Genomic Surveillance of SARS-CoV-2: Study of Cases Intradomiciliary Infection in Brazilian Amazonia

Research Article

Austin J Infect Dis. 2022; 9(1): 1065.

Genomic Surveillance of SARS-CoV-2: Study of Cases Intradomiciliary Infection in Brazilian Amazonia

Teixeira KS1,2, Sgorlon G1,3, Passos-Silva AM1,3, Roca TP1,4, Queiroz JAS1,3, Gasparelo NW1,3, Oliveira AAS1, Souza PRF1, Batista FS5, Salcedo JMV1,3,6 and Vieira DS1,3,6*

1Laboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia, FIOCRUZ/RO, Porto Velho, RO, Brazil

2Centro Universitário Aparício Carvalho, FIMCA, Porto Velho, RO, Brazil

3Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia, UNIR, Porto Velho, RO, Brazil

4Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/ IOC, FIOCRUZ, Rio de Janeiro, RJ, Brazil

5Coordenação Estadual do Covid-19, AGEVISA/RO, Porto Velho, RO, Brazil

6Centro de Pesquisa em Medicina Tropical, CEPEM/RO, Porto Velho, RO, Brazil

*Corresponding author: Deusilene Vieira, Fiocruz Rondônia, Rua da Beira, 7176, Bairro Lagoa, 76812-245 Porto Velho, Rondônia, Brazil

Received: May 05, 2022; Accepted: June 07, 2022; Published: June 14, 2022

Abstract

Studies have shown that the family environment is very favorable for SARSCOV- 2 transmission, making family groups susceptible to intra-household infection because they maintain direct contact with an infected person. We screened a cohort of 416 individuals who tested positive for SARS-CoV-2 from June to October 2021 for intradomiciliary infection. Twenty-two families with an average of 2 to 4 members were located in 12 municipalities in the state of Rondônia. Nasopharyngeal samples were collected, extracted using the QIAamp viral RNA mini kit and genomic sequencing was performed using samples with ct<25 by Illumina platform, the sequences were analyzed for phylogeny, mutations, and lineages. Among the samples analyzed 72.72% matched for VOC Delta and 27.27% for Gamma variant. The median viral load for both variants was 6.95. The main symptoms presented were cough, headache, and fever. No hospitalizations or deaths were reported. We observed that among the positive individuals, 24% were immunized with the 1st and 2nd dose, 40% were partially immunized, and 36% were not immunized. For each strain, subvariants were identified, being P.1.4 and P.1.14 for the Gamma variant and AY.43, AY.99.2 and AY.122 for Delta. The mutations mostly behaved as lineage-defining, with only eight families showing point mutations. In conclusion, it was observed that despite the low adherence to immunization, household cases were equally expressed in viral characteristics and in the low rate of hospital evolution for COVID-19, and this may be a factor associated with the permanence of infection in an isolated family environment.

Keywords: SARS-CoV-2; Variant of Concern; Gamma; Delta; Intradomiciliary Infection; Genomic Surveillance

Introduction

SARS-CoV-2 is the virus that causes a respiratory disease denominated COVID-19, it is composed of single-stranded positive sense RNA genetic material, and its transmission occurs through droplets or aerosols, which is a factor that facilitates its dissemination [1]. Furthermore, studies in China have shown that the highest rate of SARS-CoV-2 transmissibility occurred from household contacts [2], even with health prevention being carried out to prevent the spread of the virus, family groups have not managed to avoid contamination, becoming groups susceptible to infection. In the family environment, the infected person has direct contact with their relatives [3], favoring the transmissibility and infectivity of SARS-CoV-2 [4].

The high rate of recurrent infections has caused SARS-CoV-2 to accumulate numerous mutations in its genome, either by gene deletions, silent mutations, or changes in the coding of amino acids, some being responsible for altering the interaction of the Spike (S) protein with the host cell receptor angiotensin-converting enzyme 2 (ACE2). These changes in activity impair the body’s immune response against the virus, increasing transmissibility and intensifying its pathogenic potential, thus favoring the emergence of new variants and subvariants [5-7].

The appearance of the first SARS-CoV-2 variants caused a worldwide public health concern, leading the World Health Organization (WHO) to develop proposals for genomic characterization and monitoring. Recently, the Omicron variant (O.1.1.529) was classified as a Variant of Concern (VOC) due to its attributes in increasing transmissibility and potentially reducing vaccine action. Alpha (B.1.1.7), Beta (O.1.351), Gamma (P.1), and Delta (E.1.617.2) variants are also classified as VOCs, but there is no detection or a low level of circulation of some variants in this group. Lambda (C.37), Mu (O.1.621), the latter already detected in Rondônia, Brazil and other variants are classified as Variants of Interest (VOIs), and currently B.1.640 and the recombinant BA.1/AY.4 are classified as Variant Under Monitoring (VUM) [8,9].

