Viral loads observed under competing strain dynamics

Author(s): Hay JA, Kennedy-Shaffer L, Mina MJJournal: medRxiv July 2021
A plausible mechanism for the increased transmissibility of SARS-CoV-2 variants of concern (VOCs) results from VOC infections causing higher viral…

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages.

Author(s): Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, George KS, Adams MD, Grubaugh NDJournal: medRxivPMID: 34230938 July 2021
Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control…

Deep–sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial — BCPP/ Ya Tsie trial

Author(s): Magosi LE, Zhang Y, Golubchick T, Gruttola VD, Tchetgen EJT, Novitsky V, Moore J, Bachanas P, Segolodi T, Lebelonyane R, Holme MP, Moyo S, Makhema J, Lockman S, Fraser C, Essex M, Lipsitch MJournal: medRxiv June 2021
Mathematical models predict that community–wide access to HIV testing–and–treatment can rapidly and substantially reduce new HIV infections. Yet several large…

Genetic surveillance in the Greater Mekong Subregion and South Asia to support malaria control and elimination

Author(s): Jacob CG, Thuy-Nhien N, Mayxay M, Maude RJ, Quang HH, Hongvanthong B, Vanisaveth V, Duc TN, Rekol H, Pluijm RWvan der; Seidlein LV, Fairhurst RM, Nosten FH, Hossain MA, Park N, Goodwin S, Ringwald P, Chindavongsa K, Newton PN, Ashley EA, Phalivong S, Maude RR, Leang R, Huch C, Dong LT, Nguyen K.-T, Nhat TM, Hien TT, Nguyen H, Zdrojewski N, Canavati SE, Sayeed AA, Uddin D, Buckee C, Fanello CI, Onyamboko M, Peto T, Tripura R, Amaratunga C, Thu AM, Delmas G, Landier J, Parker DM, Chau NH, Lek D, Suon S, Callery JJ, Jittamala P, Hanboonkunupakarn B, Pukrittayakamee S, Phyo AP, Smithuis F, Lin K, Thant M, Hlaing TM, Satpathi P, Satpathi S, Behera PK, Tripura A, Baidya S, Valecha N, Anvikar AR, Islam Aul; Faiz A, Kunasol C, Drury E, Kekre M, Ali M, Love K, Rajatileka S, Jeffreys AE, Rowlands K, Hubbart CS, Dhorda M, Vongpromek R, Kotanan N, Wongnak P, Garcia JA, Pearson RD, Ariani CV, Chookajorn T, Malangone C, Nguyen T, Stalker J, Jeffery B, Keatley J, Johnson KJ, Muddyman D, Chan XHS, Sillitoe J, Amato R, Simpson V, Gonçalves S, Rockett K, Day NP, Dondorp AM, Kwiatkowski DP, Miotto OJournal: medRxiv June 2021
National Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for…

Metrics to relate COVID-19 wastewater data to clinical testing dynamics.

Author(s): Xiao A, Wu F, Bushman M, Zhang J, Imakaev M, Chai PR, Duvallet C, Endo N, Erickson TB, Armas F, Arnold B, Chen H, Chandra F, Ghaeli N, Gu X, Hanage WP, Lee WL, Matus M, McElroy KA, Moniz K, Rhode SF, Thompson J, Alm EJJournal: medRxivPMID: 34159339 June 2021
Wastewater surveillance has emerged as a useful tool in the public health response to the COVID-19 pandemic. While wastewater surveillance…

Viral dynamics of acute SARS-CoV-2 infection

Author(s): Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich C, Jednak S, Ott I, Vogels C, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho D, Grubaugh ND, Grad YHJournal: medRxiv June 2021
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level viral RNA shedding. The…