4 research outputs found
Cell-based culture of SARS-CoV-2 informs infectivity and safe de-isolation assessments during COVID-19
BACKGROUND: The detection of SARS-CoV-2 RNA by real-time polymerase chain reaction (PCR) in respiratory samples collected from persons recovered from COVID-19 does not necessarily indicate shedding of infective virions. By contrast, the isolation of SARS-CoV-2 using cell-based culture likely indicates infectivity, but there are limited data on the correlation between SARS-CoV-2 culture and PCR. METHODS: One hundred and ninety-five patients with varying severity of COVID-19 were tested (outpatients [n=178]), inpatients [n=12] and critically unwell patients admitted to the intensive care unit [ICU; n=5]). SARS-CoV-2 PCR positive samples were cultured in Vero C1008 cells and inspected daily for cytopathic effect (CPE). SARS-CoV-2-induced CPE was confirmed by PCR of culture supernatant. Where no CPE was observed, PCR was performed on day four to confirm absence of virus replication. Cycle threshold (Ct) of the day four PCR (Ctculture) and the PCR of the original clinical sample (Ctsample) were compared, and positive cultures were defined where Ctsample - Ctculture was ?3. FINDINGS: Of 234 samples collected, 228 (97%) were from the upper respiratory tract. SARS-CoV-2 was only successfully isolated from samples with Ctsample ?32, including in 28/181 (15%), 19/42 (45%) and 9/11 samples (82%) collected from outpatients, inpatients, and ICU patients, respectively. The mean duration from symptom onset to culture positivity was 4.5 days (range 0-18). SARS-CoV-2 was significantly more likely to be isolated from samples collected from inpatients (p<0?001) and ICU patients (p<0?0001) compared with outpatients respectively, and in samples with lower Ctsample. CONCLUSION: SARS-CoV-2 culture may be used as a surrogate marker for infectivity and inform de-isolation protocols
Global and regional molecular epidemiology of HIV-1, 1990â2015: a systematic review, global survey, and trend analysis
International audienceGlobal genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990â2015.We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published between Jan 1, 1990, and Dec 31, 2015. We collected additional unpublished HIV-1 subtyping data through a global survey. We included prevalence studies with HIV-1 subtyping data collected during 1990â2015. We grouped countries into 14 regions and analysed data for four time periods (1990â99, 2000â04, 2005â09, and 2010â15). The distribution of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV (PLHIV) in each country to generate regional and global estimates of HIV-1 diversity in each time period. The primary outcome was the number of samples designated as HIV-1 subtypes A, B, C, D, F, G, H, J, K, CRFs, and URFs. The systematic review is registered with PROSPERO, number CRD42017067164.This systematic review and global survey yielded 2203 datasets with 383â519 samples from 116 countries in 1990â2015. Globally, subtype C accounted for 46·6% (16â280â897/34â921â639 of PLHIV) of all HIV-1 infections in 2010â15. Subtype B was responsible for 12·1% (4â235â299/34â921â639) of infections, followed by subtype A (10·3%; 3â587â003/34â921â639), CRF02_AG (7·7%; 2â705â110/34â921â639), CRF01_AE (5·3%; 1â840â982/34â921â639), subtype G (4·6%; 1â591â276/34â921â639), and subtype D (2·7%; 926â255/34â921â639). Subtypes F, H, J, and K combined accounted for 0·9% (311â332/34â921â639) of infections. Other CRFs accounted for 3·7% (1â309â082/34â921â639), bringing the proportion of all CRFs to 16·7% (5â844â113/34â921â639). URFs constituted 6·1% (2â134â405/34â921â639), resulting in recombinants accounting for 22·8% (7â978â517/34â921â639) of all global HIV-1 infections. The distribution of HIV-1 subtypes and recombinants changed over time in countries, regions, and globally. At a global level during 2005â15, subtype B increased, subtypes A and D were stable, and subtypes C and G and CRF02_AG decreased. CRF01_AE, other CRFs, and URFs increased, leading to a consistent increase in the global proportion of recombinants over time.Global and regional HIV diversity is complex and evolving, and is a major challenge to HIV vaccine development. Surveillance of the global molecular epidemiology of HIV-1 remains crucial for the design, testing, and implementation of HIV vaccines
Global and regional molecular epidemiology of HIV-1, 1990-2015: a systematic review, global survey, and trend analysis
BACKGROUND: Global genetic diversity of HIV-1 is a major challenge to the development of HIV vaccines. We aimed to estimate the regional and global distribution of HIV-1 subtypes and recombinants during 1990-2015. METHODS: We searched PubMed, EMBASE (Ovid), CINAHL (Ebscohost), and Global Health (Ovid) for HIV-1 subtyping studies published between Jan 1, 1990, and Dec 31, 2015. We collected additional unpublished HIV-1 subtyping data through a global survey. We included prevalence studies with HIV-1 subtyping data collected during 1990-2015. We grouped countries into 14 regions and analysed data for four time periods (1990-99, 2000-04, 2005-09, and 2010-15). The distribution of HIV-1 subtypes, circulating recombinant forms (CRFs), and unique recombinant forms (URFs) in individual countries was weighted according to the UNAIDS estimates of the number of people living with HIV (PLHIV) in each country to generate regional and global estimates of HIV-1 diversity in each time period. The primary outcome was the number of samples designated as HIV-1 subtypes A, B, C, D, F, G, H, J, K, CRFs, and URFs. The systematic review is registered with PROSPERO, number CRD42017067164. FINDINGS: This systematic review and global survey yielded 2203 datasets with 383â519 samples from 116 countries in 1990-2015. Globally, subtype C accounted for 46·6% (16â280â897/34â921â639 of PLHIV) of all HIV-1 infections in 2010-15. Subtype B was responsible for 12·1% (4â235â299/34â921â639) of infections, followed by subtype A (10·3%; 3â587â003/34â921â639), CRF02_AG (7·7%; 2â705â110/34â921â639), CRF01_AE (5·3%; 1â840â982/34â921â639), subtype G (4·6%; 1â591â276/34â921â639), and subtype D (2·7%; 926â255/34â921â639). Subtypes F, H, J, and K combined accounted for 0·9% (311â332/34â921â639) of infections. Other CRFs accounted for 3·7% (1â309â082/34â921â639), bringing the proportion of all CRFs to 16·7% (5â844â113/34â921â639). URFs constituted 6·1% (2â134â405/34â921â639), resulting in recombinants accounting for 22·8% (7â978â517/34â921â639) of all global HIV-1 infections. The distribution of HIV-1 subtypes and recombinants changed over time in countries, regions, and globally. At a global level during 2005-15, subtype B increased, subtypes A and D were stable, and subtypes C and G and CRF02_AG decreased. CRF01_AE, other CRFs, and URFs increased, leading to a consistent increase in the global proportion of recombinants over time. INTERPRETATION: Global and regional HIV diversity is complex and evolving, and is a major challenge to HIV vaccine development. Surveillance of the global molecular epidemiology of HIV-1 remains crucial for the design, testing, and implementation of HIV vaccines. FUNDING: None.status: publishe