Gamma VOC was detected in December 2020 in Manaus, Brazil and Delta VOC was first described in India in October 2020 and was identified in Southern Brazil in April 2021, together these two VOCs favored an exponential increase in the number of infections over the course of 2021 [10-12]. In addition to the circulation of these two VOCs, evaluating the household model of transmission is a point little addressed in the increase in the number of cases, even though we know that intradomiciliary transmission is the key point of most reported infections. This type of infection provides a clear and fixed exposure of the sources of infection, which makes it a viable model to estimate the transmissibility and infectivity of the prevalent virus [13].

Given this, aware of the high rate of transmissibility of the SARS CoV-2 virus, the main objective of this study was to perform an epidemiological description of cases of intradomiciliary infection within a cohort of 416 samples sequenced from June to October 2021 in Western Amazonia, bringing the state of Rondônia as the main study site.

Materials and Methods

Ethical aspects and study site

The study was carried out at the Laboratory of Molecular Virology FIOCRUZ/RO in partnership with the Central Public Health Laboratory of Rondônia LACEN and the Laboratory of Virology of the Instituto Leônidas e Maria Deane, FIOCRUZ/AM. The proposal was submitted and approved by the Research Ethics Committee of the Centro de PesquisaemMedicina Tropical de Rondônia-CEP/ CEPEM with opinion No. 4.637.465.

Biological samples and epidemiological data

A cohort of 416 individuals positive for SARS-CoV-2 were selected in the period from June to October 2021. Biological samples were collected in primary health care units and reference centers in different municipalities of the state of Rondônia. Laboratory diagnosis was performed by RT-qPCR at the Laboratório Central de SaúdePública de Rondônia (LACEN/RO) using the One Step/ COVID-19 kit (IBMP, Brazil).

Biological samples were collected by nasopharyngeal swab technique in health care units, hospitals and reference centers located in different municipalities of the state of Rondônia. Epidemiological data were collected from electronic medical records available in the following platforms: the Laboratory Environment Manager (GAL) of Rondônia, E-SUS notifica, and SIVEP-Gripe.Screening of cases of intradomiciliary infection occurred through electronic bank tracking and home address location.

Nucleic acid isolation and RT-qPCR

Sample quantification was performed in the Molecular Virology Laboratory (FIOCRUZ/RO) where viral RNA was extracted from 140 μL of nasopharyngeal Swab samples using QIAamp® viral RNA Mini Kit (QIAGEN, Germany) according to the manufacturer’s instructions. For viral load was determined using 5μL of this extracted viral RNA using Multiplex One-Step RT-qPCR assay for detection of SARS-CoV-2, developed by Queiroz and colleagues, 2021 [14].

Complete genome sequencing of SARS-CoV-2

Samples with Ct values <25 was selected based on quantitative assays for SARS-CoV-2. Nucleotide sequencing was performed using the Illumina MiSeq or NextSeq platforms and the COVIDSEQ Kit (Illumina, San Diego, CA, USA) [15].

Análise de mutações e determinação de linhagens

The Nextclade v.1.5.4 software [16] and Pangolin COVID-19 Lineage Assigner v2.1.7 [17] were used to evaluate mutations and determine lineages.

Phylogenetic analysis

Complete genomes (n=230) of high quality (>99% N’s) sampled in Brazil and of each lineage identified were downloaded from the GISAID platform [18]. MAFFT v.7.487 was used to align the sequences [19].The data set was used to perform a maximum likelihood based phylogenetic analysis using IQ-TREE v.2.1.3 [20]. The GTR+G+I substitution model was measured by the ModelFinder tool [21]. Branching support values were obtained using 1,000 Ultrafast Bootstrap replicates. FigTree v.1.4.4 was used to visualize the maximum likelihood tree [22].

Analysis of the Secondary Attack Rate among households

The secondary attack rate was estimated from the number of infected household contacts with the overall number of cases per household. Age group, vaccination, and other criteria were not taken into consideration [23].

Statistical analysis

Descriptive analyses were represented by measures of central tendency and dispersion. The Chi-square test was used for statistical inference with a significance level of 5% (p<0.05). Statistical analysis was performed and graphs were generated using R v4.0.3 software.

Results

A total of 416 individuals with molecular diagnosis for COVID-19 were analyzed from June to October 2021 in the state of Rondônia, in which 22 families with an average of 2 to 4 members were identified, with a total of 50 (50/416) individuals. The household infections are distributed in 12 municipalities in the state of Rondônia (Figure 1) with Porto Velho (n=6) and Jaru (n=3) showing the highest frequency of cases, as they are some of the most populous municipalities in the state of Rondônia, and in a smaller proportion the cases registered in AlvoradaD’Oeste (n=1), Ariquemes (n=2), São Miguel do Guaporé (n=1), Teixeirópolis (n=1), Cacoal (n=2), Cerejeiras (n=1), Ji-paraná (n=2), MachadinhoD’Oeste (n=1), Seringueiras (n=1) and Vilhena (n=1).