

Ecuadorian population has a strong Native

South American ancestral influence, which

is considered the second highest for this re-

gion’s population

The percentage of severe cases and

deaths among individuals of Hispanic an-

cestry was higher than that reported for the

general population. For instance, in New York

City, one of the communities hardest hit by

the SARS-CoV-2 virus globally, more Hispan-

ics per capita have died from COVID-19 than

any other ethnic group. Infection rates on

the Navajo Nation Indian Reservation have

also been reported to be particularly high

Native Americans represent more than a

third of the COVID-19 cases in the state of

New Mexico, despite making up only 9% of

the population

. These ethnic differences

do not appear to be caused by socioeconomic

conditions or access to health services since

Latin American non-Sub-Saharan ancestry

was reported as a factor associated with

morbidity and mortality from COVID-19 in a

study that included health professionals with

similar economic and educational status

Latin America is one of the regions

where the impact of COVID-19 has been

most severe. Poor sanitary conditions of in-

frastructure, health personnel, and an im-

munologically vulnerable population are two

factors that influenced this impact. Ecua-

dor was one of the countries that was dra-

matically impacted at the beginning of the

pandemic. However, sustained vaccination

campaigns were able to mitigate this impact

partially. Fifteen million people, or 86% of

the population, have received at least one

dose

, with 14 million (or 79%) receiving

two or more doses

. Few genetic associa-

tion studies between COVID-19 and suscep-

tibility genes have been reported for the

Latin American populations. For this reason,

we examined the association between the

rs10774671 variant of the OAS1 gene and

the severe form of COVID-19 among Ecua-

dorian individuals.

METHODS

Design and Study Subjects

In this observational, analytical, and

case-control study, a total of 100 Ecuadorian

individuals with COVID-19 were analyzed.

The individuals were divided into two groups:

43 patients with the severe clinical picture

(group A) enrolled from October 2021 to

March 2022 and 57 subjects with the asymp-

tomatic-mild form (group B) enrolled in Jan-

uary 2021 at the Quito Sur Hospital of the

Ecuadorian Institute of Social Security, Qui-

to, Ecuador. Group A consisted of individuals

without regard to sex who had a diagnosis of

COVID-19 severe form confirmed by a posi-

tive RT-PCR test specific for SARS-CoV-2; a

chest computed tomography image showing

a pattern of viral pneumonia due to diffuse

infiltration of both lungs greater than 50%

(CORADS 6); and the presence of respirato-

ry failure and the need for mechanical venti-

lation (PaO2/FiO2 ≤ 100mmHg (with PEEP

≥ 5cm H2O) and SpO2/FiO2 ratio <315).

This group had received at least two doses of

SARS-CoV-2 vaccines. Group B subjects pre-

sented the disease’s asymptomatic or mild

clinical form, validated by a positive RT-PCR

test for SARS-CoV-2. Group B was made up of

health workers from the same hospital who

provided care for patients with the severe

172 Pilataxi et al.

Investigación Clínica 65(2): 2024

form of COVID-19 admitted to the intensive

care unit. When the subjects from Group B

were diagnosed with COVID-19, they had not

received any vaccination against COVID-19.

This method of subject selection was carried

out to identify COVID-19 protective alleles.

The exclusion criteria for both groups in-

cluded consanguineous individuals, minors,

pregnant or nursing women, and refugees or

displaced with little or no knowledge of the

Spanish language.

Molecular Analysis

Ten milliliters of peripheral blood were

drawn from each subject in an EDTA tube. In

order to reduce bias in the laboratory phase,

each tube was assigned a unique code with-

out discriminating to which clinical group

it belonged. The Column-Pure Blood Ge-

nomic DNA (ABM, Vancouver, Canada) kit

was used to extract DNA according to the

manufacturer´s instructions. The Qubit ds-

DNA BR ASSAY Kit (21000 ng 100RX (Invi-

trogen, Massachusetts, USA) was then used

to quantify the DNA using the Qubit fluo-

rometer (Invitrogen, Massachusetts, USA).

The DNA quality was determined by elec-

trophoresis in 1.5% agarose gels at 80V for

an hour, with the bands visualized using the

Microtek Bio-1000F program scanner (Mi-

crotek International Inc., Hsinchu City, Tai-

wan). The forward primer 5’-TCC-AGA-TGG-

CAT-GTC-ACA-GT-3’ and the reverse primer

5’-TAG-AAG-GCC-AGG-AGT-CAG-GA-3´ were

used to carry out the PCR, based on earlier

research

. The master mix and thermocy-

cler settings (Applied Biosystems MiniAmp,

Thermo Fisher Scientific Inc., Massachu-

setts, USA) for PCR were performed based

on a previo