Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon
It is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and as...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2025-05-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/13/5/1088 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849327318398402560 |
|---|---|
| author | Amanda Mendes Silva Cruz Jedson Ferreira Cardoso Kenny Costa Pinheiro Jessylene Almeida Ferreira Luana Soares Barbagelata Sandro Patroca Silva Wanderley Dias Chagas Junior Patrícia Santos Lobo Dielle Monteiro Teixeira Walter André Junior Inaiah Ordenes Silva Mirleide Cordeiro Santos Luana Silva Soares Farias Maisa Silva Sousa Fernando Neto Tavares |
| author_facet | Amanda Mendes Silva Cruz Jedson Ferreira Cardoso Kenny Costa Pinheiro Jessylene Almeida Ferreira Luana Soares Barbagelata Sandro Patroca Silva Wanderley Dias Chagas Junior Patrícia Santos Lobo Dielle Monteiro Teixeira Walter André Junior Inaiah Ordenes Silva Mirleide Cordeiro Santos Luana Silva Soares Farias Maisa Silva Sousa Fernando Neto Tavares |
| author_sort | Amanda Mendes Silva Cruz |
| collection | DOAJ |
| description | It is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and asymptomatic) during the outbreak of the P.1 variant of SARS-CoV-2 in Parintins, Amazonas–Brazil, in March 2021. The samples were investigated by a shotgun sequencing metagenomic approach using the NextSeq 500 Illumina® system. The samples were stratified according to the presence or absence of SARS-CoV-2, household group, sex, and age. Of the total of 63 individuals, 37 (58.73%) were positive for SARS-CoV-2 and 26 (41.27%) were negative for SARS-CoV-2 and other respiratory viruses (FLU, AdV, HBoV, HCoV, HMPV, RSV, PIV, HRV). The alpha diversity indexes Chao1, species observed, Simpson, and Inv Simpson demonstrated a significant difference (<i>p</i> < 0.05) in both the diversity of observed species and the abundance of some taxa between positive and negative individuals. We also observed an abundance of opportunists such as <i>Klebsiella pneumoniae</i>, <i>Staphylococcus</i> spp, and <i>Shigella sonnei</i>, previously associated with the severity of COVID-19. Our results suggest that SARS-CoV-2 infection causes changes in the microenvironment of the nasopharyngeal region, allowing greater proliferation of opportunistic bacteria and decreased abundance of commensal bacteria. |
| format | Article |
| id | doaj-art-4bd0f22c6d7441cb8bce59753ed2419c |
| institution | Kabale University |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj-art-4bd0f22c6d7441cb8bce59753ed2419c2025-08-20T03:47:54ZengMDPI AGMicroorganisms2076-26072025-05-01135108810.3390/microorganisms13051088Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian AmazonAmanda Mendes Silva Cruz0Jedson Ferreira Cardoso1Kenny Costa Pinheiro2Jessylene Almeida Ferreira3Luana Soares Barbagelata4Sandro Patroca Silva5Wanderley Dias Chagas Junior6Patrícia Santos Lobo7Dielle Monteiro Teixeira8Walter André Junior9Inaiah Ordenes Silva10Mirleide Cordeiro Santos11Luana Silva Soares Farias12Maisa Silva Sousa13Fernando Neto Tavares14Virology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilArbovirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilMinistry of Health, Central Public Health Laboratory of Amazonas, R. Emílio Moreira, 528—Centro, Manaus 69020-040, AM, BrazilMinistry of Health, Amazonas Health Surveillance Foundation-Dr. Rosemary Costa, Torquato Tapajós Avenue, 4010—Santo Antônio College, Manaus 69093-018, AM, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilCenter for Tropical Medicine, Federal University of Pará, Av. Generalíssimo Deodoro, 92, Umarizal, Belém 66055-240, PA, BrazilVirology Section, Evandro Chagas Institute, Secretariat for Health and Environmental Surveillance, Ministry of Health, Highway BR 316-KM 07, S/N, Levilândia, Ananindeua 67030-000, PA, BrazilIt is important to understand which bacterial taxa are most abundant during SARS-CoV-2 infection and to promote mitigation strategies for conditions subsequent to infection. Nasopharyngeal swab samples were collected from patients infected with SARS-CoV-2 and their family contacts (uninfected and asymptomatic) during the outbreak of the P.1 variant of SARS-CoV-2 in Parintins, Amazonas–Brazil, in March 2021. The samples were investigated by a shotgun sequencing metagenomic approach using the NextSeq 500 Illumina® system. The samples were stratified according to the presence or absence of SARS-CoV-2, household group, sex, and age. Of the total of 63 individuals, 37 (58.73%) were positive for SARS-CoV-2 and 26 (41.27%) were negative for SARS-CoV-2 and other respiratory viruses (FLU, AdV, HBoV, HCoV, HMPV, RSV, PIV, HRV). The alpha diversity indexes Chao1, species observed, Simpson, and Inv Simpson demonstrated a significant difference (<i>p</i> < 0.05) in both the diversity of observed species and the abundance of some taxa between positive and negative individuals. We also observed an abundance of opportunists such as <i>Klebsiella pneumoniae</i>, <i>Staphylococcus</i> spp, and <i>Shigella sonnei</i>, previously associated with the severity of COVID-19. Our results suggest that SARS-CoV-2 infection causes changes in the microenvironment of the nasopharyngeal region, allowing greater proliferation of opportunistic bacteria and decreased abundance of commensal bacteria.https://www.mdpi.com/2076-2607/13/5/1088SARS-CoV-2P.1 variantnasopharyngealalpha diversitybeta diversitymetagenomic |
| spellingShingle | Amanda Mendes Silva Cruz Jedson Ferreira Cardoso Kenny Costa Pinheiro Jessylene Almeida Ferreira Luana Soares Barbagelata Sandro Patroca Silva Wanderley Dias Chagas Junior Patrícia Santos Lobo Dielle Monteiro Teixeira Walter André Junior Inaiah Ordenes Silva Mirleide Cordeiro Santos Luana Silva Soares Farias Maisa Silva Sousa Fernando Neto Tavares Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon Microorganisms SARS-CoV-2 P.1 variant nasopharyngeal alpha diversity beta diversity metagenomic |
| title | Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon |
| title_full | Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon |
| title_fullStr | Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon |
| title_full_unstemmed | Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon |
| title_short | Impact of SARS-CoV-2 P.1 Variant Infection on the Nasopharyngeal Commensal Bacterial Microbiome of Individuals from the Brazilian Amazon |
| title_sort | impact of sars cov 2 p 1 variant infection on the nasopharyngeal commensal bacterial microbiome of individuals from the brazilian amazon |
| topic | SARS-CoV-2 P.1 variant nasopharyngeal alpha diversity beta diversity metagenomic |
| url | https://www.mdpi.com/2076-2607/13/5/1088 |
| work_keys_str_mv | AT amandamendessilvacruz impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT jedsonferreiracardoso impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT kennycostapinheiro impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT jessylenealmeidaferreira impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT luanasoaresbarbagelata impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT sandropatrocasilva impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT wanderleydiaschagasjunior impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT patriciasantoslobo impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT diellemonteiroteixeira impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT walterandrejunior impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT inaiahordenessilva impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT mirleidecordeirosantos impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT luanasilvasoaresfarias impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT maisasilvasousa impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon AT fernandonetotavares impactofsarscov2p1variantinfectiononthenasopharyngealcommensalbacterialmicrobiomeofindividualsfromthebrazilianamazon |