Duplex real-time RT-PCR assay for detection and subgroup-specific identification of human respiratory syncytial virus

Wang, Limin; Piedra, Pedro A.; Avadhanula, Vasanthi; Durigon, Edison Luiz; Machablishvili, Ann; López, María-Renée; Thornburg, Natalie J.; Peret, Teresa C. T.

doi:10.1016/j.jviromet.2019.113676

Cited by 33 publications

(37 citation statements)

References 38 publications

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“… 9 , 10 We used reverse transcriptase quantitative PCR to identify RSV following the protocol developed by the respiratory viruses branch at the US Centers for Disease Control and Prevention (CDC). 11 We tested each sample for the constitutive human enzyme RNAseP to show adequate sampling and the absence of PCR inhibitors.…”

Section: Methodsmentioning

confidence: 99%

Infant deaths from respiratory syncytial virus in Lusaka, Zambia from the ZPRIME study: a 3-year, systematic, post-mortem surveillance project

Gill¹,

Mwananyanda²,

MacLeod³

et al. 2022

The Lancet Global Health

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Summary Background Respiratory syncytial virus (RSV) is the leading cause of acute lower respiratory tract infections and a key driver of childhood mortality. Previous RSV burden of disease estimates used hospital-based surveillance data and modelled, rather than directly measured, community deaths. Given this uncertainty, we conducted a 3-year post-mortem prevalence study among young infants at a busy morgue in Lusaka, Zambia—the Zambia Pertussis RSV Infant Mortality Estimation (ZPRIME) study. Methods Infants were eligible for inclusion if they were aged between 4 days and less than 6 months and were enrolled within 48 h of death. Enrolment occurred mainly at the University Teaching Hospital of the University of Zambia Medical School (Lusaka, Zambia), the largest teaching hospital in Zambia. We extracted demographic and clinical data from medical charts and official death certificates, and we conducted verbal autopsies with the guardian or next of kin. RSV was identified using reverse transcriptase quantitative PCR and stratified by age, time of year, and setting (community vs facility deaths). By combining the PCR prevalence data with syndromic presentation, we estimated the proportion of all infant deaths that were due to RSV. Findings The ZPRIME study ran from Aug 31, 2017, to Aug 31, 2020, except for from April 1 to May 6, 2020, during which data were not collected due to restrictions on human research at this time (linked to COVID-19). We enrolled 2286 deceased infants, representing 79% of total infant deaths in Lusaka. RSV was detected in 162 (7%) of 2286 deceased infants. RSV was detected in 102 (9%) of 1176 community deaths, compared with 10 (4%) of 236 early facility deaths (<48 h from admission) and 36 (5%) of 737 late facility deaths (≥48 h from admission). RSV deaths were concentrated in infants younger than 3 months (116 [72%] of 162 infants), and were clustered in the first half of each year and in the poorest and most densely populated Lusaka townships. RSV caused at least 2·8% (95% CI 1·0–4·6) of all infant deaths and 4·7% (1·3–8·1) of community deaths. Interpretation RSV was a major seasonal cause of overall infant mortality, particularly among infants younger than 3 months of age. Because most RSV deaths occurred in the community and would have been missed through hospital-based surveillance, the global burden of fatal RSV has probably been underestimated. Funding Bill & Melinda Gates Foundation.

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Section: Methodsmentioning

confidence: 99%

Infant deaths from respiratory syncytial virus in Lusaka, Zambia from the ZPRIME study: a 3-year, systematic, post-mortem surveillance project

Gill¹,

Mwananyanda²,

MacLeod³

et al. 2022

The Lancet Global Health

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“…Although this situation appears relatively infrequently, usually in <1% of HRSV-positive respiratory samples ( 2 , 3 ), some sources describe higher levels of codetection (e.g., 3.4% in a study from Senegal [ 4 ]). Dual infections may also be more frequently identified when subtype-specific PCR is introduced, as they have been in phase 2 of the World Health Organization RSV program ( 5 , 6 ). We offer an approach to clarify nomenclature in such instances of codetection.…”

mentioning

confidence: 99%

Addendum to Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level

Barr¹,

Williams²,

Salimi³

et al. 2022

Emerg. Infect. Dis.

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“…RNP is a the constitutively expressed gene that we used to assess successful sample collection, storage, DNA extraction, and lack of PCR inhibition. The B. pertussis assay was a singleplex TaqMan qPCR reactions targeting the IS481 insertion sequence [46], and the RSV assay used a reverse-transcriptase qPCR reaction [47]. Samples were run on 96-well qPCR plates; each plate contained approximately 46 samples (one each of IS481 and RNP), along with one positive and one negative control per plate.…”

Section: Laboratory Methodsmentioning

confidence: 99%

Young Zambian infants with symptomatic RSV and pertussis infections are frequently prescribed inappropriate antibiotics

Gunning

Rohani

Mwananyanda

et al. 2021

Preprint

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Pediatric community-acquired pneumonia (CAP) remains a pressing global health concern, particularly in low-resource settings where diagnosis and treatment rely on empiric, symptoms-based guidelines such as the WHO's Integrated Management of Childhood Illness (IMCI). This study details the delivery of IMCI-based health care in a cohort of 1,320 young infants and their mothers in a low-resource urban community in Lusaka, Zambia. We prospectively monitored mother/infant pairs across infants' first four months of life, recording symptoms of respiratory infection and antibiotics prescriptions (predominantly penicillins), and tested nasopharyngeal (NP) samples for Respiratory syncytial virus (RSV) and Bordetella pertussis. Symptoms and antibiotics use were more common in infants (43% and 15.7%) than in mothers (16.6% and 8%), while RSV and B. pertussis were observed at similar rates in infants (2.7% and 32.5%) and mothers (2% and 35.5%), albeit frequently at very low levels. In infants, we observed strong associations between symptoms, pathogen detection, and antibiotics use. Critically, we demonstrate that non-macrolide antibiotics were commonly prescribed for pertussis infections, some of which persisted across many weeks. We speculate that improved diagnostic specificity and/or clinician education paired with timely, appropriate treatment of pertussis could substantially reduce the burden of this disease while reducing the off-target use of penicillins.

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Duplex real-time RT-PCR assay for detection and subgroup-specific identification of human respiratory syncytial virus

Cited by 33 publications

References 38 publications

Infant deaths from respiratory syncytial virus in Lusaka, Zambia from the ZPRIME study: a 3-year, systematic, post-mortem surveillance project

Infant deaths from respiratory syncytial virus in Lusaka, Zambia from the ZPRIME study: a 3-year, systematic, post-mortem surveillance project

Addendum to Proposal for Human Respiratory Syncytial Virus Nomenclature below the Species Level

Young Zambian infants with symptomatic RSV and pertussis infections are frequently prescribed inappropriate antibiotics

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