Title Typical epidemiology of respiratory virus infections in a Brazilian slum.
Author Goes, Luiz Gustavo Bentim; Zerbinati, Rodrigo Melim; Tateno, Adriana Fumie; de Souza, Andrea Vieira; Ebach, Fabian; Corman, Victor M; Moreira-Filho, Carlos Alberto; Durigon, Edison Luiz; da Silva Filho, Luiz Vicente Ribeiro Ferreira; Drexler, Jan Felix
Journal J Med Virol Publication Year/Month 2020-Aug
PMID 31769524 PMCID PMC7228228
Affiliation + expend 1.Institute of Virology, Charite-Universitatsmedizin Berlin, corporate Member of Freie Universitat Berlin, Humboldt-Universitat zu Berlin, and Berlin Institute of Health, Berlin, Germany.

Host population size, density, immune status, age structure, and contact rates are critical elements of virus epidemiology. Slum populations stand out from other settings and may present differences in the epidemiology of acute viral infections. We collected nasopharyngeal specimens from 282 children aged </=5 years with acute respiratory tract infection (ARI) during 2005 to 2006 in one of the largest Brazilian slums. We conducted real-time reverse transcription-polymerase chain reaction (RT-PCR) for 16 respiratory viruses, nested RT-PCR-based typing of rhinoviruses (HRVs), and collected clinical symptoms. Viruses were common causes of respiratory disease; with >/=1 virus being detected in 65.2% of patients. We detected 15 different viruses during 1 year with a predominance of HRV (33.0%) and human respiratory syncytial virus (hRSV, 12.1%) infections, and a high rate of viral coinfections (28.3%). We observed seasonality of hRSV, HRV and human coronavirus infections, more severe symptoms in hRSV and influenza virus (FLU) infections and prolonged circulation of seven HRV clusters likely representing distinct serotypes according to genomic sequence distances. Potentially unusual findings included the absence of human metapneumovirus detections and lack of typical FLU seasonal patterns, which may be linked to the population size and density of the slum. Nonetheless, most epidemiological patterns were similar to other studies globally, suggesting surprising similarities of virus-associated ARI across highly diverse settings and a complex impact of population characteristics on respiratory virus epidemiology.

StrainID RV Species Serotype Length(nt) Country Year Strain Name
UNS05648 Unclassified None 434 Brazil 2005 1382
UNS05649 Unclassified None 434 Brazil 2005 1293
UNS05650 Unclassified None 434 Brazil 2005 1167
UNS05651 Unclassified None 434 Brazil 2005 1299
UNS05652 Unclassified None 434 Brazil 2005 1281
UNS05653 Unclassified None 428 Brazil 2005 1289
UNS05654 Unclassified None 428 Brazil 2005 1345
UNS05655 Unclassified None 428 Brazil 2005 1239
UNS05656 Unclassified None 428 Brazil 2005 1256
UNS05657 Unclassified None 428 Brazil 2005 1290
UNS05658 Unclassified None 428 Brazil 2005 1319
UNS05659 Unclassified None 428 Brazil 2005 1118
UNS05660 Unclassified None 428 Brazil 2005 1145
UNS05661 Unclassified None 428 Brazil 2005 1159
UNS05662 Unclassified None 428 Brazil 2005 1216
UNS05663 Unclassified None 428 Brazil 2005 1246
UNS05664 Unclassified None 428 Brazil 2005 1260
UNS05665 Unclassified None 428 Brazil 2005 1358
UNS05666 Unclassified None 428 Brazil 2005 1359
UNS05667 Unclassified None 428 Brazil 2005 1270
UNS05668 Unclassified None 428 Brazil 2005 1214
UNS05669 Unclassified None 428 Brazil 2005 1128
UNS05670 Unclassified None 428 Brazil 2006 1390
UNS05671 Unclassified None 428 Brazil 2006 1397
UNS05672 Unclassified None 428 Brazil 2006 1401
UNS05673 Unclassified None 428 Brazil 2005 1135
UNS05674 Unclassified None 428 Brazil 2005 1238
UNS05675 Unclassified None 428 Brazil 2005 1314
UNS05676 Unclassified None 428 Brazil 2005 1194
UNS05677 Unclassified None 428 Brazil 2005 1215
UNS05678 Unclassified None 428 Brazil 2005 1219
UNS05679 Unclassified None 428 Brazil 2005 1275
UNS05680 Unclassified None 428 Brazil 2005 1265
UNS05681 Unclassified None 428 Brazil 2005 1268
UNS05682 Unclassified None 428 Brazil 2005 1304
UNS05683 Unclassified None 428 Brazil 2005 1288
UNS05684 Unclassified None 434 Brazil 2005 1301
UNS05685 Unclassified None 434 Brazil 2005 1154
UNS05686 Unclassified None 434 Brazil 2005 1197
UNS05687 Unclassified None 379 Brazil 2005 1306
UNS05688 Unclassified None 434 Brazil 2005 1348
UNS05689 Unclassified None 434 Brazil 2005 1351
UNS05690 Unclassified None 434 Brazil 2005 1367
UNS05691 Unclassified None 434 Brazil 2005 1368
UNS05692 Unclassified None 434 Brazil 2005 1326
UNS05693 Unclassified None 434 Brazil 2005 1357
UNS05694 Unclassified None 434 Brazil 2005 1369
UNS05695 Unclassified None 434 Brazil 2005 1343
UNS05696 Unclassified None 434 Brazil 2005 1361
UNS05697 Unclassified None 434 Brazil 2005 1161
UNS05698 Unclassified None 434 Brazil 2005 1171
UNS05699 Unclassified None 434 Brazil 2005 1175
UNS05700 Unclassified None 434 Brazil 2005 1280
UNS05701 Unclassified None 434 Brazil 2005 1117
UNS05702 Unclassified None 434 Brazil 2005 1370
UNS05703 Unclassified None 434 Brazil 2006 1389
UNS05704 Unclassified None 434 Brazil 2006 1395
UNS05705 Unclassified None 434 Brazil 2005 1196
UNS05706 Unclassified None 434 Brazil 2005 1223
UNS05707 Unclassified None 434 Brazil 2005 1244
UNS05708 Unclassified None 434 Brazil 2005 1282
UNS05709 Unclassified None 434 Brazil 2005 1168
UNS05710 Unclassified None 434 Brazil 2005 1191
UNS05711 Unclassified None 434 Brazil 2005 1277
UNS05712 Unclassified None 434 Brazil 2005 1303
UNS05713 Unclassified None 434 Brazil 2005 1354
UNS05714 Unclassified None 434 Brazil 2005 1254
UNS05715 Unclassified None 434 Brazil 2006 1393
UNS05716 Unclassified None 434 Brazil 2005 1302
UNS05717 Unclassified None 434 Brazil 2005 1285
UNS05718 Unclassified None 434 Brazil 2005 1131
UNS05719 Unclassified None 434 Brazil 2005 1325
UNS05720 Unclassified None 434 Brazil 2005 1315
UNS05721 Unclassified None 434 Brazil 2005 1342
UNS05722 Unclassified None 434 Brazil 2005 1279
UNS05723 Unclassified None 434 Brazil 2005 1295
UNS05724 Unclassified None 434 Brazil 2005 1338
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