The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Anastomotic leaks after anterior resection for mid and low rectal cancer: survey of the Italian Society of Colorectal Surgery

Abstract BACKGROUND: The aim of the survey was to assess the incidence of anastomotic leaks (AL) and to identify risk factors predicting incidence and gravity of AL after low anterior resection (LAR) for rectal cancer performed by colorectal surgeons of the Italian Society of Colorectal Surgery (SICCR). METHODS: Information about patients with rectal cancers less than 12 cm from the anal verge who underwent LAR during 2005 was collected retrospectively. AL was classified as grade I to IV according to gravity. Fifteen clinical variables were examined by univariate and multivariate analyses. Further analysis was conducted on patients with AL to identify factors correlated with gravity. RESULTS: There were 520 patients representing 64% of LAR for rectal cancer performed by SICCR members. The overall rate of AL was 15.2%. Mortality was 2.7% including 0.6% from AL. The incidence of AL was correlated with higher age (p<0.05), lower (<20 per year) centre case volume (p<0.05), obesity (p<0.05), malnutrition (p<0.01) and intraoperative contamination (p<0.05), and was lower in patients with a colonic J-pouch reservoir (p<0.05). In the multivariate analysis age, malnutrition and intraoperative contamination were independent predictors. The only predictor of severe (grade III/IV) AL was alcohol/smoking habits (p<0.05) while the absence of a diverting stoma was borderline significant (p<0.07). CONCLUSION: Our retrospective survey identified several risk factors for AL. This survey was a necessary step to construct prospective interventional studies and to establish benchmark standards for outcome studies

FISSIT (Fistula Surgery in Italy) study: A retrospective survey on the surgical management of anal fistulas in Italy over the last 15 years

Background: Surgical treatment of anal fistulas is still a challenge. The aims of this study were to evaluate the adoption and healing rates for the different surgical techniques used in Italy over the past 15 years. Methods: This was a multicenter retrospective observational study of patients affected by simple and complex anal fistulas of cryptoglandular origin who were surgically treated in the period 2003\u20132017. Surgical techniques were grouped as sphincter-cutting or sphincter-sparing and as technology-assisted or techno-free. All patients included in the study were followed for at least 12 months. Results: A total of 9,536 patients (5,520 simple; 4,016 complex fistulas) entered the study. For simple fistulas, fistulotomy was the most frequently used procedure, although its adoption significantly decreased over the years (P < .0005), with an increase in sphincter-sparing approaches; the overall healing rate in simple fistulas was 81.1%, with a significant difference between sphincter-cutting (91.9%) and sphincter-sparing (65.1%) techniques (P = .001). For complex fistulas, the adoption of sphincter-cutting approaches decreased, while sphincter-sparing techniques were mildly preferred (P < .0005). Moreover, there was a significant trend toward the use of technology-assisted procedures. The overall healing rate for complex fistulas was 69.0%, with a measurable difference between sphincter-cutting (81.1%) and sphincter-sparing (61.4%; P = .001) techniques and between techno-free and technology-assisted techniques (72.5% and 55.0%, respectively; P = .001). Conclusion: Surgical treatment of anal fistulas has changed, with a trend toward the use of sphincter-sparing techniques. The overall cure rate has remained stable, even if the most innovative procedures have achieved a lower success rate

Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy

Background: Next-generation sequencing (NGS) is gradually replacing Sanger sequencing for HIV genotypic drug resistance testing (GRT). This work evaluated the concordance among different NGS-GRT interpretation tools in a real-life setting. Methods: Routine NGS-GRT data were generated from viral RNA at 11 Italian laboratories with the AD4SEQ HIV-1 Solution v2 commercial kit. NGS results were interpreted by the SmartVir system provided by the kit and by two online tools (HyDRA Web and Stanford HIVdb). NGS-GRT was considered valid when the coverage was &gt;100 reads (100×) at each PR/RT/IN resistance-associated position listed in the HIVdb 9.5.1 algorithm. Results: Among 629 NGS-GRT, 75.2%, 74.2%, and 70.9% were valid according to SmartVir, HyDRA Web, and HIVdb. Considering at least two interpretation tools, 463 (73.6%) NGS-GRT had a valid coverage for resistance analyses. The proportion of valid samples was affected by viremia &lt;10,000-1000 copies/mL and non-B subtypes. Mutations at an NGS frequency &gt;10% showed fair concordance among different interpretation tools. Conclusion: This Italian survey on NGS resistance testing suggests that viremia levels and HIV subtype affect NGS-GRT coverage. Within the current routine method for NGS-GRT, only mutations with frequency &gt;10% seem reliably detected across different interpretation tools

Time trend in the surgical management of obstructed defecation syndrome: a multicenter experience on behalf of the Italian Society of Colorectal Surgery (SICCR)

Background: Surgical management of obstructed defecation syndrome (ODS) is challenging, with several surgical options showing inconsistent functional results over time. The aim of this study was to evaluate the trend in surgical management of ODS in a 10-year timeframe across Italian referral centers. Methods: Surgeons from referral centers for the management of pelvic floor disorders and affiliated to the Italian Society of Colorectal Surgery provided data on the yearly volume of procedures for ODS from 2010 to 2019. Six common clinical scenarios of ODS were captured, including details on patient’s anal sphincter function and presence of rectocele and/or rectal intussusception. Perineal repair, ventral rectopexy (VRP), transanal repair (internal Delorme), stapled transanal rectal resection (STARR), Contour Transtar, and transvaginal repair were considered in each clinical scenario. Results: Twenty-five centers were included providing data on 2943 surgical patients. Procedure volumes ranged from 10–20 (54%) to 21–50 (46%) per year across centers. The most performed techniques in patients with good sphincter function were transanal repair for isolated rectocele (243/716 [34%]), transanal repair for isolated rectal intussusception (287/677 [42%]) and VRP for combined abnormalities (464/976 [48%]). When considering poor sphincter function, these were perineal repair (112/194 [57.8%]) for isolated rectocele, and VRP for the other two scenarios (60/120 [50%] and 97/260 [37%], respectively). The use of STARR and Contour Transtar decreased over time in patients with impaired sphincter function. Conclusions: The complexity of ODS treatment is confirmed by the variety of clinical scenarios that can occur and by the changing trend of surgical management over the last 10&nbsp;years

E-consensus on telemedicine in colorectal surgery: a RAND/UCLA-modified study

Coronavirus disease 2019 (COVID-19) is revolutionizing healthcare delivery. The aim of the study was to reach consensus among experts on the possible applications of telemedicine in colorectal surgery. A group of 48 clinical practice recommendations (CPRs) was developed by a clinical guidance group based on coalescence of evidence and expert opinion. The Telemedicine in Colorectal Surgery Italian Working Group included 54 colorectal surgeons affiliated to the Italian Society of Colo-Rectal Surgery (SICCR) who were involved in the evaluation of the appropriateness of each CPR, based on published RAND/UCLA methodology, in two rounds. Stakeholders’ median age was 44.5 (IQR 36–60) years, and 44 (81%) were males. Agreement was obtained on the applicability of telemonitoring and telemedicine for multidisciplinary pre-operative evaluation. The panel voted against the use of telemedicine for a first consultation. 15/48 statements deemed uncertain on round 1 and were re-elaborated and assessed by 51/54 (94%) panelists on round 2. Consensus was achieved in all but one statement concerning the cost of a teleconsultation. There was strong agreement on the usefulness of teleconsultation during follow-up of patients with diverticular disease after an in-person visit. This e-consensus provides the boundaries of telemedicine in colorectal surgery in Italy. Standardization of infrastructures and costs remains to be better elucidated